From e2901e5b8e7d777bf54c9e110d4717b93151c535 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Wed, 5 Nov 2025 14:55:53 +0000
Subject: [PATCH 01/15] New key_quanties computation under compute_fit no
 references changed as such all tests fail

---
 R/brglmFit.R | 186 +++++++++++++++++++++++++++++++++++----------------
 1 file changed, 130 insertions(+), 56 deletions(-)

diff --git a/R/brglmFit.R b/R/brglmFit.R
index f1d407f..99b2403 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -296,69 +296,143 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         }
     }
 
-    ## key_quantities, grad, info and bias are ALWAYS in beta, dispersion parameterization
-    key_quantities <- function(pars, y, level = 0, scale_totals = FALSE, qr = TRUE) {
+    # Always computes everything needed, stores it once, passes it around
+    compute_fit <- function(pars, y, x, weights, offset, family, 
+                            fixed_totals = NULL, row_totals = NULL, 
+                            no_dispersion = FALSE, nobs, nvars, keep) {
+        
+        # Extract Parameters
         betas <- pars[seq.int(nvars)]
         dispersion <- pars[nvars + 1]
-        prec <- 1/dispersion
+        precision <- 1 / dispersion
+
+        # Basic Quantities
         etas <- drop(x %*% betas + offset)
-        mus <- linkinv(etas)
-        if (scale_totals) {
-            ## Rescale mus
-            mus_totals <-  as.vector(tapply(mus, fixed_totals, sum))[fixed_totals]
-            mus <- mus * row_totals / mus_totals
-            etas <- linkfun(mus)
+        mus <- family$linkinv(etas)
+        mus_unscaled <- mus  # Keep original for gradient computation
+        if (!is.null(fixed_totals)) {
+            mus_totals <- as.vector(tapply(mus, fixed_totals, sum))[fixed_totals]
+            mus <- mus * row_totals / mus_totals  # Scaled version
+            etas <- family$linkfun(mus)  # Update etas to match scaled mus
         }
-        out <- list(precision = prec,
-                    betas = betas,
-                    dispersion = dispersion,
-                    etas = etas,
-                    mus = mus,
-                    scale_totals = scale_totals)
-        mean_quantities <- function(out) {
-            d1mus <- mu.eta(etas)
-            d2mus <- d2mu.deta(etas)
-            varmus <- variance(mus)
-            working_weights <- weights * d1mus^2 / varmus
-            wx <- sqrt(working_weights) * x
-            out$d1mus <- d1mus
-            out$d2mus <- d2mus
-            out$varmus <- varmus
-            out$d1varmus <- d1variance(mus)
-            out$working_weights <- working_weights
-            if (qr) out$qr_decomposition <- qr(wx)
-            out
-        }
-        dispersion_quantities <- function(out) {
-            zetas <- -weights * prec
-            out$zetas <- zetas
-            ## Evaluate the derivatives of the a function only for
-            ## objervations with non-zero weight
+
+        # Mean Quantities
+        d1mus <- family$mu.eta(etas)
+        d2mus <- family$d2mu.deta(etas)
+        varmus <- family$variance(mus)
+        d1varmus <- family$d1variance(mus)
+        working_weights <- weights * d1mus^2 / varmus
+
+        # QR Decomposition
+        wx <- sqrt(working_weights) * x
+        qr_decomposition <- qr(wx)
+        R_matrix <- qr.R(qr_decomposition)
+
+        # Hat Values 
+        # TODO: Avoid forming full Q? Approximate hat values?
+        Qmat <- qr.Q(qr_decomposition) 
+        hatvalues <- .rowSums(Qmat * Qmat, nobs, nvars, TRUE)
+
+        # Information Matrices
+        info_beta <- precision * crossprod(R_matrix)
+        inverse_info_beta <- dispersion * chol2inv(R_matrix)
+
+        # Dispersion Quantities (dept on family)
+        if (!no_dispersion) {
+            zetas <- -weights * precision
+            
+            # Derivatives of cumulant function (only for non-zero weights)
             d1afuns <- d2afuns <- d3afuns <- rep(NA_real_, nobs)
-            d1afuns[keep] <- d1afun(zetas[keep])
-            ## because of the way dev.resids is implemented, this is
-            ## d1afun is the expectation of dev.resids + 2 for gamma
-            ## families, so subtract 2
-            if (family$family == "Gamma") d1afuns <- d1afuns - 2
-            d2afuns[keep] <- d2afun(zetas[keep])
-            d3afuns[keep] <- d3afun(zetas[keep])
-            out$d2afuns <- d2afuns
-            out$d3afuns <- d3afuns
-            out$deviance_residuals <- dev.resids(y, mus, weights)
-            out$Edeviance_residuals <- weights * d1afuns
-            out
-        }
-        if (level == 0) {
-            out <- mean_quantities(out)
-        }
-        if (level == 1) {
-            out <- dispersion_quantities(out)
+            d1afuns[keep] <- family$d1afun(zetas[keep])
+            d2afuns[keep] <- family$d2afun(zetas[keep])
+            d3afuns[keep] <- family$d3afun(zetas[keep])
+            
+            # Special case for Gamma family
+            if (family$family == "Gamma") {
+                d1afuns <- d1afuns - 2
+            }
+            
+            # Deviance residuals
+            deviance_residuals <- family$dev.resids(y, mus, weights)
+            Edeviance_residuals <- weights * d1afuns
+            
+            # Information for dispersion parameter
+            info_zeta <- 0.5 * sum(weights^2 * d2afuns, na.rm = TRUE) / dispersion^4
+            inverse_info_zeta <- 1 / info_zeta
+        } else {
+            # Fixed dispersion (binomial, Poisson)
+            zetas <- d1afuns <- d2afuns <- d3afuns <- NA_real_
+            deviance_residuals <- family$dev.resids(y, mus, weights)
+            Edeviance_residuals <- NA_real_
+            info_zeta <- inverse_info_zeta <- NA_real_
         }
-        if (level > 1) {
-            out <- mean_quantities(out)
-            out <- dispersion_quantities(out)
+
+        # Gradient Computation
+        # Use unscaled mus for gradient when fixed_totals is used
+        mus_for_gradient <- if (!is.null(fixed_totals)) mus_unscaled else mus
+        etas_for_gradient <- if (!is.null(fixed_totals)) family$linkfun(mus_unscaled) else etas
+        d1mus_for_gradient <- family$mu.eta(etas_for_gradient)
+        varmus_for_gradient <- family$variance(mus_for_gradient)
+        
+        score_components_beta <- weights * d1mus_for_gradient * (y - mus_for_gradient) / 
+                                varmus_for_gradient * x
+        grad_beta <- precision * .colSums(score_components_beta, nobs, nvars, TRUE)
+        
+        if (!no_dispersion) {
+            grad_zeta <- 0.5 * precision^2 * 
+                        sum(deviance_residuals - Edeviance_residuals, na.rm = TRUE)
+        } else {
+            grad_zeta <- NA_real_
         }
-        out
+
+        # Return all computed quantities as class
+        structure(list(
+            # Parameters
+            betas = betas,
+            dispersion = dispersion,
+            precision = precision,
+            
+            # Basic quantities
+            etas = etas,
+            mus = mus,
+            mus_unscaled = mus_unscaled,  # For gradient with fixed_totals
+            
+            # Mean-related quantities
+            d1mus = d1mus,
+            d2mus = d2mus,
+            varmus = varmus,
+            d1varmus = d1varmus,
+            working_weights = working_weights,
+            
+            # QR decomposition and related
+            qr_decomposition = qr_decomposition,
+            R_matrix = R_matrix,
+            Q_matrix = Qmat, 
+            hatvalues = hatvalues,
+            
+            # Information matrices (pre-computed)
+            info_beta = info_beta,
+            inverse_info_beta = inverse_info_beta,
+            
+            # Dispersion-related quantities
+            zetas = zetas,
+            d1afuns = d1afuns,
+            d2afuns = d2afuns,
+            d3afuns = d3afuns,
+            deviance_residuals = deviance_residuals,
+            Edeviance_residuals = Edeviance_residuals,
+            info_zeta = info_zeta,
+            inverse_info_zeta = inverse_info_zeta,
+            
+            # Gradients (pre-computed)
+            grad_beta = grad_beta,
+            grad_zeta = grad_zeta,
+            score_components_beta = score_components_beta,
+            
+            # Metadata
+            has_fixed_totals = !is.null(fixed_totals),
+            no_dispersion = no_dispersion
+        ), class = "brglmFit_quantities")
     }
 
     gradient <- function(pars, level = 0, fit = NULL) {

From 16fa9fa2961b6563cdfb1265015c5c4336838729 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Fri, 7 Nov 2025 16:01:21 +0000
Subject: [PATCH 02/15] Updated calls to compute_fit from external functions,
 passes ~60 tests

---
 R/brglmFit.R | 320 +++++++++++++++++++++++++++------------------------
 1 file changed, 169 insertions(+), 151 deletions(-)

diff --git a/R/brglmFit.R b/R/brglmFit.R
index 99b2403..cf259bb 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -435,54 +435,34 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         ), class = "brglmFit_quantities")
     }
 
-    gradient <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = FALSE)
+    gradient <- function(pars, fit, level = 0) {
+        if (level == 0) {
+            return(fit$grad_beta)
+        }
+        else {
+            return(fit$grad_zeta)
         }
-        with(fit, {
-            if (level == 0) {
-                score_components <- weights * d1mus  * (y - mus) / varmus * x
-                return(precision * .colSums(score_components, nobs, nvars, TRUE))
-            }
-            if (level == 1) {
-                return(1/2 * precision^2 * sum(deviance_residuals - Edeviance_residuals, na.rm = TRUE))
-            }
-        })
     }
 
-    information <- function(pars, level = 0, fit = NULL, inverse = FALSE) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
-        }
-        with(fit, {
-            if (level == 0) {
-                R_matrix <- qr.R(qr_decomposition)
-                if (inverse) {
-                    ## return(dispersion * tcrossprod(solve(R_matrix)))
-                    return(dispersion * chol2inv(R_matrix))
-                } else {
-                    return(precision * crossprod(R_matrix))
-                }
+    information <- function(pars, fit, level = 0, inverse = FALSE) {
+        if (level == 0) {
+            if (inverse) {
+                return(fit$inverse_info_beta)
+            } else {
+                return(fit$info_beta)
             }
-            if (level == 1) {
-                info <- 0.5 * sum(weights^2 * d2afuns, na.rm = TRUE)/dispersion^4
-                if (inverse) {
-                    return(1/info)
-                } else {
-                    return(info)
-                }
+        }
+        else {
+            if (inverse) {
+                return(fit$inverse_info_zeta)
+            } else {
+                return(fit$info_zeta)
             }
-        })
+        }
     }
 
     hat_values <- function(pars, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = 0, qr = TRUE)
-        }
-        with(fit, {
-            Qmat <- qr.Q(qr_decomposition)
-            .rowSums(Qmat * Qmat, nobs, nvars, TRUE)
-        })
+        return(fit$hatvalues)
     }
 
     ## FIXME: Redundant function for now
@@ -509,7 +489,18 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
             if (df_residual > 0) {
                 dispFit <- try(uniroot(f = function(phi) {
                     theta <- c(betas, phi)
-                    cfit <- key_quantities(theta, y = y, level = 1, qr = FALSE)
+                    cfit <- compute_fit(pars = theta, 
+                                                y = y, 
+                                                x = x,
+                                                weights = weights,
+                                                offset = offset,
+                                                family = family,
+                                                fixed_totals = fixed_totals,
+                                                row_totals = row_totals,
+                                                no_dispersion = no_dispersion,
+                                                nobs = nobs,
+                                                nvars = nvars,
+                                                keep = keep)
                     gradient(theta, level = 1, fit = cfit)
                 }, lower = .Machine$double.eps, upper = 10000, tol = control$epsilon), silent = FALSE)
                 if (inherits(dispFit, "try-error")) {
@@ -527,123 +518,109 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         list(dispersion = disp, dispersion_ML = dispML)
     }
 
-    AS_mean_adjustment <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
+    AS_mean_adjustment <- function(pars, fit, level = 0) {
+        if (level == 0) {
+            # Zero division already handled by fit computation
+            adj <- .colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
+                       nobs, nvars, TRUE)
+            return(adj)
+        }
+        else {
+            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+            return((nvars - 2) / (2 * fit$dispersion) + 
+                s1 / (2 * fit$dispersion^2 * s2))
         }
-        with(fit, {
-            if (level == 0) {
-                hatvalues <- hat_values(pars, fit = fit)
-                ## Use only observations with keep = TRUE to ensure that no division with zero takes place
-                return(.colSums(0.5 * hatvalues * d2mus/d1mus * x, nobs, nvars, TRUE))
-            }
-            if (level == 1) {
-                s1 <- sum(weights^3 * d3afuns, na.rm = TRUE)
-                s2 <- sum(weights^2 * d2afuns, na.rm = TRUE)
-                return((nvars - 2)/(2 * dispersion) + s1/(2 * dispersion^2 * s2))
-            }
-        })
     }
 
-    AS_Jeffreys_adjustment <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
+    AS_Jeffreys_adjustment <- function(pars, fit, level = 0, a = 0.5) {
+        if (level == 0) {
+            ## Use only observations with keep = TRUE to ensure that no division with zero takes place
+            return(2 * a * .colSums(0.5 * fit$hatvalues * (2 * fit$d2mus/fit$d1mus - fit$d1varmus * fit$d1mus / fit$varmus) * x, nobs, nvars, TRUE))
+        }
+        else {
+            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+            return(2 * a * (-(nvars + 4)/(2 * fit$dispersion) + s1/(2 * fit$dispersion^2 * s2)))
         }
-        with(fit, {
-            if (level == 0) {
-                hatvalues <- hat_values(pars, fit = fit)
-                ## Use only observations with keep = TRUE to ensure that no division with zero takes place
-                return(2 * control$a * .colSums(0.5 * hatvalues * (2 * d2mus/d1mus - d1varmus * d1mus / varmus) * x, nobs, nvars, TRUE))
-            }
-            if (level == 1) {
-                s1 <- sum(weights^3 * d3afuns, na.rm = TRUE)
-                s2 <- sum(weights^2 * d2afuns, na.rm = TRUE)
-                return(2 * control$a * (-(nvars + 4)/(2 * dispersion) + s1/(2 * dispersion^2 * s2)))
-            }
-        })
     }
 
-    AS_median_adjustment <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
-        }
-        with(fit, {
-            if (level == 0) {
-                hatvalues <- hat_values(pars, fit = fit)
-                R_matrix <- qr.R(qr_decomposition)
-                info_unscaled <- crossprod(R_matrix)
-                inverse_info_unscaled <- chol2inv(R_matrix)
-                ## FIXME: There is 1) definitely a better way to do this, 2) no time...
-                b_vector <- numeric(nvars)
-                for (j in seq.int(nvars)) {
-                    inverse_info_unscaled_j <- inverse_info_unscaled[j, ]
-                    vcov_j <- tcrossprod(inverse_info_unscaled_j) / inverse_info_unscaled_j[j]
-                    hats_j <- .rowSums((x %*% vcov_j) * x, nobs, nvars, TRUE) * working_weights
-                    b_vector[j] <- inverse_info_unscaled_j %*% .colSums(x * (hats_j * (d1mus * d1varmus / (6 * varmus) - 0.5 * d2mus/d1mus)), nobs, nvars, TRUE)
-                }
-                return(.colSums(0.5 * hatvalues * d2mus / d1mus * x, nobs, nvars, TRUE) +
-                       info_unscaled %*% b_vector)
-            }
-            if (level == 1) {
-                s1 <- sum(weights^3 * d3afuns, na.rm = TRUE)
-                s2 <- sum(weights^2 * d2afuns, na.rm = TRUE)
-                return(nvars/(2 * dispersion) + s1/(6 * dispersion^2 * s2))
+    AS_median_adjustment <- function(pars, fit, level = 0) {
+        if (level == 0) {
+            info_unscaled <- fit$info_beta / fit$precision
+            inverse_info_unscaled <- fit$inverse_info_beta / fit$dispersion
+
+            ## TODO: Below fixme? 
+            ## FIXME: There is 1) definitely a better way to do this, 2) no time... 
+            b_vector <- numeric(nvars)
+            for (j in seq.int(nvars)) {
+                inverse_info_unscaled_j <- inverse_info_unscaled[j, ]
+                vcov_j <- tcrossprod(inverse_info_unscaled_j) / inverse_info_unscaled_j[j]
+                hats_j <- .rowSums((x %*% vcov_j) * x, nobs, nvars, TRUE) * fit$working_weights
+                b_vector[j] <- inverse_info_unscaled_j %*% .colSums(x * (hats_j * (fit$d1mus * fit$d1varmus / (6 * fit$varmus) - 0.5 * fit$d2mus/fit$d1mus)), nobs, nvars, TRUE)
             }
-        })
+            return(.colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
+                       nobs, nvars, TRUE) + 
+               info_unscaled %*% b_vector)
+        }
+        else {
+            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+            return(nvars / (2 * fit$dispersion) + 
+                s1 / (6 * fit$dispersion^2 * s2))
+        }
     }
 
     AS_mixed_adjustment <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
+        if (level == 0) {
+            ## Use only observations with keep = TRUE to ensure that no division with zero takes place
+            return(.colSums(0.5 * fit$hatvalues * fit$d2mus/fit$d1mus * x, nobs, nvars, TRUE))
+        }
+        else {
+            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+            return(nvars / (2 * fit$dispersion) + 
+                s1 / (6 * fit$dispersion^2 * s2))
         }
-        with(fit, {
-            if (level == 0) {
-                hatvalues <- hat_values(pars, fit = fit)
-                ## Use only observations with keep = TRUE to ensure that no division with zero takes place
-                return(.colSums(0.5 * hatvalues * d2mus/d1mus * x, nobs, nvars, TRUE))
-            }
-            if (level == 1) {
-                s1 <- sum(weights^3 * d3afuns, na.rm = TRUE)
-                s2 <- sum(weights^2 * d2afuns, na.rm = TRUE)
-                return(nvars/(2 * dispersion) + s1/(6 * dispersion^2 * s2))
-            }
-        })
     }
 
 
     ## compute_step_components does everything on the scale of the /transformed/ dispersion
-    compute_step_components <- function(pars, level = 0, fit = NULL) {
-        if (is.null(fit)) {
-            fit <- key_quantities(pars, y = y, level = level, qr = TRUE)
-        }
+    compute_step_components <- function(pars, fit, level = 0, adjustment_function, control) {
+
         if (level == 0) {
-            grad <-  gradient(pars, fit = if (has_fixed_totals) NULL else fit, level = 0)
-            inverse_info <- try(information(pars, inverse = TRUE, fit = fit, level = 0))
-            failed_inversion <- inherits(inverse_info, "try-error")
+            # Beta components
+            grad <- fit$grad_beta
+            inverse_info <- fit$inverse_info_beta
             adjustment <- adjustment_function(pars, fit = fit, level = 0)
+            
             failed_adjustment <- any(is.na(adjustment))
+            failed_inversion <- FALSE  # Already computed successfully
         }
-        if (level == 1) {
-            if (no_dispersion | df_residual < 1) {
+        else {
+            # Dispersion components
+            if (fit$no_dispersion || df_residual < 1) {
                 grad <- adjustment <- inverse_info <- NA_real_
                 failed_adjustment <- failed_inversion <- FALSE
             } else {
-                d1zeta <- eval(d1_transformed_dispersion)
-                d2zeta <- eval(d2_transformed_dispersion)
-                grad <-  gradient(theta, fit = fit, level = 1)/d1zeta
-                inverse_info <- 1/information(theta, inverse = FALSE, fit = fit, level = 1) * d1zeta^2
+                d1zeta <- eval(control$d1_transformed_dispersion)
+                d2zeta <- eval(control$d2_transformed_dispersion)
+                
+                grad <- fit$grad_zeta / d1zeta
+                inverse_info <- fit$inverse_info_zeta * d1zeta^2
+                adjustment <- adjustment_function(pars, fit = fit, level = 1) / d1zeta - 
+                            0.5 * d2zeta / d1zeta^2
+                
                 failed_inversion <- !is.finite(inverse_info)
-                ## adjustment <- adjustment_function(theta, fit = fit, level = 1)/d1zeta - if (is_ML | is_AS_median) 0 else 0.5 * d2zeta / d1zeta^2
-                adjustment <- adjustment_function(theta, fit = fit, level = 1)/d1zeta - 0.5 * d2zeta / d1zeta^2
                 failed_adjustment <- is.na(adjustment)
             }
         }
-        out <- list(grad = grad,
-                    inverse_info = inverse_info,
-                    adjustment = adjustment,
-                    failed_adjustment = failed_adjustment,
-                    failed_inversion = failed_inversion)
-        out
+        
+        list(grad = grad,
+             inverse_info = inverse_info,
+             adjustment = adjustment,
+             failed_adjustment = failed_adjustment,
+             failed_inversion = failed_inversion)
     }
 
     customTransformation <- is.list(control$transformation) & length(control$transformation) == 2
@@ -910,13 +887,27 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         ## Evaluate at the starting values
         theta <- c(betas, dispersion)
         transformed_dispersion <- eval(control$Trans)
-        ## Mean quantities
-        ## If fixed_totals is provided (i.e. multinomial regression
-        ## via the Poisson trick) then evaluate everything expect
-        ## the score function at the scaled fitted means
-        quantities <- key_quantities(theta, y = y, level = 2 * !no_dispersion, scale_totals = has_fixed_totals, qr = TRUE)
-        step_components_beta <- compute_step_components(theta, level = 0, fit = quantities)
-        step_components_zeta <- compute_step_components(theta, level = 1, fit = quantities)
+
+        ## Compute fit
+        fit <- compute_fit(pars = theta, 
+                    y = y, 
+                    x = x,
+                    weights = weights,
+                    offset = offset,
+                    family = family,
+                    fixed_totals = fixed_totals,
+                    row_totals = row_totals,
+                    no_dispersion = no_dispersion,
+                    nobs = nobs,
+                    nvars = nvars,
+                    keep = keep)
+
+        step_components_beta <- compute_step_components(theta, level = 0, fit = fit, 
+                                                       adjustment_function = adjustment_function,
+                                                       control = control)
+        step_components_zeta <- compute_step_components(theta, level = 1, fit = fit,
+                                                       adjustment_function = adjustment_function,
+                                                       control = control)
         if (step_components_beta$failed_inversion) {
             warning("failed to invert the information matrix")
         }
@@ -977,16 +968,32 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                     transformed_dispersion <- eval(control$Trans)
 
                     ## Mean quantities
-                    quantities <- try(key_quantities(theta, y = y, level = 2 * !no_dispersion, scale_totals = has_fixed_totals, qr = TRUE), silent = TRUE)
+                    fit <- try(compute_fit(pars = theta, 
+                                                    y = y, 
+                                                    x = x,
+                                                    weights = weights,
+                                                    offset = offset,
+                                                    family = family,
+                                                    fixed_totals = fixed_totals,
+                                                    row_totals = row_totals,
+                                                    no_dispersion = no_dispersion,
+                                                    nobs = nobs,
+                                                    nvars = nvars,
+                                                    keep = keep), silent = TRUE)
+
                     ## This is to capture qr failing and revering to previous estimates
-                    if (failed_adjustment_beta <- inherits(quantities, "try-error")) {
+                    if (failed_adjustment_beta <- inherits(fit, "try-error")) {
                         ## betas <- betas0
                         ## dispersion <- dispersion0
                         warning("failed to calculate score adjustment")
                         break
                     }
-                    step_components_beta <- compute_step_components(theta, level = 0, fit = quantities)
-                    step_components_zeta <- compute_step_components(theta, level = 1, fit = quantities)
+                    step_components_beta <- compute_step_components(theta, level = 0, fit = fit,
+                                                                   adjustment_function = adjustment_function,
+                                                                   control = control)
+                    step_components_zeta <- compute_step_components(theta, level = 1, fit = fit,
+                                                                   adjustment_function = adjustment_function,
+                                                                   control = control)
                     if (failed_inversion_beta <- step_components_beta$failed_inversion) {
                         warning("failed to invert the information matrix")
                         break
@@ -1068,15 +1075,26 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         ## calculating QR decompositions, fitted values, etas,
         ## residuals and working_weights
 
-        quantities <- key_quantities(c(betas, dispersion), y = y, level = 2 * !no_dispersion, scale_totals = has_fixed_totals, qr = TRUE)
-
-        qr.Wx <- quantities$qr_decomposition
-
-        mus <- quantities$mus
-        etas <- quantities$etas
+        fit <- compute_fit(pars = c(betas, dispersion), 
+                        y = y, 
+                        x = x,
+                        weights = weights,
+                        offset = offset,
+                        family = family,
+                        fixed_totals = fixed_totals,
+                        row_totals = row_totals,
+                        no_dispersion = no_dispersion,
+                        nobs = nobs,
+                        nvars = nvars,
+                        keep = keep)
+
+        qr.Wx <- fit$qr_decomposition
+
+        mus <- fit$mus
+        etas <- fit$etas
         ## Residuals
-        residuals <- with(quantities, (y - mus)/d1mus)
-        working_weights <- quantities$working_weights
+        residuals <- with(fit, (y - mus)/d1mus)
+        working_weights <- fit$working_weights
 
         ## info_transformed_dispersion will be NA if is_ML | is_AS_median | is_AS_mixed
         info_transformed_dispersion <- 1/step_components_zeta$inverse_info

From 89574ba510ffd9929cb48ce80e1714ea64c312c0 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Fri, 7 Nov 2025 16:28:12 +0000
Subject: [PATCH 03/15] Tests passing, not utilising scope with control

---
 R/brglmFit.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/brglmFit.R b/R/brglmFit.R
index cf259bb..35629bb 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -603,14 +603,14 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                 grad <- adjustment <- inverse_info <- NA_real_
                 failed_adjustment <- failed_inversion <- FALSE
             } else {
-                d1zeta <- eval(control$d1_transformed_dispersion)
-                d2zeta <- eval(control$d2_transformed_dispersion)
+                d1zeta <- eval(d1_transformed_dispersion)
+                d2zeta <- eval(d2_transformed_dispersion)
                 
                 grad <- fit$grad_zeta / d1zeta
                 inverse_info <- fit$inverse_info_zeta * d1zeta^2
                 adjustment <- adjustment_function(pars, fit = fit, level = 1) / d1zeta - 
                             0.5 * d2zeta / d1zeta^2
-                
+
                 failed_inversion <- !is.finite(inverse_info)
                 failed_adjustment <- is.na(adjustment)
             }

From e98f8a589f441eb1d896f9c14775bf0e7bd646ff Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Fri, 7 Nov 2025 23:07:41 +0000
Subject: [PATCH 04/15] Tests passing with no errors or warnings. Added
 parameters that specify whether qr decomp and hatvalues are needed for
 computation

---
 R/brglmFit.R | 50 +++++++++++++++++++++++++++++++++-----------------
 1 file changed, 33 insertions(+), 17 deletions(-)

diff --git a/R/brglmFit.R b/R/brglmFit.R
index 35629bb..a67b28d 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -299,7 +299,8 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
     # Always computes everything needed, stores it once, passes it around
     compute_fit <- function(pars, y, x, weights, offset, family, 
                             fixed_totals = NULL, row_totals = NULL, 
-                            no_dispersion = FALSE, nobs, nvars, keep) {
+                            no_dispersion = FALSE, nobs, nvars, keep,
+                            need_qr = TRUE, need_hatvalues = TRUE) {
         
         # Extract Parameters
         betas <- pars[seq.int(nvars)]
@@ -323,19 +324,26 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         d1varmus <- family$d1variance(mus)
         working_weights <- weights * d1mus^2 / varmus
 
-        # QR Decomposition
-        wx <- sqrt(working_weights) * x
-        qr_decomposition <- qr(wx)
-        R_matrix <- qr.R(qr_decomposition)
+        # QR Decomposition and Hat Values (only if needed)
+        qr_decomposition <- R_matrix <- Q_matrix <- hatvalues <- NULL
+        info_beta <- inverse_info_beta <- NULL
 
-        # Hat Values 
         # TODO: Avoid forming full Q? Approximate hat values?
-        Qmat <- qr.Q(qr_decomposition) 
-        hatvalues <- .rowSums(Qmat * Qmat, nobs, nvars, TRUE)
-
-        # Information Matrices
-        info_beta <- precision * crossprod(R_matrix)
-        inverse_info_beta <- dispersion * chol2inv(R_matrix)
+        if (need_qr) {
+            wx <- sqrt(working_weights) * x
+            qr_decomposition <- qr(wx)
+            R_matrix <- qr.R(qr_decomposition)
+            
+            # Information Matrices
+            info_beta <- precision * crossprod(R_matrix)
+            inverse_info_beta <- dispersion * chol2inv(R_matrix)
+            
+            # Hat Values (only if needed and we have QR)
+            if (need_hatvalues) {
+                Q_matrix <- qr.Q(qr_decomposition) 
+                hatvalues <- .rowSums(Q_matrix * Q_matrix, nobs, nvars, TRUE)
+            }
+        }
 
         # Dispersion Quantities (dept on family)
         if (!no_dispersion) {
@@ -407,7 +415,7 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
             # QR decomposition and related
             qr_decomposition = qr_decomposition,
             R_matrix = R_matrix,
-            Q_matrix = Qmat, 
+            Q_matrix = Q_matrix, 
             hatvalues = hatvalues,
             
             # Information matrices (pre-computed)
@@ -500,7 +508,9 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                                                 no_dispersion = no_dispersion,
                                                 nobs = nobs,
                                                 nvars = nvars,
-                                                keep = keep)
+                                                keep = keep,
+                                                need_qr = FALSE,
+                                                need_hatvalues = FALSE)
                     gradient(theta, level = 1, fit = cfit)
                 }, lower = .Machine$double.eps, upper = 10000, tol = control$epsilon), silent = FALSE)
                 if (inherits(dispFit, "try-error")) {
@@ -900,7 +910,9 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                     no_dispersion = no_dispersion,
                     nobs = nobs,
                     nvars = nvars,
-                    keep = keep)
+                    keep = keep,
+                    need_qr = TRUE,
+                    need_hatvalues = TRUE)
 
         step_components_beta <- compute_step_components(theta, level = 0, fit = fit, 
                                                        adjustment_function = adjustment_function,
@@ -979,7 +991,9 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                                                     no_dispersion = no_dispersion,
                                                     nobs = nobs,
                                                     nvars = nvars,
-                                                    keep = keep), silent = TRUE)
+                                                    keep = keep, 
+                                                    need_qr = TRUE,
+                                                    need_hatvalues = TRUE), silent = TRUE)
 
                     ## This is to capture qr failing and revering to previous estimates
                     if (failed_adjustment_beta <- inherits(fit, "try-error")) {
@@ -1086,7 +1100,9 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                         no_dispersion = no_dispersion,
                         nobs = nobs,
                         nvars = nvars,
-                        keep = keep)
+                        keep = keep,
+                        need_qr = TRUE,
+                        need_hatvalues = FALSE)
 
         qr.Wx <- fit$qr_decomposition
 

From 0537b8799a2f56ea57bc96c47f3f09ce7755f473 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Mon, 10 Nov 2025 10:36:26 +0000
Subject: [PATCH 05/15] Cleaned up compute_step_components as unnecessary
 parameters passed

---
 R/brglmFit.R | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/R/brglmFit.R b/R/brglmFit.R
index a67b28d..b33ab8d 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -596,7 +596,7 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
 
 
     ## compute_step_components does everything on the scale of the /transformed/ dispersion
-    compute_step_components <- function(pars, fit, level = 0, adjustment_function, control) {
+    compute_step_components <- function(pars, fit, level = 0) {
 
         if (level == 0) {
             # Beta components
@@ -914,12 +914,8 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                     need_qr = TRUE,
                     need_hatvalues = TRUE)
 
-        step_components_beta <- compute_step_components(theta, level = 0, fit = fit, 
-                                                       adjustment_function = adjustment_function,
-                                                       control = control)
-        step_components_zeta <- compute_step_components(theta, level = 1, fit = fit,
-                                                       adjustment_function = adjustment_function,
-                                                       control = control)
+        step_components_beta <- compute_step_components(theta, level = 0, fit = fit)
+        step_components_zeta <- compute_step_components(theta, level = 1, fit = fit)
         if (step_components_beta$failed_inversion) {
             warning("failed to invert the information matrix")
         }
@@ -1002,12 +998,8 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                         warning("failed to calculate score adjustment")
                         break
                     }
-                    step_components_beta <- compute_step_components(theta, level = 0, fit = fit,
-                                                                   adjustment_function = adjustment_function,
-                                                                   control = control)
-                    step_components_zeta <- compute_step_components(theta, level = 1, fit = fit,
-                                                                   adjustment_function = adjustment_function,
-                                                                   control = control)
+                    step_components_beta <- compute_step_components(theta, level = 0, fit = fit)
+                    step_components_zeta <- compute_step_components(theta, level = 1, fit = fit)
                     if (failed_inversion_beta <- step_components_beta$failed_inversion) {
                         warning("failed to invert the information matrix")
                         break

From ed72ddd9f43c82dcc70739888b32ee1d317538a2 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Mon, 10 Nov 2025 14:40:06 +0000
Subject: [PATCH 06/15] Add benchmarking suite for fit-streamline feature

---
 benchmarks/check_setup.R                      | 203 ++++++++++++
 benchmarks/main_benchmark.R                   | 293 ++++++++++++++++++
 .../20251110_142635/benchmark_data.RData      | Bin 0 -> 2082 bytes
 .../20251110_142635/benchmark_results.txt     | 165 ++++++++++
 .../plots/01_lizards_comparison.png           | Bin 0 -> 581 bytes
 .../plots/02_endometrial_comparison.png       | Bin 0 -> 581 bytes
 .../plots/03_speedup_summary.png              | Bin 0 -> 581 bytes
 .../plots/04_absolute_timing.png              | Bin 0 -> 581 bytes
 .../plots/05_lizards_distribution.png         | Bin 0 -> 581 bytes
 .../plots/summary_statistics.csv              |   5 +
 .../results/20251110_142635/test_results.txt  |   3 +
 benchmarks/run_all.R                          |  69 +++++
 benchmarks/setup.R                            | 134 ++++++++
 benchmarks/visualize_results.R                | 168 ++++++++++
 14 files changed, 1040 insertions(+)
 create mode 100644 benchmarks/check_setup.R
 create mode 100644 benchmarks/main_benchmark.R
 create mode 100644 benchmarks/results/20251110_142635/benchmark_data.RData
 create mode 100644 benchmarks/results/20251110_142635/benchmark_results.txt
 create mode 100644 benchmarks/results/20251110_142635/plots/01_lizards_comparison.png
 create mode 100644 benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png
 create mode 100644 benchmarks/results/20251110_142635/plots/03_speedup_summary.png
 create mode 100644 benchmarks/results/20251110_142635/plots/04_absolute_timing.png
 create mode 100644 benchmarks/results/20251110_142635/plots/05_lizards_distribution.png
 create mode 100644 benchmarks/results/20251110_142635/plots/summary_statistics.csv
 create mode 100644 benchmarks/results/20251110_142635/test_results.txt
 create mode 100644 benchmarks/run_all.R
 create mode 100644 benchmarks/setup.R
 create mode 100644 benchmarks/visualize_results.R

diff --git a/benchmarks/check_setup.R b/benchmarks/check_setup.R
new file mode 100644
index 0000000..365bcd7
--- /dev/null
+++ b/benchmarks/check_setup.R
@@ -0,0 +1,203 @@
+# Setup Verification Script
+# Run this first to check that everything is configured correctly
+
+cat("\n")
+cat(strrep("=", 70), "\n")
+cat("BRGLM2 BENCHMARK SETUP VERIFICATION\n")
+cat(strrep("=", 70), "\n\n")
+
+# ====== Check R Version ======
+cat("1. Checking R version...\n")
+r_version <- R.version.string
+cat("   ", r_version, "\n")
+if (getRversion() < "4.0.0") {
+  cat("WARNING: R version 4.0.0 or higher recommended\n")
+}
+cat("OK\n\n")
+
+# ====== Check Required Packages ======
+cat("2. Checking required packages...\n")
+required_pkgs <- c("tictoc", "rbenchmark", "microbenchmark", "ggplot2", "tinytest")
+
+missing_pkgs <- c()
+for (pkg in required_pkgs) {
+  if (requireNamespace(pkg, quietly = TRUE)) {
+    cat("OK", pkg, "installed\n")
+  } else {
+    cat("FAIL", pkg, "NOT FOUND\n")
+    missing_pkgs <- c(missing_pkgs, pkg)
+  }
+}
+
+if (length(missing_pkgs) > 0) {
+  cat("\nInstalling missing packages...\n")
+  install.packages(missing_pkgs)
+  cat("OK Installation complete\n")
+} else {
+  cat("OK All packages available\n")
+}
+cat("\n")
+
+# ====== Check Library Paths ======
+cat("3. Checking library paths...\n")
+
+# Read paths from setup.R if it exists
+setup_file <- "benchmarks/setup.R"
+if (file.exists(setup_file)) {
+  source(setup_file, local = TRUE)
+  
+  cat("Original library:", LIB_ORIGINAL, "\n")
+  if (dir.exists(LIB_ORIGINAL)) {
+    cat("OK Original library exists\n")
+    
+    # Check if brglm2 is there
+    if (file.exists(file.path(LIB_ORIGINAL, "brglm2"))) {
+      cat("OK brglm2 package found in original library\n")
+    } else {
+      cat("FAIL brglm2 package NOT found in original library\n")
+    }
+  } else {
+    cat("FAIL Original library path does NOT exist\n")
+    cat("Please update LIB_ORIGINAL in benchmarks/setup.R\n")
+  }
+  
+  cat("\nNew library:", LIB_NEW, "\n")
+  if (dir.exists(LIB_NEW)) {
+    cat("OK New library exists\n")
+    
+    # Check if brglm2 is there
+    if (file.exists(file.path(LIB_NEW, "brglm2"))) {
+      cat("OK brglm2 package found in new library\n")
+    } else {
+      cat("FAIL brglm2 package NOT found in new library\n")
+    }
+  } else {
+    cat("FAIL New library path does NOT exist\n")
+    cat("Please update LIB_NEW in benchmarks/setup.R\n")
+  }
+} else {
+  cat("FAIL setup.R not found\n")
+  cat("Please ensure you're in the project root directory\n")
+}
+cat("\n")
+
+# ====== Check Package Path (for tests) ======
+cat("4. Checking package path for tests...\n")
+pkg_path <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/brglm2"
+
+if (dir.exists(pkg_path)) {
+  cat("OK Package directory exists:", pkg_path, "\n")
+  
+  # Check for key files
+  key_files <- c("DESCRIPTION", "NAMESPACE", "R", "tests")
+  for (f in key_files) {
+    if (file.exists(file.path(pkg_path, f))) {
+      cat("OK", f, "found\n")
+    } else {
+      cat("FAIL", f, "NOT found\n")
+    }
+  }
+} else {
+  cat("FAIL Package directory does NOT exist\n")
+  cat("Please update pkg_path in main_benchmark.R\n")
+}
+cat("\n")
+
+# ====== Check Datasets ======
+cat("5. Checking dataset availability...\n")
+
+# Try to load brglm2 from somewhere to access datasets
+tryCatch({
+  suppressWarnings(library(brglm2))
+  
+  # Check each dataset
+  datasets_to_check <- c("lizards", "endometrial", "MultipleFeatures")
+  for (ds in datasets_to_check) {
+    tryCatch({
+      data(list = ds, package = "brglm2")
+      if (exists(ds)) {
+        cat("OK", ds, "dataset accessible\n")
+      }
+    }, error = function(e) {
+      cat("FAIL", ds, "dataset NOT accessible\n")
+    })
+  }
+  
+  cat("OK All datasets available\n")
+}, error = function(e) {
+  cat("Could not load brglm2 to check datasets\n")
+  cat("This is OK if you're setting up for the first time\n")
+})
+cat("\n")
+
+# ====== Check Results Directory ======
+cat("6. Checking results directory...\n")
+results_dir <- "benchmarks/results"
+
+if (!dir.exists(results_dir)) {
+  cat("Creating results directory...\n")
+  dir.create(results_dir, recursive = TRUE)
+  cat("OK Results directory created\n")
+} else {
+  cat("OK Results directory exists\n")
+  
+  # Check for previous results
+  existing_results <- list.dirs(results_dir, recursive = FALSE)
+  if (length(existing_results) > 0) {
+    cat("Found", length(existing_results), "previous benchmark run(s)\n")
+    latest <- existing_results[which.max(file.info(existing_results)$mtime)]
+    cat("Latest:", basename(latest), "\n")
+  }
+}
+cat("\n")
+
+# ====== Summary ======
+cat(strrep("=", 70), "\n")
+cat("VERIFICATION SUMMARY\n")
+cat(strrep("=", 70), "\n\n")
+
+# Collect all checks
+checks <- list(
+  "R version" = TRUE,  # We always have R running this
+  "Packages" = length(missing_pkgs) == 0,
+  "Library paths" = exists("LIB_ORIGINAL") && exists("LIB_NEW") && 
+                    dir.exists(LIB_ORIGINAL) && dir.exists(LIB_NEW),
+  "Package path" = dir.exists(pkg_path),
+  "Results directory" = dir.exists(results_dir)
+)
+
+all_ok <- all(unlist(checks))
+
+if (all_ok) {
+  cat("ALL CHECKS PASSED\n\n")
+  cat("You're ready to run benchmarks!\n\n")
+  cat("Run the full suite with:\n")
+  cat("  source('benchmarks/run_all.R')\n\n")
+  cat("Or run individual components:\n")
+  cat("  source('benchmarks/main_benchmark.R')  # Main benchmarks\n")
+  cat("  source('benchmarks/visualize_results.R')  # Generate plots\n")
+} else {
+  cat("SOME CHECKS FAILED\n\n")
+  cat("Please fix the issues above before running benchmarks.\n\n")
+  
+  cat("Common fixes:\n")
+  cat("1. Update library paths in benchmarks/setup.R\n")
+  cat("2. Install missing packages\n")
+  cat("3. Ensure you're in the correct working directory\n")
+  cat("4. Check that brglm2 is installed in both library locations\n")
+}
+
+cat("\n", strrep("=", 70), "\n\n")
+
+# ====== Helpful Commands ======
+cat("Helpful commands:\n\n")
+cat("Check current working directory:\n")
+cat("  getwd()\n\n")
+cat("Change working directory:\n")
+cat("  setwd('path/to/project')\n\n")
+cat("Install a package:\n")
+cat("  install.packages('package_name')\n\n")
+cat("List installed packages:\n")
+cat("  installed.packages()[,c('Package', 'LibPath')]\n\n")
+cat("Check where package is installed:\n")
+cat("  find.package('brglm2')\n\n")
\ No newline at end of file
diff --git a/benchmarks/main_benchmark.R b/benchmarks/main_benchmark.R
new file mode 100644
index 0000000..441df5a
--- /dev/null
+++ b/benchmarks/main_benchmark.R
@@ -0,0 +1,293 @@
+# Add microbenchmark library
+library(microbenchmark)
+
+# Create results directory with timestamp
+timestamp <- format(Sys.time(), "%Y%m%d_%H%M%S")
+results_dir <- file.path("benchmarks", "results", timestamp)
+dir.create(results_dir, recursive = TRUE)
+
+# Redirect output to file
+sink(file.path(results_dir, "benchmark_results.txt"), split = TRUE)
+
+tryCatch({
+  separator <- strrep("=", 70)
+  
+  cat(separator, "\n")
+  cat("BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS\n")
+  cat("Timestamp:", timestamp, "\n")
+  cat(separator, "\n\n")
+  
+# ====== SECTION 1: Test Suite Execution ======
+cat("\n", separator, "\n")
+cat("SECTION 1: TEST SUITE EXECUTION\n")
+cat(separator, "\n\n")
+
+pkg_path <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/brglm2"
+
+# Ensure DD is available in case internal calls need it
+if (!exists("DD", mode = "function")) {
+  DD <- function(expr, name, order = 1) {
+    if(order < 1) stop("'order' must be >= 1")
+    if(order == 1) D(expr, name)
+    else DD(D(expr, name), name, order - 1)
+  }
+}
+
+run_test_suite <- function(libpath, label) {
+  cat("Running test suite for", label, "version...\n")
+  cat("Library path:", libpath, "\n\n")
+  
+  # Load brglm2 version
+  library(brglm2, lib.loc = libpath)
+  library(tinytest)
+  
+  # Run test suite, timing total duration
+  start <- Sys.time()
+  result <- test_all(pkg_path)
+  elapsed <- as.numeric(difftime(Sys.time(), start, units = "secs"))
+  
+  # Summarise results safely
+  sum_df <- as.data.frame(result)
+  if ("ok" %in% names(sum_df)) {
+    passes <- sum(sum_df$ok)
+    fails <- sum(!sum_df$ok)
+  } else {
+    # fallback if tinytest version differs
+    passes <- NA
+    fails <- NA
+    warning("Could not extract passes/fails from test results")
+  }
+  
+  cat(sprintf("All ok, %d results (%.1fs)\n\n", passes + fails, elapsed))
+  
+  invisible(list(result = result, passes = passes, fails = fails, elapsed = elapsed))
+}
+
+# --- Run NEW version ---
+new_results <- run_test_suite(LIB_NEW, "NEW")
+
+# --- Run ORIGINAL version ---
+orig_results <- run_test_suite(LIB_ORIGINAL, "ORIGINAL")
+
+# --- Save summary file (concise) ---
+test_output_file <- file.path(results_dir, "test_results.txt")
+cat(sprintf(
+  "Original: %d tests (%.1fs)\nNew: %d tests (%.1fs)\nSpeedup: %.2fx faster\n",
+  orig_results$passes + orig_results$fails, orig_results$elapsed,
+  new_results$passes + new_results$fails, new_results$elapsed,
+  orig_results$elapsed / new_results$elapsed
+), file = test_output_file)
+
+cat("\nDetailed test results saved to:", test_output_file, "\n")
+  
+  # ====== SECTION 2: Microbenchmark Comparison ======
+  cat("\n", separator, "\n")
+  cat("SECTION 2: MICROBENCHMARK COMPARISON\n")
+  cat("(100 evaluations with unit: seconds)\n")
+  cat(separator, "\n\n")
+  
+  cat("Test: Lizards dataset (small)\n")
+  lizards_bench <- microbenchmark(
+    original = glm(full_fm, data = lizards,
+                   family = binomial(),
+                   method = brglm2_original,
+                   maxit = 200),
+    new = glm(full_fm, data = lizards,
+              family = binomial(),
+              method = brglm2_new,
+              maxit = 200),
+    times = 100,
+    unit = "s"
+  )
+  print(lizards_bench)
+  
+  cat("\n\nSpeedup factor:", 
+      median(lizards_bench$time[lizards_bench$expr == "original"]) / 
+        median(lizards_bench$time[lizards_bench$expr == "new"]), "x\n")
+  
+  # ====== SECTION 3: Endometrial Dataset Test ======
+  cat("\n", separator, "\n")
+  cat("SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)\n")
+  cat(separator, "\n\n")
+  
+  data("endometrial", package = "brglm2")
+  endo_fm <- HG ~ NV + PI + EH
+  
+  cat("Microbenchmark (50 evaluations):\n")
+  endo_bench <- microbenchmark(
+    original = glm(endo_fm, data = endometrial,
+                   family = binomial("probit"),
+                   method = brglm2_original,
+                   maxit = 200),
+    new = glm(endo_fm, data = endometrial,
+              family = binomial("probit"),
+              method = brglm2_new,
+              maxit = 200),
+    times = 50,
+    unit = "s"
+  )
+  print(endo_bench)
+  
+  cat("\n\nSpeedup factor:", 
+      median(endo_bench$time[endo_bench$expr == "original"]) / 
+        median(endo_bench$time[endo_bench$expr == "new"]), "x\n")
+  
+  # ====== SECTION 4: MultipleFeatures Dataset (Large, High-Dimensional) ======
+  cat("\n", separator, "\n")
+  cat("SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)\n")
+  cat("Reference: Sterzinger & Kosmidis (2024, Section 8)\n")
+  cat(separator, "\n\n")
+
+  if (exists("MultipleFeatures", envir = .GlobalEnv)) {
+    rm(MultipleFeatures, envir = .GlobalEnv)
+  }
+  data("MultipleFeatures", package = "brglm2")
+  
+  # Prepare data following the documentation example
+  vars <- grep("fou|kar", names(MultipleFeatures), value = TRUE)
+  train_id <- which(MultipleFeatures$training)
+  MultipleFeatures[train_id, vars] <- scale(MultipleFeatures[train_id, vars], scale = FALSE)
+  
+  # Calculate kappa for MDYPL
+  kappa <- length(vars) / sum(MultipleFeatures$training)
+  
+  # Create formula for full model
+  full_mf_fm <- formula(paste("I(digit == 7) ~", paste(vars, collapse = " + ")))
+  
+  cat("Dataset info:\n")
+  cat("  Total observations:", nrow(MultipleFeatures), "\n")
+  cat("  Training observations:", sum(MultipleFeatures$training), "\n")
+  cat("  Number of features:", length(vars), "\n")
+  cat("  Dimensionality ratio (kappa):", round(kappa, 4), "\n\n")
+  
+  cat("Running single timing test...\n\n")
+  
+  cat("Original version timing:\n")
+  time_mf_orig <- system.time({
+    fit_mf_orig <- glm(full_mf_fm, data = MultipleFeatures, 
+                       family = binomial(),
+                       method = brglm2_original, 
+                       subset = training, 
+                       maxit = 200)
+  })
+  print(time_mf_orig)
+  cat("\n")
+  
+  cat("New version timing:\n")
+  time_mf_new <- system.time({
+    fit_mf_new <- glm(full_mf_fm, data = MultipleFeatures, 
+                      family = binomial(),
+                      method = brglm2_new, 
+                      subset = training, 
+                      maxit = 200)
+  })
+  print(time_mf_new)
+  cat("\n")
+  
+  cat("MultipleFeatures speedup:", 
+      time_mf_orig["elapsed"] / time_mf_new["elapsed"], "x\n")
+  
+  # Verify coefficients match
+  cat("\nNumerical verification:\n")
+  cat("  Coefficients match:", 
+      isTRUE(all.equal(coef(fit_mf_orig), coef(fit_mf_new), tolerance = 1e-10)), "\n")
+  cat("  Max coefficient difference:", 
+      max(abs(coef(fit_mf_orig) - coef(fit_mf_new))), "\n")
+  cat("  Deviance match:",
+      isTRUE(all.equal(fit_mf_orig$deviance, fit_mf_new$deviance, tolerance = 1e-10)), "\n")
+  
+  # ====== SECTION 5: MDYPL Method Test ======
+  cat("\n", separator, "\n")
+  cat("SECTION 5: MDYPL METHOD (MultipleFeatures)\n")
+  cat("Maximum Diaconis-Ylvisaker Prior Penalized Likelihood\n")
+  cat(separator, "\n\n")
+  
+  # Load both versions with mdyplFit
+  library(brglm2, lib.loc = LIB_ORIGINAL)
+  mdypl_original <- brglm2::mdyplFit
+  
+  detach("package:brglm2", unload = TRUE)
+  library(brglm2, lib.loc = LIB_NEW)
+  mdypl_new <- brglm2::mdyplFit
+  
+  cat("Testing mdyplFit method with alpha = 1/(1 + kappa)\n")
+  alpha_val <- 1 / (1 + kappa)
+  cat("  Alpha value:", round(alpha_val, 4), "\n\n")
+  
+  cat("Original mdyplFit timing:\n")
+  time_mdypl_orig <- system.time({
+    fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
+                          family = binomial(),
+                          method = mdypl_original,
+                          alpha = alpha_val,
+                          subset = training,
+                          maxit = 200)
+  })
+  print(time_mdypl_orig)
+  cat("\n")
+  
+  cat("New mdyplFit timing:\n")
+  time_mdypl_new <- system.time({
+    fit_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
+                         family = binomial(),
+                         method = mdypl_new,
+                         alpha = alpha_val,
+                         subset = training,
+                         maxit = 200)
+  })
+  print(time_mdypl_new)
+  cat("\n")
+  
+  cat("MDYPL speedup:", 
+      time_mdypl_orig["elapsed"] / time_mdypl_new["elapsed"], "x\n")
+  
+  cat("\nNumerical verification (MDYPL):\n")
+  cat("  Coefficients match:", 
+      isTRUE(all.equal(coef(fit_mdypl_orig), coef(fit_mdypl_new), tolerance = 1e-10)), "\n")
+  cat("  Max coefficient difference:", 
+      max(abs(coef(fit_mdypl_orig) - coef(fit_mdypl_new))), "\n")
+  
+  # ====== SECTION 6: Summary Statistics ======
+  cat("\n", separator, "\n")
+  cat("SECTION 6: OVERALL SUMMARY\n")
+  cat(separator, "\n\n")
+  
+  speedups <- c(
+    "Lizards (small)" = median(lizards_bench$time[lizards_bench$expr == "original"]) / 
+      median(lizards_bench$time[lizards_bench$expr == "new"]),
+    "Endometrial (medium)" = median(endo_bench$time[endo_bench$expr == "original"]) / 
+      median(endo_bench$time[endo_bench$expr == "new"]),
+    "MultipleFeatures (large)" = time_mf_orig["elapsed"] / time_mf_new["elapsed"],
+    "MDYPL (large)" = time_mdypl_orig["elapsed"] / time_mdypl_new["elapsed"]
+  )
+  
+  cat("Speedup Summary:\n")
+  for (i in seq_along(speedups)) {
+    cat(sprintf("  %-25s: %.2fx faster\n", names(speedups)[i], speedups[i]))
+  }
+  
+  cat("\nMean speedup:", round(mean(speedups), 2), "x\n")
+  cat("Median speedup:", round(median(speedups), 2), "x\n")
+  
+  # Save benchmark objects for plotting
+  save(lizards_bench, endo_bench, 
+       time_mf_orig, time_mf_new, 
+       time_mdypl_orig, time_mdypl_new,
+       speedups,
+       file = file.path(results_dir, "benchmark_data.RData"))
+  
+  cat("\n", separator, "\n")
+  cat("BENCHMARKING COMPLETE\n")
+  cat("All results saved to:", results_dir, "\n")
+  cat(separator, "\n")
+  
+}, error = function(e) {
+  cat("\n\nERROR OCCURRED:\n")
+  cat(conditionMessage(e), "\n")
+  cat(traceback(), "\n")
+}, finally = {
+  sink()
+})
+
+cat("\nResults saved to:", file.path(results_dir, "benchmark_results.txt"), "\n")
+cat("Benchmark data saved to:", file.path(results_dir, "benchmark_data.RData"), "\n")
\ No newline at end of file
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diff --git a/benchmarks/results/20251110_142635/benchmark_results.txt b/benchmarks/results/20251110_142635/benchmark_results.txt
new file mode 100644
index 0000000..b1f5744
--- /dev/null
+++ b/benchmarks/results/20251110_142635/benchmark_results.txt
@@ -0,0 +1,165 @@
+====================================================================== 
+BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
+Timestamp: 20251110_142635 
+====================================================================== 
+
+
+ ====================================================================== 
+SECTION 1: TEST SUITE EXECUTION
+====================================================================== 
+
+Running test suite for NEW version...
+Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/new 
+
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.9s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 1.1s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.9s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 56ms
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.1s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.8s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.7s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.0s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.3s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 38.4s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 2.2s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.3s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.8s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 41.1s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 14.0s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.6s
+All ok, NA results (113.3s)
+
+Running test suite for ORIGINAL version...
+Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/original 
+
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.8s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 2.4s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.7s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.3s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 83ms
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.7s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.6s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.7s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.4s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.2s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 32.9s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 2.3s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.4s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.7s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 33.3s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.2s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 6.7s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
+All ok, NA results (89.3s)
+
+
+Detailed test results saved to: benchmarks/results/20251110_142635/test_results.txt 
+
+ ====================================================================== 
+SECTION 2: MICROBENCHMARK COMPARISON
+(100 evaluations with unit: seconds)
+====================================================================== 
+
+Test: Lizards dataset (small)
+Unit: seconds
+     expr         min         lq       mean    median         uq       max neval
+ original 0.007249401 0.01269455 0.01776941 0.0172211 0.02214865 0.0369909   100
+      new 0.006609902 0.01268585 0.01728913 0.0163083 0.02137415 0.0353854   100
+
+
+Speedup factor: 1.055971 x
+
+ ====================================================================== 
+SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
+====================================================================== 
+
+Microbenchmark (50 evaluations):
+Unit: seconds
+     expr         min        lq       mean     median        uq       max neval
+ original 0.008669302 0.0124377 0.01720837 0.01515210 0.0203757 0.0430905    50
+      new 0.009150701 0.0143091 0.01781808 0.01756955 0.0208440 0.0287275    50
+
+
+Speedup factor: 0.8624068 x
+
+ ====================================================================== 
+SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
+Reference: Sterzinger & Kosmidis (2024, Section 8)
+====================================================================== 
+
+Dataset info:
+  Total observations: 2000 
+  Training observations: 1000 
+  Number of features: 140 
+  Dimensionality ratio (kappa): 0.14 
+
+Running single timing test...
+
+Original version timing:
+   user  system elapsed 
+  20.47    0.58   21.79 
+
+New version timing:
+   user  system elapsed 
+  19.33    0.60   20.72 
+
+MultipleFeatures speedup: 1.051641 x
+
+Numerical verification:
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+  Deviance match: TRUE 
+
+ ====================================================================== 
+SECTION 5: MDYPL METHOD (MultipleFeatures)
+Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
+====================================================================== 
+
+Testing mdyplFit method with alpha = 1/(1 + kappa)
+  Alpha value: 0.8772 
+
+Original mdyplFit timing:
+   user  system elapsed 
+   0.20    0.03    0.22 
+
+New mdyplFit timing:
+   user  system elapsed 
+   0.25    0.00    0.29 
+
+MDYPL speedup: 0.7586207 x
+
+Numerical verification (MDYPL):
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+
+ ====================================================================== 
+SECTION 6: OVERALL SUMMARY
+====================================================================== 
+
+Speedup Summary:
+  Lizards (small)          : 1.06x faster
+  Endometrial (medium)     : 0.86x faster
+  MultipleFeatures (large).elapsed: 1.05x faster
+  MDYPL (large).elapsed    : 0.76x faster
+
+Mean speedup: 0.93 x
+Median speedup: 0.96 x
+
+ ====================================================================== 
+BENCHMARKING COMPLETE
+All results saved to: benchmarks/results/20251110_142635 
+====================================================================== 
diff --git a/benchmarks/results/20251110_142635/plots/01_lizards_comparison.png b/benchmarks/results/20251110_142635/plots/01_lizards_comparison.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

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diff --git a/benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png b/benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png
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diff --git a/benchmarks/results/20251110_142635/plots/03_speedup_summary.png b/benchmarks/results/20251110_142635/plots/03_speedup_summary.png
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diff --git a/benchmarks/results/20251110_142635/plots/04_absolute_timing.png b/benchmarks/results/20251110_142635/plots/04_absolute_timing.png
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diff --git a/benchmarks/results/20251110_142635/plots/05_lizards_distribution.png b/benchmarks/results/20251110_142635/plots/05_lizards_distribution.png
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diff --git a/benchmarks/results/20251110_142635/plots/summary_statistics.csv b/benchmarks/results/20251110_142635/plots/summary_statistics.csv
new file mode 100644
index 0000000..a298af0
--- /dev/null
+++ b/benchmarks/results/20251110_142635/plots/summary_statistics.csv
@@ -0,0 +1,5 @@
+"Dataset","Version","Median","Mean","SD"
+"Lizards","Original",0.0172211005,0.01776941499,0.00652682193196431
+"Lizards","New",0.016308301,0.01728913399,0.00651137518225907
+"Endometrial","Original",0.015152101,0.01720837496,0.0067319175452717
+"Endometrial","New",0.017569551,0.01781808104,0.00452952984679089
diff --git a/benchmarks/results/20251110_142635/test_results.txt b/benchmarks/results/20251110_142635/test_results.txt
new file mode 100644
index 0000000..8cf4c1d
--- /dev/null
+++ b/benchmarks/results/20251110_142635/test_results.txt
@@ -0,0 +1,3 @@
+Original: NA tests (89.3s)
+New: NA tests (113.3s)
+Speedup: 0.79x faster
diff --git a/benchmarks/run_all.R b/benchmarks/run_all.R
new file mode 100644
index 0000000..4614f3c
--- /dev/null
+++ b/benchmarks/run_all.R
@@ -0,0 +1,69 @@
+# Master script to run all benchmarks
+# This script runs the complete benchmarking suite and generates visualizations
+
+cat("======================================================================\n")
+cat("BRGLM2 COMPREHENSIVE BENCHMARK SUITE\n")
+cat("======================================================================\n\n")
+
+cat("This will run:\n")
+cat("  1. Test suite validation\n")
+cat("  2. Microbenchmark comparisons (small & medium datasets)\n")
+cat("  3. Large dataset tests (MultipleFeatures)\n")
+cat("  4. MDYPL method comparison\n")
+cat("  5. Visualization generation\n\n")
+
+cat("Expected runtime: ~ 5 minutes depending on system\n\n")
+
+response <- readline(prompt = "Continue? (y/n): ")
+
+if (tolower(response) != "y") {
+  cat("Benchmark cancelled.\n")
+  quit(save = "no")
+}
+
+cat("\n======================================================================\n")
+cat("PHASE 1: Running validation and setup\n")
+cat("======================================================================\n\n")
+
+# Verify and Setup
+source("benchmarks/check_setup.R")
+source("benchmarks/setup.R")
+
+cat("\n======================================================================\n")
+cat("PHASE 2: Running main benchmark script\n")
+cat("======================================================================\n\n")
+
+# Run main benchmark
+start_time <- Sys.time()
+source("benchmarks/main_benchmark.R")
+end_time <- Sys.time()
+
+cat("\n======================================================================\n")
+cat("PHASE 3: Generating visualizations\n")
+cat("======================================================================\n\n")
+
+# Generate plots
+source("benchmarks/visualize_results.R")
+
+cat("\n======================================================================\n")
+cat("BENCHMARK SUITE COMPLETE\n")
+cat("======================================================================\n\n")
+
+cat("Total runtime:", format(difftime(end_time, start_time)), "\n")
+cat("Results directory:", file.path("benchmarks", "results"), "\n\n")
+
+cat("Next steps:\n")
+cat("  1. Review benchmark_results.txt for detailed timing\n")
+cat("  2. Check plots/ directory for visualizations\n")
+cat("  3. Review test_results.txt for test suite output\n\n")
+
+cat("Summary of improvements:\n")
+results_dir <- file.path("benchmarks", "results")
+dirs <- list.dirs(results_dir, recursive = FALSE)
+latest_dir <- dirs[which.max(file.info(dirs)$mtime)]
+load(file.path(latest_dir, "benchmark_data.RData"))
+
+for (i in seq_along(speedups)) {
+  cat(sprintf("  %-30s: %.2fx faster\n", names(speedups)[i], speedups[i]))
+}
+cat(sprintf("  %-30s: %.2fx faster\n", "Average", mean(speedups)))
\ No newline at end of file
diff --git a/benchmarks/setup.R b/benchmarks/setup.R
new file mode 100644
index 0000000..38a921c
--- /dev/null
+++ b/benchmarks/setup.R
@@ -0,0 +1,134 @@
+# Configuration for all benchmark scripts
+
+# ====== Library Paths ======
+LIB_ORIGINAL <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/original"
+LIB_NEW <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/new"
+
+# ====== Load Required Packages ======
+cat("Loading benchmark packages...\n")
+
+required_packages <- c("tictoc", "rbenchmark", "microbenchmark", "ggplot2")
+
+for (pkg in required_packages) {
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    cat("Installing", pkg, "...\n")
+    install.packages(pkg)
+  }
+  library(pkg, character.only = TRUE)
+}
+
+cat("All packages loaded successfully.\n\n")
+
+# ====== Load Both Versions of brglm2 ======
+cat("Loading brglm2 versions...\n")
+
+# Load original version
+if (!dir.exists(LIB_ORIGINAL)) {
+  stop("Original library path does not exist: ", LIB_ORIGINAL)
+}
+
+library(brglm2, lib.loc = LIB_ORIGINAL)
+brglm2_original <- brglm2::brglmFit
+cat("  Original brglmFit loaded from:", LIB_ORIGINAL, "\n")
+
+# Detach and load new version
+detach("package:brglm2", unload = TRUE)
+
+if (!dir.exists(LIB_NEW)) {
+  stop("New library path does not exist: ", LIB_NEW)
+}
+
+library(brglm2, lib.loc = LIB_NEW)
+brglm2_new <- brglm2::brglmFit
+cat("  New brglmFit loaded from:", LIB_NEW, "\n\n")
+
+# ====== Verify Version Loading ======
+if (!exists("brglm2_original") || !exists("brglm2_new")) {
+  stop("Failed to load one or both brglm2 versions")
+}
+
+# ====== Setup Test Data ======
+cat("Loading test datasets...\n")
+
+# Lizards dataset (small)
+data("lizards", package = "brglm2")
+full_fm <- cbind(grahami, opalinus) ~ height + diameter + light + time
+cat("  Lizards dataset loaded (n =", nrow(lizards), ")\n")
+
+# Endometrial dataset (medium)
+data("endometrial", package = "brglm2")
+cat("  Endometrial dataset loaded (n =", nrow(endometrial), ")\n")
+
+# MultipleFeatures dataset (large, high-dimensional)
+if (exists("MultipleFeatures", envir = .GlobalEnv)) {
+  rm(MultipleFeatures, envir = .GlobalEnv)
+}
+data("MultipleFeatures", package = "brglm2")
+cat("  MultipleFeatures dataset loaded (n =", nrow(MultipleFeatures), ")\n")
+
+# ====== Configuration Summary ======
+cat("\n")
+cat(strrep("=", 70), "\n")
+cat("BENCHMARK SETUP COMPLETE\n")
+cat(strrep("=", 70), "\n")
+cat("Original library:", LIB_ORIGINAL, "\n")
+cat("New library:", LIB_NEW, "\n")
+cat("Datasets loaded: lizards, endometrial, MultipleFeatures\n")
+cat("Packages loaded:", paste(required_packages, collapse = ", "), "\n")
+cat(strrep("=", 70), "\n\n")
+
+# ====== Utility Functions ======
+
+# Function to safely run and time code
+safe_time <- function(expr, name = "Expression") {
+  cat("Timing:", name, "...\n")
+  tryCatch({
+    timing <- system.time(result <- expr)
+    cat("  Completed in", timing["elapsed"], "seconds\n")
+    list(result = result, timing = timing, success = TRUE)
+  }, error = function(e) {
+    cat("  ERROR:", conditionMessage(e), "\n")
+    list(result = NULL, timing = NULL, success = FALSE, error = e)
+  })
+}
+
+# Function to compare two fits for numerical equality
+compare_fits <- function(fit1, fit2, tolerance = 1e-10, verbose = TRUE) {
+  checks <- list(
+    coefficients = all.equal(coef(fit1), coef(fit2), tolerance = tolerance),
+    fitted_values = all.equal(fitted(fit1), fitted(fit2), tolerance = tolerance),
+    deviance = all.equal(fit1$deviance, fit2$deviance, tolerance = tolerance)
+  )
+  
+  if (verbose) {
+    cat("\nNumerical Comparison:\n")
+    cat("  Coefficients match:", isTRUE(checks$coefficients), "\n")
+    if (!isTRUE(checks$coefficients)) {
+      cat("    Max difference:", max(abs(coef(fit1) - coef(fit2))), "\n")
+    }
+    cat("  Fitted values match:", isTRUE(checks$fitted_values), "\n")
+    if (!isTRUE(checks$fitted_values)) {
+      cat("    Max difference:", max(abs(fitted(fit1) - fitted(fit2))), "\n")
+    }
+    cat("  Deviance match:", isTRUE(checks$deviance), "\n")
+    if (!isTRUE(checks$deviance)) {
+      cat("    Difference:", abs(fit1$deviance - fit2$deviance), "\n")
+    }
+  }
+  
+  all(sapply(checks, isTRUE))
+}
+
+# Function to format speedup nicely
+format_speedup <- function(time_old, time_new) {
+  speedup <- time_old / time_new
+  improvement_pct <- (1 - 1/speedup) * 100
+  
+  list(
+    speedup = speedup,
+    improvement_pct = improvement_pct,
+    text = sprintf("%.2fx faster (%.1f%% improvement)", speedup, improvement_pct)
+  )
+}
+
+cat("Setup complete! Ready to run benchmarks.\n\n")
\ No newline at end of file
diff --git a/benchmarks/visualize_results.R b/benchmarks/visualize_results.R
new file mode 100644
index 0000000..c8ce165
--- /dev/null
+++ b/benchmarks/visualize_results.R
@@ -0,0 +1,168 @@
+# Benchmark visualization script
+# Run this after the main benchmark script completes
+
+library(ggplot2)
+library(microbenchmark)
+
+# Find the most recent results directory
+results_base <- "benchmarks/results"
+dirs <- list.dirs(results_base, recursive = FALSE)
+latest_dir <- dirs[which.max(file.info(dirs)$mtime)]
+
+cat("Loading benchmark data from:", latest_dir, "\n")
+
+# Load the benchmark data
+load(file.path(latest_dir, "benchmark_data.RData"))
+
+# Create plots directory
+plots_dir <- file.path(latest_dir, "plots")
+dir.create(plots_dir, showWarnings = FALSE)
+
+# ====== Plot 1: Microbenchmark comparison (Lizards) ======
+png(file.path(plots_dir, "01_lizards_comparison.png"), 
+    width = 800, height = 600, res = 100)
+autoplot(lizards_bench) + 
+  labs(title = "Lizards Dataset: Original vs New Implementation",
+       subtitle = "100 evaluations each",
+       y = "Time (seconds)") +
+  theme_minimal(base_size = 12)
+dev.off()
+
+# ====== Plot 2: Microbenchmark comparison (Endometrial) ======
+png(file.path(plots_dir, "02_endometrial_comparison.png"), 
+    width = 800, height = 600, res = 100)
+autoplot(endo_bench) + 
+  labs(title = "Endometrial Dataset: Original vs New Implementation",
+       subtitle = "50 evaluations each",
+       y = "Time (seconds)") +
+  theme_minimal(base_size = 12)
+dev.off()
+
+# ====== Plot 3: Speedup summary bar chart ======
+speedup_df <- data.frame(
+  Test = factor(names(speedups), levels = names(speedups)),
+  Speedup = as.numeric(speedups),
+  Category = c("Small", "Medium", "Large", "Large (MDYPL)")
+)
+
+png(file.path(plots_dir, "03_speedup_summary.png"), 
+    width = 800, height = 600, res = 100)
+ggplot(speedup_df, aes(x = Test, y = Speedup, fill = Category)) +
+  geom_bar(stat = "identity") +
+  geom_text(aes(label = sprintf("%.2fx", Speedup)), 
+            vjust = -0.5, size = 4) +
+  geom_hline(yintercept = 1, linetype = "dashed", color = "red") +
+  labs(title = "Performance Improvement: New vs Original Implementation",
+       subtitle = "Higher is better",
+       x = "Test Case",
+       y = "Speedup Factor") +
+  scale_fill_brewer(palette = "Set2") +
+  theme_minimal(base_size = 12) +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1),
+        legend.position = "top")
+dev.off()
+
+# ====== Plot 4: Absolute timing comparison ======
+timing_df <- data.frame(
+  Test = rep(c("Lizards", "Endometrial", "MultipleFeatures", "MDYPL"), each = 2),
+  Version = rep(c("Original", "New"), 4),
+  Time = c(
+    median(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
+    median(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9,
+    median(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
+    median(endo_bench$time[endo_bench$expr == "new"]) / 1e9,
+    time_mf_orig["elapsed"],
+    time_mf_new["elapsed"],
+    time_mdypl_orig["elapsed"],
+    time_mdypl_new["elapsed"]
+  )
+)
+
+png(file.path(plots_dir, "04_absolute_timing.png"), 
+    width = 800, height = 600, res = 100)
+ggplot(timing_df, aes(x = Test, y = Time, fill = Version)) +
+  geom_bar(stat = "identity", position = "dodge") +
+  geom_text(aes(label = sprintf("%.2fs", Time)), 
+            position = position_dodge(width = 0.9),
+            vjust = -0.5, size = 3) +
+  labs(title = "Absolute Execution Time Comparison",
+       subtitle = "Lower is better",
+       x = "Test Case",
+       y = "Time (seconds)") +
+  scale_fill_manual(values = c("Original" = "#E41A1C", "New" = "#4DAF4A")) +
+  theme_minimal(base_size = 12) +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1),
+        legend.position = "top")
+dev.off()
+
+# ====== Plot 5: Distribution comparison (Lizards) ======
+lizards_df <- data.frame(
+  Time = lizards_bench$time / 1e9,  # Convert to seconds
+  Version = lizards_bench$expr
+)
+
+png(file.path(plots_dir, "05_lizards_distribution.png"), 
+    width = 800, height = 600, res = 100)
+ggplot(lizards_df, aes(x = Time, fill = Version)) +
+  geom_density(alpha = 0.6) +
+  geom_vline(data = aggregate(Time ~ Version, lizards_df, median),
+             aes(xintercept = Time, color = Version),
+             linetype = "dashed", size = 1) +
+  labs(title = "Execution Time Distribution: Lizards Dataset",
+       subtitle = "Dashed lines show median values",
+       x = "Time (seconds)",
+       y = "Density") +
+  scale_fill_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+  scale_color_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+  theme_minimal(base_size = 12) +
+  theme(legend.position = "top")
+dev.off()
+
+# ====== Summary statistics table ======
+summary_stats <- rbind(
+  data.frame(
+    Dataset = "Lizards",
+    Version = c("Original", "New"),
+    Median = c(
+      median(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
+      median(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
+    ),
+    Mean = c(
+      mean(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
+      mean(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
+    ),
+    SD = c(
+      sd(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
+      sd(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
+    )
+  ),
+  data.frame(
+    Dataset = "Endometrial",
+    Version = c("Original", "New"),
+    Median = c(
+      median(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
+      median(endo_bench$time[endo_bench$expr == "new"]) / 1e9
+    ),
+    Mean = c(
+      mean(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
+      mean(endo_bench$time[endo_bench$expr == "new"]) / 1e9
+    ),
+    SD = c(
+      sd(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
+      sd(endo_bench$time[endo_bench$expr == "new"]) / 1e9
+    )
+  )
+)
+
+write.csv(summary_stats, 
+          file.path(plots_dir, "summary_statistics.csv"),
+          row.names = FALSE)
+
+cat("\nAll plots saved to:", plots_dir, "\n")
+cat("\nGenerated plots:\n")
+cat("  1. Lizards microbenchmark comparison\n")
+cat("  2. Endometrial microbenchmark comparison\n")
+cat("  3. Overall speedup summary\n")
+cat("  4. Absolute timing comparison\n")
+cat("  5. Lizards timing distribution\n")
+cat("  6. Summary statistics (CSV)\n")
\ No newline at end of file

From 7dcce20c8573a0f98ea583b193f45eb62ed3066e Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Mon, 10 Nov 2025 14:40:10 +0000
Subject: [PATCH 07/15] Ignore benchmark results

---
 .gitignore | Bin 1539 -> 1703 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/.gitignore b/.gitignore
index b4e86b59c501f04261317ed809031c28c8549c01..96f6aa29f20d70367189527585818ffdf61dce45 100644
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From 15272d27434372f7a18c3824f0aefc2f3be524fd Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Mon, 10 Nov 2025 15:04:33 +0000
Subject: [PATCH 08/15] Ignore benchmark results

---
 .gitignore | Bin 1703 -> 1835 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/.gitignore b/.gitignore
index 96f6aa29f20d70367189527585818ffdf61dce45..34e8aee44d2445c61b8eab759de538a5790c1b33 100644
GIT binary patch
delta 19
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delta 7
OcmZ3@x14vway9@9;{wY7


From e0b84045fc3d02fede9918ee019f642169496377 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Mon, 10 Nov 2025 15:04:52 +0000
Subject: [PATCH 09/15] Further amendments to benchmarking files

---
 benchmarks/main_benchmark.R                   |  95 +++++-----
 .../20251110_144218/benchmark_data.RData      | Bin 0 -> 2111 bytes
 .../20251110_144218/benchmark_results.txt     | 165 ++++++++++++++++++
 .../plots/01_lizards_comparison.png           | Bin 0 -> 581 bytes
 .../plots/02_endometrial_comparison.png       | Bin 0 -> 581 bytes
 .../plots/03_speedup_summary.png              | Bin 0 -> 581 bytes
 .../plots/04_absolute_timing.png              | Bin 0 -> 581 bytes
 .../plots/05_lizards_distribution.png         | Bin 0 -> 581 bytes
 .../plots/summary_statistics.csv              |   5 +
 .../results/20251110_144218/test_results.txt  |   3 +
 .../20251110_144957/benchmark_data.RData      | Bin 0 -> 2129 bytes
 .../20251110_144957/benchmark_results.txt     | 164 +++++++++++++++++
 .../plots/01_lizards_comparison.png           | Bin 0 -> 581 bytes
 .../plots/02_endometrial_comparison.png       | Bin 0 -> 581 bytes
 .../plots/03_speedup_summary.png              | Bin 0 -> 581 bytes
 .../plots/04_absolute_timing.png              | Bin 0 -> 581 bytes
 .../plots/05_lizards_distribution.png         | Bin 0 -> 581 bytes
 .../plots/summary_statistics.csv              |   5 +
 benchmarks/run_all.R                          |   5 -
 19 files changed, 383 insertions(+), 59 deletions(-)
 create mode 100644 benchmarks/results/20251110_144218/benchmark_data.RData
 create mode 100644 benchmarks/results/20251110_144218/benchmark_results.txt
 create mode 100644 benchmarks/results/20251110_144218/plots/01_lizards_comparison.png
 create mode 100644 benchmarks/results/20251110_144218/plots/02_endometrial_comparison.png
 create mode 100644 benchmarks/results/20251110_144218/plots/03_speedup_summary.png
 create mode 100644 benchmarks/results/20251110_144218/plots/04_absolute_timing.png
 create mode 100644 benchmarks/results/20251110_144218/plots/05_lizards_distribution.png
 create mode 100644 benchmarks/results/20251110_144218/plots/summary_statistics.csv
 create mode 100644 benchmarks/results/20251110_144218/test_results.txt
 create mode 100644 benchmarks/results/20251110_144957/benchmark_data.RData
 create mode 100644 benchmarks/results/20251110_144957/benchmark_results.txt
 create mode 100644 benchmarks/results/20251110_144957/plots/01_lizards_comparison.png
 create mode 100644 benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png
 create mode 100644 benchmarks/results/20251110_144957/plots/03_speedup_summary.png
 create mode 100644 benchmarks/results/20251110_144957/plots/04_absolute_timing.png
 create mode 100644 benchmarks/results/20251110_144957/plots/05_lizards_distribution.png
 create mode 100644 benchmarks/results/20251110_144957/plots/summary_statistics.csv

diff --git a/benchmarks/main_benchmark.R b/benchmarks/main_benchmark.R
index 441df5a..4d6f2c0 100644
--- a/benchmarks/main_benchmark.R
+++ b/benchmarks/main_benchmark.R
@@ -17,68 +17,55 @@ tryCatch({
   cat("Timestamp:", timestamp, "\n")
   cat(separator, "\n\n")
   
-# ====== SECTION 1: Test Suite Execution ======
-cat("\n", separator, "\n")
-cat("SECTION 1: TEST SUITE EXECUTION\n")
-cat(separator, "\n\n")
+  # ====== SECTION 1: Test Suite Execution ======
+  cat("\n", separator, "\n")
+  cat("SECTION 1: TEST SUITE EXECUTION\n")
+  cat(separator, "\n\n")
 
-pkg_path <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/brglm2"
+  pkg_path <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/brglm2"
 
-# Ensure DD is available in case internal calls need it
-if (!exists("DD", mode = "function")) {
-  DD <- function(expr, name, order = 1) {
-    if(order < 1) stop("'order' must be >= 1")
-    if(order == 1) D(expr, name)
-    else DD(D(expr, name), name, order - 1)
+  # Ensure DD exists for internal brglm2 calls
+  if (!exists("DD", mode = "function")) {
+    DD <- function(expr, name, order = 1) {
+      if(order < 1) stop("'order' must be >= 1")
+      if(order == 1) D(expr, name)
+      else DD(D(expr, name), name, order - 1)
+    }
   }
-}
 
-run_test_suite <- function(libpath, label) {
-  cat("Running test suite for", label, "version...\n")
-  cat("Library path:", libpath, "\n\n")
-  
-  # Load brglm2 version
-  library(brglm2, lib.loc = libpath)
-  library(tinytest)
-  
-  # Run test suite, timing total duration
-  start <- Sys.time()
-  result <- test_all(pkg_path)
-  elapsed <- as.numeric(difftime(Sys.time(), start, units = "secs"))
-  
-  # Summarise results safely
-  sum_df <- as.data.frame(result)
-  if ("ok" %in% names(sum_df)) {
-    passes <- sum(sum_df$ok)
-    fails <- sum(!sum_df$ok)
-  } else {
-    # fallback if tinytest version differs
-    passes <- NA
-    fails <- NA
-    warning("Could not extract passes/fails from test results")
+  run_test_suite <- function(libpath, label) {
+    library(brglm2, lib.loc = libpath)
+    library(tinytest)
+    
+    cat("Running test suite for", label, "version...\n")
+    start <- Sys.time()
+    
+    result <- test_all(pkg_path)
+    elapsed <- as.numeric(difftime(Sys.time(), start, units = "secs"))
+    
+    # Summarise
+    sum_df <- as.data.frame(result)
+    n_passed <- sum(sum_df$ok)
+    n_total  <- nrow(sum_df)
+    
+    cat(sprintf("%s: %d/%d tests OK (%.1fs)\n\n", label, n_passed, n_total, elapsed))
+    
+    invisible(list(result = result, passes = n_passed, total = n_total, elapsed = elapsed))
   }
-  
-  cat(sprintf("All ok, %d results (%.1fs)\n\n", passes + fails, elapsed))
-  
-  invisible(list(result = result, passes = passes, fails = fails, elapsed = elapsed))
-}
-
-# --- Run NEW version ---
-new_results <- run_test_suite(LIB_NEW, "NEW")
 
-# --- Run ORIGINAL version ---
-orig_results <- run_test_suite(LIB_ORIGINAL, "ORIGINAL")
+  # Run NEW version
+  new_results <- run_test_suite(LIB_NEW, "NEW")
 
-# --- Save summary file (concise) ---
-test_output_file <- file.path(results_dir, "test_results.txt")
-cat(sprintf(
-  "Original: %d tests (%.1fs)\nNew: %d tests (%.1fs)\nSpeedup: %.2fx faster\n",
-  orig_results$passes + orig_results$fails, orig_results$elapsed,
-  new_results$passes + new_results$fails, new_results$elapsed,
-  orig_results$elapsed / new_results$elapsed
-), file = test_output_file)
+  # Run ORIGINAL version
+  orig_results <- run_test_suite(LIB_ORIGINAL, "ORIGINAL")
 
-cat("\nDetailed test results saved to:", test_output_file, "\n")
+  # Optional summary in CLI
+  cat(sprintf(
+    "Summary:\n  Original: %d/%d tests OK (%.1fs)\n  New: %d/%d tests OK (%.1fs)\n  Speedup: %.2fx faster\n\n",
+    orig_results$passes, orig_results$total, orig_results$elapsed,
+    new_results$passes, new_results$total, new_results$elapsed,
+    orig_results$elapsed / new_results$elapsed
+  ))
   
   # ====== SECTION 2: Microbenchmark Comparison ======
   cat("\n", separator, "\n")
diff --git a/benchmarks/results/20251110_144218/benchmark_data.RData b/benchmarks/results/20251110_144218/benchmark_data.RData
new file mode 100644
index 0000000000000000000000000000000000000000..76637f1bb1dedd22b1bab241148a13300ee879e8
GIT binary patch
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diff --git a/benchmarks/results/20251110_144218/benchmark_results.txt b/benchmarks/results/20251110_144218/benchmark_results.txt
new file mode 100644
index 0000000..8642dc4
--- /dev/null
+++ b/benchmarks/results/20251110_144218/benchmark_results.txt
@@ -0,0 +1,165 @@
+====================================================================== 
+BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
+Timestamp: 20251110_144218 
+====================================================================== 
+
+
+ ====================================================================== 
+SECTION 1: TEST SUITE EXECUTION
+====================================================================== 
+
+Running test suite for NEW version...
+Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/new 
+
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.7s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.7s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.0s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 66ms
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.8s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.7s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.8s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.4s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.2s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 36.4s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 1.8s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.3s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.7s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 36.0s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 8.3s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
+All ok, NA results (97.8s)
+
+Running test suite for ORIGINAL version...
+Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/original 
+
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.3s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 2.0s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.5s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 4.0s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 68ms
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.1s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 2.6s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.8s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.9s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.1s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.2s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 50.1s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 3.2s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.5s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 1.4s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 58.5s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.2s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 9.9s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
+All ok, NA results (137.4s)
+
+
+Detailed test results saved to: benchmarks/results/20251110_144218/test_results.txt 
+
+ ====================================================================== 
+SECTION 2: MICROBENCHMARK COMPARISON
+(100 evaluations with unit: seconds)
+====================================================================== 
+
+Test: Lizards dataset (small)
+Unit: seconds
+     expr         min         lq       mean     median         uq       max neval
+ original 0.007330301 0.01378855 0.02005687 0.01725985 0.02418465 0.1216547   100
+      new 0.008511801 0.01436165 0.02051142 0.01865905 0.02408140 0.0660474   100
+
+
+Speedup factor: 0.9250123 x
+
+ ====================================================================== 
+SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
+====================================================================== 
+
+Microbenchmark (50 evaluations):
+Unit: seconds
+     expr       min        lq       mean    median        uq       max neval
+ original 0.0139655 0.0263821 0.03291419 0.0325623 0.0400453 0.0557061    50
+      new 0.0134326 0.0235499 0.02991951 0.0293484 0.0363481 0.0509676    50
+
+
+Speedup factor: 1.109509 x
+
+ ====================================================================== 
+SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
+Reference: Sterzinger & Kosmidis (2024, Section 8)
+====================================================================== 
+
+Dataset info:
+  Total observations: 2000 
+  Training observations: 1000 
+  Number of features: 140 
+  Dimensionality ratio (kappa): 0.14 
+
+Running single timing test...
+
+Original version timing:
+   user  system elapsed 
+  30.63    1.30   35.05 
+
+New version timing:
+   user  system elapsed 
+  31.48    1.72   36.10 
+
+MultipleFeatures speedup: 0.9709141 x
+
+Numerical verification:
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+  Deviance match: TRUE 
+
+ ====================================================================== 
+SECTION 5: MDYPL METHOD (MultipleFeatures)
+Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
+====================================================================== 
+
+Testing mdyplFit method with alpha = 1/(1 + kappa)
+  Alpha value: 0.8772 
+
+Original mdyplFit timing:
+   user  system elapsed 
+   0.45    0.03    0.50 
+
+New mdyplFit timing:
+   user  system elapsed 
+   0.45    0.00    0.49 
+
+MDYPL speedup: 1.020408 x
+
+Numerical verification (MDYPL):
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+
+ ====================================================================== 
+SECTION 6: OVERALL SUMMARY
+====================================================================== 
+
+Speedup Summary:
+  Lizards (small)          : 0.93x faster
+  Endometrial (medium)     : 1.11x faster
+  MultipleFeatures (large).elapsed: 0.97x faster
+  MDYPL (large).elapsed    : 1.02x faster
+
+Mean speedup: 1.01 x
+Median speedup: 1 x
+
+ ====================================================================== 
+BENCHMARKING COMPLETE
+All results saved to: benchmarks/results/20251110_144218 
+====================================================================== 
diff --git a/benchmarks/results/20251110_144218/plots/01_lizards_comparison.png b/benchmarks/results/20251110_144218/plots/01_lizards_comparison.png
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diff --git a/benchmarks/results/20251110_144218/plots/05_lizards_distribution.png b/benchmarks/results/20251110_144218/plots/05_lizards_distribution.png
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diff --git a/benchmarks/results/20251110_144218/plots/summary_statistics.csv b/benchmarks/results/20251110_144218/plots/summary_statistics.csv
new file mode 100644
index 0000000..ea87d87
--- /dev/null
+++ b/benchmarks/results/20251110_144218/plots/summary_statistics.csv
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+"Dataset","Version","Median","Mean","SD"
+"Lizards","Original",0.0172598505,0.02005687496,0.0127806048378596
+"Lizards","New",0.0186590505,0.02051141999,0.00995345879697426
+"Endometrial","Original",0.032562301,0.03291419496,0.0106647091686285
+"Endometrial","New",0.029348401,0.02991950706,0.00952642493897422
diff --git a/benchmarks/results/20251110_144218/test_results.txt b/benchmarks/results/20251110_144218/test_results.txt
new file mode 100644
index 0000000..ed74bc5
--- /dev/null
+++ b/benchmarks/results/20251110_144218/test_results.txt
@@ -0,0 +1,3 @@
+Original: NA tests (137.4s)
+New: NA tests (97.8s)
+Speedup: 1.40x faster
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diff --git a/benchmarks/results/20251110_144957/benchmark_results.txt b/benchmarks/results/20251110_144957/benchmark_results.txt
new file mode 100644
index 0000000..cfbd471
--- /dev/null
+++ b/benchmarks/results/20251110_144957/benchmark_results.txt
@@ -0,0 +1,164 @@
+====================================================================== 
+BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
+Timestamp: 20251110_144957 
+====================================================================== 
+
+
+ ====================================================================== 
+SECTION 1: TEST SUITE EXECUTION
+====================================================================== 
+
+Running test suite for NEW version...
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.3s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.9s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 4.9s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 89ms
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.4s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 2.8s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.3s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 1.0s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.3s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.6s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 1.1s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 6.5s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 1.4s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 2.2s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 1.1s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.4s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 12.8s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.8s
+NEW: 0/394 tests OK (168.8s)
+
+Running test suite for ORIGINAL version...
+
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.4s
+
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.0s
+
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.8s
+
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 7.1s
+
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 0.4s
+
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.8s
+
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
+
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 3.4s
+
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.3s
+
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 1.0s
+
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
+
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.3s
+
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.5s
+
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.5s
+
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
+
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 54.4s
+
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 3.0s
+
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.6s
+
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 1.3s
+
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 57.2s
+
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
+
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
+
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 12.2s
+
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.4s
+ORIGINAL: 0/394 tests OK (150.2s)
+
+Summary:
+  Original: 0/394 tests OK (150.2s)
+  New: 0/394 tests OK (168.8s)
+  Speedup: 0.89x faster
+
+
+ ====================================================================== 
+SECTION 2: MICROBENCHMARK COMPARISON
+(100 evaluations with unit: seconds)
+====================================================================== 
+
+Test: Lizards dataset (small)
+Unit: seconds
+     expr       min         lq       mean     median         uq       max neval
+ original 0.0187133 0.02525975 0.02957711 0.02941280 0.03280180 0.0476508   100
+      new 0.0199584 0.02579680 0.02939260 0.02859835 0.03194715 0.0505933   100
+
+
+Speedup factor: 1.028479 x
+
+ ====================================================================== 
+SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
+====================================================================== 
+
+Microbenchmark (50 evaluations):
+Unit: seconds
+     expr       min        lq       mean     median        uq       max neval
+ original 0.0260116 0.0341137 0.04680443 0.04065590 0.0510011 0.1197933    50
+      new 0.0276428 0.0368329 0.05011108 0.04384985 0.0529795 0.1234211    50
+
+
+Speedup factor: 0.9271617 x
+
+ ====================================================================== 
+SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
+Reference: Sterzinger & Kosmidis (2024, Section 8)
+====================================================================== 
+
+Dataset info:
+  Total observations: 2000 
+  Training observations: 1000 
+  Number of features: 140 
+  Dimensionality ratio (kappa): 0.14 
+
+Running single timing test...
+
+Original version timing:
+   user  system elapsed 
+  33.13    1.89   38.67 
+
+New version timing:
+   user  system elapsed 
+  33.34    1.32   36.52 
+
+MultipleFeatures speedup: 1.058872 x
+
+Numerical verification:
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+  Deviance match: TRUE 
+
+ ====================================================================== 
+SECTION 5: MDYPL METHOD (MultipleFeatures)
+Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
+====================================================================== 
+
+Testing mdyplFit method with alpha = 1/(1 + kappa)
+  Alpha value: 0.8772 
+
+Original mdyplFit timing:
+   user  system elapsed 
+   0.51    0.08    0.66 
+
+New mdyplFit timing:
+   user  system elapsed 
+   0.54    0.00    0.56 
+
+MDYPL speedup: 1.178571 x
+
+Numerical verification (MDYPL):
+  Coefficients match: TRUE 
+  Max coefficient difference: 0 
+
+ ====================================================================== 
+SECTION 6: OVERALL SUMMARY
+====================================================================== 
+
+Speedup Summary:
+  Lizards (small)          : 1.03x faster
+  Endometrial (medium)     : 0.93x faster
+  MultipleFeatures (large).elapsed: 1.06x faster
+  MDYPL (large).elapsed    : 1.18x faster
+
+Mean speedup: 1.05 x
+Median speedup: 1.04 x
+
+ ====================================================================== 
+BENCHMARKING COMPLETE
+All results saved to: benchmarks/results/20251110_144957 
+====================================================================== 
diff --git a/benchmarks/results/20251110_144957/plots/01_lizards_comparison.png b/benchmarks/results/20251110_144957/plots/01_lizards_comparison.png
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diff --git a/benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png b/benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png
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diff --git a/benchmarks/results/20251110_144957/plots/03_speedup_summary.png b/benchmarks/results/20251110_144957/plots/03_speedup_summary.png
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diff --git a/benchmarks/results/20251110_144957/plots/04_absolute_timing.png b/benchmarks/results/20251110_144957/plots/04_absolute_timing.png
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diff --git a/benchmarks/results/20251110_144957/plots/05_lizards_distribution.png b/benchmarks/results/20251110_144957/plots/05_lizards_distribution.png
new file mode 100644
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diff --git a/benchmarks/results/20251110_144957/plots/summary_statistics.csv b/benchmarks/results/20251110_144957/plots/summary_statistics.csv
new file mode 100644
index 0000000..752d2e6
--- /dev/null
+++ b/benchmarks/results/20251110_144957/plots/summary_statistics.csv
@@ -0,0 +1,5 @@
+"Dataset","Version","Median","Mean","SD"
+"Lizards","Original",0.029412801,0.02957711407,0.00609669878307209
+"Lizards","New",0.028598351,0.029392598,0.00532998275559886
+"Endometrial","Original",0.040655901,0.04680443282,0.0205270555333662
+"Endometrial","New",0.043849851,0.05011108294,0.022082500465604
diff --git a/benchmarks/run_all.R b/benchmarks/run_all.R
index 4614f3c..cf16b7c 100644
--- a/benchmarks/run_all.R
+++ b/benchmarks/run_all.R
@@ -52,11 +52,6 @@ cat("======================================================================\n\n"
 cat("Total runtime:", format(difftime(end_time, start_time)), "\n")
 cat("Results directory:", file.path("benchmarks", "results"), "\n\n")
 
-cat("Next steps:\n")
-cat("  1. Review benchmark_results.txt for detailed timing\n")
-cat("  2. Check plots/ directory for visualizations\n")
-cat("  3. Review test_results.txt for test suite output\n\n")
-
 cat("Summary of improvements:\n")
 results_dir <- file.path("benchmarks", "results")
 dirs <- list.dirs(results_dir, recursive = FALSE)

From 813eba171c4642850494350868f1ee24365f0cd6 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Fri, 14 Nov 2025 11:14:03 +0000
Subject: [PATCH 10/15] Benchmarking scripts complete with readme for local
 installation

---
 .gitignore                     | Bin 1835 -> 1572 bytes
 benchmarks/benchmark_readme.md | 384 +++++++++++++++++++++++++++++++++
 benchmarks/check_setup.R       |  15 +-
 benchmarks/main_benchmark.R    |  87 ++++----
 benchmarks/run_all.R           |   4 +-
 benchmarks/visualize_results.R | 317 +++++++++++++++------------
 6 files changed, 604 insertions(+), 203 deletions(-)
 create mode 100644 benchmarks/benchmark_readme.md

diff --git a/.gitignore b/.gitignore
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diff --git a/benchmarks/benchmark_readme.md b/benchmarks/benchmark_readme.md
new file mode 100644
index 0000000..20a4f6b
--- /dev/null
+++ b/benchmarks/benchmark_readme.md
@@ -0,0 +1,384 @@
+# BRGLM2 Benchmarking Suite
+
+Comprehensive performance benchmarking framework for comparing original and optimized versions of the brglm2 R package.
+
+## Overview
+
+This suite compares the performance of two versions of brglm2:
+- **Original**: Main branch implementation
+- **New**: Optimized implementation with performance improvements
+
+The benchmarks test across multiple datasets (small, medium, and large) and different fitting methods (brglmFit and mdyplFit).
+
+## Repository Structure
+```
+parent-directory/
+├── brglm2/                      # Your working branch 
+│   ├── benchmarks/
+│   │   ├── benchmark_readme.md  # You're here (if this wasnt obvious)
+│   │   ├── setup.R              # Configuration and setup
+│   │   ├── check_setup.R        # Validation script
+│   │   ├── main_benchmark.R     # Core benchmarking tests
+│   │   ├── visualize_results.R  # Plot generation
+│   │   ├── run_all.R            # Master execution script
+│   │   └── results/             # Output directory (auto-created)
+│   │       └── YYYYMMDD_HHMMSS/ # Timestamped results
+│   │           ├── benchmark_results.txt
+│   │           ├── benchmark_data.RData
+│   │           └── plots/
+│   ├── R/                       # Your source code
+│   ├── tests/
+│   └── ...
+│
+├── brglm2-original/             # Clone of main branch (reference)
+│   └── ...
+│
+└── benchmark_libs/              # Installed package versions
+    ├── original/
+    │   └── brglm2/              # Compiled original version
+    │       ├── R/
+    │       ├── data/
+    │       ├── libs/
+    │       ├── Meta/
+    │       ├── DESCRIPTION
+    │       └── ...
+    └── new/
+        └── brglm2/              # Compiled optimized version
+            ├── R/
+            ├── data/
+            ├── libs/
+            ├── Meta/
+            ├── DESCRIPTION
+            └── ...
+```
+
+The `benchmark_libs` folder contains **installed (compiled) R packages**. This is essential for dual loading for comparison.
+
+## Initial Setup
+
+### 1. Directory Structure Setup
+
+Starting from your parent directory (containing all projects):
+
+```bash
+# Navigate to parent directory
+cd /path/to/parent-directory
+
+# If not already present, create benchmark_libs
+mkdir -p benchmark_libs/original
+mkdir -p benchmark_libs/new
+
+# Clone main branch for reference (if not already done)
+git clone <repository-url> brglm2-original
+cd brglm2-original
+git checkout main
+cd ..
+
+# Your working branch (if not already present)
+git clone <repository-url> brglm2
+cd brglm2
+git checkout -b benchmark-testing  # or your optimization branch
+
+# Create results directory
+mkdir -p benchmarks/results
+```
+
+### 2. Install Package Versions to `benchmark_libs`
+
+From the parent directory:
+
+```bash
+# Install original version from main branch clone
+cd brglm2-original
+R CMD INSTALL . --library=../benchmark_libs/original
+
+# Install new version from your working branch
+cd ../brglm2
+R CMD INSTALL . --library=../benchmark_libs/new
+```
+
+**Important**: After making changes to your optimized code, reinstall to `benchmark_libs/new`:
+
+```bash
+cd brglm2
+R CMD INSTALL . --library=../benchmark_libs/new
+```
+
+### 3. Configure Paths
+
+Edit `brglm2/benchmarks/setup.R` to point to the correct locations.
+
+**If running from `brglm2/` directory** (recommended), use relative paths:
+
+```r
+# Paths relative to brglm2/ directory
+LIB_ORIGINAL <- "../benchmark_libs/original"
+LIB_NEW <- "../benchmark_libs/new"
+```
+
+**Or use absolute paths**:
+
+```r
+# Example absolute paths (adjust for your system)
+LIB_ORIGINAL <- "C:/path/to/parent-directory/benchmark_libs/original"
+LIB_NEW <- "C:/path/to/parent-directory/benchmark_libs/new"
+```
+
+Also update the package path in `brglm2/benchmarks/check_setup.R`:
+
+```r
+# Absolute path to your working brglm2 source
+pkg_path <- "C:/path/to/parent-directory/brglm2"
+```
+
+### 4. Install Required R Packages
+
+```r
+install.packages(c("tictoc", "rbenchmark", "microbenchmark", 
+                   "ggplot2", "tinytest"))
+```
+
+### 5. Verify Setup
+
+From the `brglm2/` directory:
+
+```r
+setwd("C:/path/to/parent-directory/brglm2")  # Set working directory
+source("benchmarks/check_setup.R")
+```
+
+This will verify:
+- R version compatibility
+- Required packages installed
+- Library paths exist and contain brglm2
+- Test datasets accessible
+- Results directory structure
+
+## Running Benchmarks
+
+### Quick Start
+
+**From the `brglm2/` directory** (your working branch):
+
+```r
+# Set working directory (if not already there)
+setwd("C:/path/to/parent-directory/brglm2")
+
+# Run complete benchmark suite
+source("benchmarks/run_all.R")
+```
+
+This executes:
+1. Setup validation
+2. Test suite execution (both versions)
+3. Microbenchmark comparisons (100 evaluations)
+4. Large dataset tests
+5. MDYPL method comparison
+6. Visualization generation
+
+Expected runtime: ~5 minutes (default settings)
+
+### Individual Components
+
+Run specific benchmark sections:
+
+```r
+# Setup and configuration
+source("benchmarks/setup.R")
+
+# Main benchmarks only
+source("benchmarks/main_benchmark.R")
+
+# Generate plots from existing results
+source("benchmarks/visualize_results.R")
+```
+
+### Workflow After Code Changes
+
+When you modify your optimized code:
+
+```bash
+# 1. Reinstall the new version
+cd /path/to/parent-directory/brglm2
+R CMD INSTALL . --library=../benchmark_libs/new
+
+# 2. Re-run benchmarks
+# In R:
+setwd("C:/path/to/parent-directory/brglm2")
+source("benchmarks/run_all.R")
+```
+
+## Benchmark Components
+
+### 1. Test Suite Validation
+- Runs complete tinytest suite for both versions
+- Verifies numerical correctness
+- Reports pass/fail rates and execution time
+
+### 2. Microbenchmark Tests
+
+#### Small Dataset (Lizards)
+- Dataset: 409 observations, binomial GLM
+- Default: 100 evaluations
+- Tests: brglmFit method
+
+#### Medium Dataset (Endometrial)
+- Dataset: 79 observations, probit link
+- Default: 50 evaluations
+- Tests: brglmFit method
+
+### 3. Large Dataset Tests
+
+#### MultipleFeatures Dataset
+- Dataset: 2000 observations, 432 features
+- High-dimensional classification problem
+- Single timing test (computationally intensive)
+- Tests: brglmFit and mdyplFit methods
+
+### 4. Visualizations
+
+Generated plots:
+- `01_lizards_comparison.png` - Boxplot comparison
+- `02_endometrial_comparison.png` - Boxplot comparison
+- `03_speedup_summary.png` - Speedup factor bar chart
+- `04_absolute_timing.png` - Absolute execution times
+- `05_lizards_distribution.png` - Distribution densities
+
+## Increasing Evaluation Counts
+
+To improve consistency and reduce variability:
+
+### In `main_benchmark.R`
+
+**Lizards microbenchmark** (Line ~68):
+```r
+lizards_bench <- microbenchmark(
+  # ... 
+  times = 1000,  # Change to increase/decrease test numbers
+  unit = "s"
+)
+```
+
+**Endometrial microbenchmark** (Line ~91):
+```r
+endo_bench <- microbenchmark(
+  # ...
+  times = 500,  # Change to increase/decrease test numbers
+  unit = "s"
+)
+```
+
+**MultipleFeatures tests** (Lines ~138-162):
+For more robust timing on large datasets, increase replications.
+
+```r
+time_mf_orig <- system.time({
+  replicate(5, {  # Change from 5 replications
+    fit_mf_orig <- glm(full_mf_fm, data = MultipleFeatures, 
+                       family = binomial(),
+                       method = brglm2_original, 
+                       subset = training, 
+                       maxit = 200)
+  })
+})
+
+# Divide elapsed time by number of replications for average
+cat("Average time per run:", time_mf_orig["elapsed"] / 5, "s\n")
+```
+
+**MDYPL tests** (Lines ~195-221):
+Similarly change replications:
+
+```r
+time_mdypl_orig <- system.time({
+  replicate(5, {  # Change from 5 replications
+    fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
+                          family = binomial(),
+                          method = mdypl_original,
+                          alpha = alpha_val,
+                          subset = training,
+                          maxit = 200)
+  })
+})
+```
+
+### Recommended Settings for 10-Minute Runtime
+
+```r
+# Microbenchmarks
+lizards:     times = 400 
+endometrial: times = 200  
+
+# Large dataset tests
+MultipleFeatures (brglmFit): replicate(5, ...) 
+MDYPL:                       replicate(5, ...) 
+```
+
+## Output Files
+
+### Results Directory Structure
+
+Each run creates a timestamped directory:
+
+```
+benchmarks/results/YYYYMMDD_HHMMSS/
+├── benchmark_results.txt      # Complete text output
+├── benchmark_data.RData       # R objects for plotting
+└── plots/
+    ├── 01_lizards_comparison.png
+    ├── 02_endometrial_comparison.png
+    ├── 03_speedup_summary.png
+    ├── 04_absolute_timing.png
+    └── 05_lizards_distribution.png
+```
+
+### Key Metrics Reported
+
+- **Speedup factors**: New vs Original execution time ratios
+- **Absolute timings**: Median/mean execution times
+- **Test results**: Pass/fail counts for validation
+- **Numerical accuracy**: Coefficient and deviance comparisons
+
+## Troubleshooting
+
+### Common Issues
+
+**"Original library path does not exist"**
+- Update `LIB_ORIGINAL` in `benchmarks/setup.R`
+- Ensure brglm2 is installed: `R CMD INSTALL . --library=path/to/original`
+
+**"brglm2 package NOT found"**
+- Reinstall packages in both library locations
+- Verify installation: `library(brglm2, lib.loc="path/to/lib")`
+
+**"Package directory does NOT exist"**
+- Update `pkg_path` in `benchmarks/check_setup.R` and `main_benchmark.R`
+- Ensure you're running from project root
+
+**Plots fail to generate**
+- Check that `benchmark_data.RData` was created
+- Verify ggplot2 is installed
+- Review error messages in console output
+
+### Verifying Results
+
+Successful benchmarks should show:
+- All tests passing (or matching pass rate between versions)
+- Speedup factors > 1.0 (new faster than original)
+- Numerical accuracy: coefficient differences < 1e-10
+
+## Notes
+
+- The test suite execution times are included in overall speedup metrics
+- Large dataset tests use single evaluations due to computational cost
+- All visualizations use consistent color scheme: Red (original), Green (new)
+- Benchmark data is saved for regenerating plots without re-running tests
+
+## Citations
+
+- Kosmidis, I., & Firth, D. (2021). Jeffreys-prior penalty, finiteness and shrinkage in binomial-response generalized linear models. *Biometrika*, 108(1), 71-82.
+- Sterzinger, P., & Kosmidis, I. (2024). An iteratively reweighted least squares algorithm for the maximum Diaconis-Ylvisaker prior penalized likelihood in binomial-response generalized linear models.
+
+## License
+
+Same as parent brglm2 package.
\ No newline at end of file
diff --git a/benchmarks/check_setup.R b/benchmarks/check_setup.R
index 365bcd7..115f5b7 100644
--- a/benchmarks/check_setup.R
+++ b/benchmarks/check_setup.R
@@ -187,17 +187,4 @@ if (all_ok) {
   cat("4. Check that brglm2 is installed in both library locations\n")
 }
 
-cat("\n", strrep("=", 70), "\n\n")
-
-# ====== Helpful Commands ======
-cat("Helpful commands:\n\n")
-cat("Check current working directory:\n")
-cat("  getwd()\n\n")
-cat("Change working directory:\n")
-cat("  setwd('path/to/project')\n\n")
-cat("Install a package:\n")
-cat("  install.packages('package_name')\n\n")
-cat("List installed packages:\n")
-cat("  installed.packages()[,c('Package', 'LibPath')]\n\n")
-cat("Check where package is installed:\n")
-cat("  find.package('brglm2')\n\n")
\ No newline at end of file
+cat("\n", strrep("=", 70), "\n\n")
\ No newline at end of file
diff --git a/benchmarks/main_benchmark.R b/benchmarks/main_benchmark.R
index 4d6f2c0..f064602 100644
--- a/benchmarks/main_benchmark.R
+++ b/benchmarks/main_benchmark.R
@@ -24,15 +24,6 @@ tryCatch({
 
   pkg_path <- "C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/brglm2"
 
-  # Ensure DD exists for internal brglm2 calls
-  if (!exists("DD", mode = "function")) {
-    DD <- function(expr, name, order = 1) {
-      if(order < 1) stop("'order' must be >= 1")
-      if(order == 1) D(expr, name)
-      else DD(D(expr, name), name, order - 1)
-    }
-  }
-
   run_test_suite <- function(libpath, label) {
     library(brglm2, lib.loc = libpath)
     library(tinytest)
@@ -40,12 +31,15 @@ tryCatch({
     cat("Running test suite for", label, "version...\n")
     start <- Sys.time()
     
+    sink(NULL)
     result <- test_all(pkg_path)
+    sink(file.path(results_dir, "benchmark_results.txt"), append = TRUE, split = TRUE)
+
     elapsed <- as.numeric(difftime(Sys.time(), start, units = "secs"))
     
     # Summarise
     sum_df <- as.data.frame(result)
-    n_passed <- sum(sum_df$ok)
+    n_passed <- sum(sum_df$result == TRUE)
     n_total  <- nrow(sum_df)
     
     cat(sprintf("%s: %d/%d tests OK (%.1fs)\n\n", label, n_passed, n_total, elapsed))
@@ -70,7 +64,7 @@ tryCatch({
   # ====== SECTION 2: Microbenchmark Comparison ======
   cat("\n", separator, "\n")
   cat("SECTION 2: MICROBENCHMARK COMPARISON\n")
-  cat("(100 evaluations with unit: seconds)\n")
+  cat("(1000 evaluations with unit: seconds)\n")
   cat(separator, "\n\n")
   
   cat("Test: Lizards dataset (small)\n")
@@ -83,7 +77,7 @@ tryCatch({
               family = binomial(),
               method = brglm2_new,
               maxit = 200),
-    times = 100,
+    times = 1000,
     unit = "s"
   )
   print(lizards_bench)
@@ -100,7 +94,7 @@ tryCatch({
   data("endometrial", package = "brglm2")
   endo_fm <- HG ~ NV + PI + EH
   
-  cat("Microbenchmark (50 evaluations):\n")
+  cat("Microbenchmark (500 evaluations):\n")
   endo_bench <- microbenchmark(
     original = glm(endo_fm, data = endometrial,
                    family = binomial("probit"),
@@ -110,7 +104,7 @@ tryCatch({
               family = binomial("probit"),
               method = brglm2_new,
               maxit = 200),
-    times = 50,
+    times = 500,
     unit = "s"
   )
   print(endo_bench)
@@ -147,29 +141,34 @@ tryCatch({
   cat("  Number of features:", length(vars), "\n")
   cat("  Dimensionality ratio (kappa):", round(kappa, 4), "\n\n")
   
-  cat("Running single timing test...\n\n")
+  cat("Running timing tests...\n\n")
   
   cat("Original version timing:\n")
   time_mf_orig <- system.time({
+  replicate(10, {
     fit_mf_orig <- glm(full_mf_fm, data = MultipleFeatures, 
                        family = binomial(),
                        method = brglm2_original, 
                        subset = training, 
                        maxit = 200)
   })
-  print(time_mf_orig)
-  cat("\n")
+})
+
+  cat("Average time per run:", time_mf_orig["elapsed"] / 10, "s\n\n")
   
   cat("New version timing:\n")
   time_mf_new <- system.time({
-    fit_mf_new <- glm(full_mf_fm, data = MultipleFeatures, 
-                      family = binomial(),
-                      method = brglm2_new, 
-                      subset = training, 
-                      maxit = 200)
+    replicate(10, {  # Change from 10 replications
+      fit_mf_new <- glm(full_mf_fm, data = MultipleFeatures, 
+                        family = binomial(),
+                        method = brglm2_new, 
+                        subset = training, 
+                        maxit = 200)
+    })
   })
-  print(time_mf_new)
-  cat("\n")
+
+  # Divide elapsed time by number of replications for average
+  cat("Average time per run:", time_mf_orig["elapsed"] / 10, "s\n")
   
   cat("MultipleFeatures speedup:", 
       time_mf_orig["elapsed"] / time_mf_new["elapsed"], "x\n")
@@ -203,26 +202,30 @@ tryCatch({
   
   cat("Original mdyplFit timing:\n")
   time_mdypl_orig <- system.time({
-    fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
-                          family = binomial(),
-                          method = mdypl_original,
-                          alpha = alpha_val,
-                          subset = training,
-                          maxit = 200)
+    replicate(50, { 
+      fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
+                            family = binomial(),
+                            method = mdypl_original,
+                            alpha = alpha_val,
+                            subset = training,
+                            maxit = 200)
+    })
   })
-  print(time_mdypl_orig)
+  cat("Average time per run:", time_mdypl_orig["elapsed"] / 50, "s\n")
   cat("\n")
   
   cat("New mdyplFit timing:\n")
   time_mdypl_new <- system.time({
-    fit_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
+    replicate(50, {
+      fit_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
                          family = binomial(),
                          method = mdypl_new,
                          alpha = alpha_val,
                          subset = training,
                          maxit = 200)
+    })
   })
-  print(time_mdypl_new)
+  cat("Average time per run:", time_mdypl_new["elapsed"] / 50, "s\n")
   cat("\n")
   
   cat("MDYPL speedup:", 
@@ -234,11 +237,6 @@ tryCatch({
   cat("  Max coefficient difference:", 
       max(abs(coef(fit_mdypl_orig) - coef(fit_mdypl_new))), "\n")
   
-  # ====== SECTION 6: Summary Statistics ======
-  cat("\n", separator, "\n")
-  cat("SECTION 6: OVERALL SUMMARY\n")
-  cat(separator, "\n\n")
-  
   speedups <- c(
     "Lizards (small)" = median(lizards_bench$time[lizards_bench$expr == "original"]) / 
       median(lizards_bench$time[lizards_bench$expr == "new"]),
@@ -248,14 +246,6 @@ tryCatch({
     "MDYPL (large)" = time_mdypl_orig["elapsed"] / time_mdypl_new["elapsed"]
   )
   
-  cat("Speedup Summary:\n")
-  for (i in seq_along(speedups)) {
-    cat(sprintf("  %-25s: %.2fx faster\n", names(speedups)[i], speedups[i]))
-  }
-  
-  cat("\nMean speedup:", round(mean(speedups), 2), "x\n")
-  cat("Median speedup:", round(median(speedups), 2), "x\n")
-  
   # Save benchmark objects for plotting
   save(lizards_bench, endo_bench, 
        time_mf_orig, time_mf_new, 
@@ -274,7 +264,4 @@ tryCatch({
   cat(traceback(), "\n")
 }, finally = {
   sink()
-})
-
-cat("\nResults saved to:", file.path(results_dir, "benchmark_results.txt"), "\n")
-cat("Benchmark data saved to:", file.path(results_dir, "benchmark_data.RData"), "\n")
\ No newline at end of file
+})
\ No newline at end of file
diff --git a/benchmarks/run_all.R b/benchmarks/run_all.R
index cf16b7c..c2311d6 100644
--- a/benchmarks/run_all.R
+++ b/benchmarks/run_all.R
@@ -52,12 +52,14 @@ cat("======================================================================\n\n"
 cat("Total runtime:", format(difftime(end_time, start_time)), "\n")
 cat("Results directory:", file.path("benchmarks", "results"), "\n\n")
 
-cat("Summary of improvements:\n")
+cat("Summary of benchmarks:\n")
 results_dir <- file.path("benchmarks", "results")
 dirs <- list.dirs(results_dir, recursive = FALSE)
 latest_dir <- dirs[which.max(file.info(dirs)$mtime)]
 load(file.path(latest_dir, "benchmark_data.RData"))
 
+speedups <- c("Test suite" = orig_results$elapsed / new_results$elapsed, speedups)
+
 for (i in seq_along(speedups)) {
   cat(sprintf("  %-30s: %.2fx faster\n", names(speedups)[i], speedups[i]))
 }
diff --git a/benchmarks/visualize_results.R b/benchmarks/visualize_results.R
index c8ce165..fcff078 100644
--- a/benchmarks/visualize_results.R
+++ b/benchmarks/visualize_results.R
@@ -1,5 +1,5 @@
-# Benchmark visualization script
-# Run this after the main benchmark script completes
+# Fixed Benchmark Visualization Script
+# This version properly handles the benchmark data structure
 
 library(ggplot2)
 library(microbenchmark)
@@ -18,151 +18,192 @@ load(file.path(latest_dir, "benchmark_data.RData"))
 plots_dir <- file.path(latest_dir, "plots")
 dir.create(plots_dir, showWarnings = FALSE)
 
+cat("\n=== Checking loaded data ===\n")
+cat("lizards_bench dimensions:", nrow(lizards_bench), "rows\n")
+cat("endo_bench dimensions:", nrow(endo_bench), "rows\n")
+cat("Speedups vector:", names(speedups), "\n")
+cat("Speedup values:", speedups, "\n\n")
+
 # ====== Plot 1: Microbenchmark comparison (Lizards) ======
-png(file.path(plots_dir, "01_lizards_comparison.png"), 
-    width = 800, height = 600, res = 100)
-autoplot(lizards_bench) + 
-  labs(title = "Lizards Dataset: Original vs New Implementation",
-       subtitle = "100 evaluations each",
-       y = "Time (seconds)") +
-  theme_minimal(base_size = 12)
-dev.off()
+cat("Creating Plot 1: Lizards comparison...\n")
+tryCatch({
+  png(file.path(plots_dir, "01_lizards_comparison.png"), 
+      width = 800, height = 600, res = 100)
+  
+  # Manual boxplot approach (more reliable than autoplot)
+  lizards_df <- data.frame(
+    time_seconds = lizards_bench$time / 1e9,
+    version = lizards_bench$expr
+  )
+  
+  p1 <- ggplot(lizards_df, aes(x = version, y = time_seconds, fill = version)) +
+    geom_boxplot() +
+    labs(title = "Lizards Dataset: Original vs New Implementation",
+         subtitle = "100 evaluations each",
+         x = "Version",
+         y = "Time (seconds)") +
+    scale_fill_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+    theme_minimal(base_size = 12) +
+    theme(legend.position = "none")
+  
+  print(p1)
+  dev.off()
+  cat("Plot 1 saved\n")
+}, error = function(e) {
+  cat("Error in Plot 1:", conditionMessage(e), "\n")
+  dev.off()
+})
 
 # ====== Plot 2: Microbenchmark comparison (Endometrial) ======
-png(file.path(plots_dir, "02_endometrial_comparison.png"), 
-    width = 800, height = 600, res = 100)
-autoplot(endo_bench) + 
-  labs(title = "Endometrial Dataset: Original vs New Implementation",
-       subtitle = "50 evaluations each",
-       y = "Time (seconds)") +
-  theme_minimal(base_size = 12)
-dev.off()
+cat("Creating Plot 2: Endometrial comparison...\n")
+tryCatch({
+  png(file.path(plots_dir, "02_endometrial_comparison.png"), 
+      width = 800, height = 600, res = 100)
+  
+  endo_df <- data.frame(
+    time_seconds = endo_bench$time / 1e9,
+    version = endo_bench$expr
+  )
+  
+  p2 <- ggplot(endo_df, aes(x = version, y = time_seconds, fill = version)) +
+    geom_boxplot() +
+    labs(title = "Endometrial Dataset: Original vs New Implementation",
+         subtitle = "50 evaluations each",
+         x = "Version",
+         y = "Time (seconds)") +
+    scale_fill_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+    theme_minimal(base_size = 12) +
+    theme(legend.position = "none")
+  
+  print(p2)
+  dev.off()
+  cat("Plot 2 saved\n")
+}, error = function(e) {
+  cat("Error in Plot 2:", conditionMessage(e), "\n")
+  dev.off()
+})
 
 # ====== Plot 3: Speedup summary bar chart ======
-speedup_df <- data.frame(
-  Test = factor(names(speedups), levels = names(speedups)),
-  Speedup = as.numeric(speedups),
-  Category = c("Small", "Medium", "Large", "Large (MDYPL)")
-)
-
-png(file.path(plots_dir, "03_speedup_summary.png"), 
-    width = 800, height = 600, res = 100)
-ggplot(speedup_df, aes(x = Test, y = Speedup, fill = Category)) +
-  geom_bar(stat = "identity") +
-  geom_text(aes(label = sprintf("%.2fx", Speedup)), 
-            vjust = -0.5, size = 4) +
-  geom_hline(yintercept = 1, linetype = "dashed", color = "red") +
-  labs(title = "Performance Improvement: New vs Original Implementation",
-       subtitle = "Higher is better",
-       x = "Test Case",
-       y = "Speedup Factor") +
-  scale_fill_brewer(palette = "Set2") +
-  theme_minimal(base_size = 12) +
-  theme(axis.text.x = element_text(angle = 45, hjust = 1),
-        legend.position = "top")
-dev.off()
-
-# ====== Plot 4: Absolute timing comparison ======
-timing_df <- data.frame(
-  Test = rep(c("Lizards", "Endometrial", "MultipleFeatures", "MDYPL"), each = 2),
-  Version = rep(c("Original", "New"), 4),
-  Time = c(
-    median(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
-    median(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9,
-    median(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
-    median(endo_bench$time[endo_bench$expr == "new"]) / 1e9,
-    time_mf_orig["elapsed"],
-    time_mf_new["elapsed"],
-    time_mdypl_orig["elapsed"],
-    time_mdypl_new["elapsed"]
+cat("Creating Plot 3: Speedup summary...\n")
+tryCatch({
+  # Clean up speedup names if they have .elapsed suffix
+  clean_names <- gsub("\\.elapsed$", "", names(speedups))
+  
+  speedup_df <- data.frame(
+    Test = factor(clean_names, levels = clean_names),
+    Speedup = as.numeric(speedups),
+    Category = c("Small", "Medium", "Large", "Large (MDYPL)")
   )
-)
+  
+  png(file.path(plots_dir, "03_speedup_summary.png"), 
+      width = 800, height = 600, res = 100)
+  
+  p3 <- ggplot(speedup_df, aes(x = Test, y = Speedup, fill = Category)) +
+    geom_bar(stat = "identity", width = 0.7) +
+    geom_text(aes(label = sprintf("%.2fx", Speedup)), 
+              vjust = -0.5, size = 4) +
+    geom_hline(yintercept = 1, linetype = "dashed", color = "red", size = 0.8) +
+    labs(title = "Performance Improvement: New vs Original Implementation",
+         subtitle = "Higher is better (baseline = 1.0)",
+         x = "Test Case",
+         y = "Speedup Factor") +
+    scale_fill_brewer(palette = "Set2") +
+    ylim(0, max(speedup_df$Speedup) * 1.15) +
+    theme_minimal(base_size = 12) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1),
+          legend.position = "top")
+  
+  print(p3)
+  dev.off()
+  cat("Plot 3 saved\n")
+}, error = function(e) {
+  cat("Error in Plot 3:", conditionMessage(e), "\n")
+  dev.off()
+})
 
-png(file.path(plots_dir, "04_absolute_timing.png"), 
-    width = 800, height = 600, res = 100)
-ggplot(timing_df, aes(x = Test, y = Time, fill = Version)) +
-  geom_bar(stat = "identity", position = "dodge") +
-  geom_text(aes(label = sprintf("%.2fs", Time)), 
-            position = position_dodge(width = 0.9),
-            vjust = -0.5, size = 3) +
-  labs(title = "Absolute Execution Time Comparison",
-       subtitle = "Lower is better",
-       x = "Test Case",
-       y = "Time (seconds)") +
-  scale_fill_manual(values = c("Original" = "#E41A1C", "New" = "#4DAF4A")) +
-  theme_minimal(base_size = 12) +
-  theme(axis.text.x = element_text(angle = 45, hjust = 1),
-        legend.position = "top")
-dev.off()
-
-# ====== Plot 5: Distribution comparison (Lizards) ======
-lizards_df <- data.frame(
-  Time = lizards_bench$time / 1e9,  # Convert to seconds
-  Version = lizards_bench$expr
-)
-
-png(file.path(plots_dir, "05_lizards_distribution.png"), 
-    width = 800, height = 600, res = 100)
-ggplot(lizards_df, aes(x = Time, fill = Version)) +
-  geom_density(alpha = 0.6) +
-  geom_vline(data = aggregate(Time ~ Version, lizards_df, median),
-             aes(xintercept = Time, color = Version),
-             linetype = "dashed", size = 1) +
-  labs(title = "Execution Time Distribution: Lizards Dataset",
-       subtitle = "Dashed lines show median values",
-       x = "Time (seconds)",
-       y = "Density") +
-  scale_fill_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
-  scale_color_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
-  theme_minimal(base_size = 12) +
-  theme(legend.position = "top")
-dev.off()
-
-# ====== Summary statistics table ======
-summary_stats <- rbind(
-  data.frame(
-    Dataset = "Lizards",
-    Version = c("Original", "New"),
-    Median = c(
+# ====== Plot 4: Absolute timing comparison ======
+cat("Creating Plot 4: Absolute timing...\n")
+tryCatch({
+  timing_df <- data.frame(
+    Test = rep(c("Lizards", "Endometrial", "MultipleFeatures", "MDYPL"), each = 2),
+    Version = rep(c("Original", "New"), 4),
+    Time = c(
       median(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
-      median(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
-    ),
-    Mean = c(
-      mean(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
-      mean(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
-    ),
-    SD = c(
-      sd(lizards_bench$time[lizards_bench$expr == "original"]) / 1e9,
-      sd(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9
-    )
-  ),
-  data.frame(
-    Dataset = "Endometrial",
-    Version = c("Original", "New"),
-    Median = c(
+      median(lizards_bench$time[lizards_bench$expr == "new"]) / 1e9,
       median(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
-      median(endo_bench$time[endo_bench$expr == "new"]) / 1e9
-    ),
-    Mean = c(
-      mean(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
-      mean(endo_bench$time[endo_bench$expr == "new"]) / 1e9
-    ),
-    SD = c(
-      sd(endo_bench$time[endo_bench$expr == "original"]) / 1e9,
-      sd(endo_bench$time[endo_bench$expr == "new"]) / 1e9
+      median(endo_bench$time[endo_bench$expr == "new"]) / 1e9,
+      as.numeric(time_mf_orig["elapsed"]),
+      as.numeric(time_mf_new["elapsed"]),
+      as.numeric(time_mdypl_orig["elapsed"]),
+      as.numeric(time_mdypl_new["elapsed"])
     )
   )
-)
+  
+  png(file.path(plots_dir, "04_absolute_timing.png"), 
+      width = 800, height = 600, res = 100)
+  
+  p4 <- ggplot(timing_df, aes(x = Test, y = Time, fill = Version)) +
+    geom_bar(stat = "identity", position = "dodge", width = 0.7) +
+    geom_text(aes(label = sprintf("%.3fs", Time)), 
+              position = position_dodge(width = 0.7),
+              vjust = -0.5, size = 3) +
+    labs(title = "Absolute Execution Time Comparison",
+         subtitle = "Lower is better",
+         x = "Test Case",
+         y = "Time (seconds)") +
+    scale_fill_manual(values = c("Original" = "#E41A1C", "New" = "#4DAF4A")) +
+    theme_minimal(base_size = 12) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1),
+          legend.position = "top")
+  
+  print(p4)
+  dev.off()
+  cat("Plot 4 saved\n")
+}, error = function(e) {
+  cat("Error in Plot 4:", conditionMessage(e), "\n")
+  dev.off()
+})
 
-write.csv(summary_stats, 
-          file.path(plots_dir, "summary_statistics.csv"),
-          row.names = FALSE)
-
-cat("\nAll plots saved to:", plots_dir, "\n")
-cat("\nGenerated plots:\n")
-cat("  1. Lizards microbenchmark comparison\n")
-cat("  2. Endometrial microbenchmark comparison\n")
-cat("  3. Overall speedup summary\n")
-cat("  4. Absolute timing comparison\n")
-cat("  5. Lizards timing distribution\n")
-cat("  6. Summary statistics (CSV)\n")
\ No newline at end of file
+# ====== Plot 5: Distribution comparison (Lizards) ======
+cat("Creating Plot 5: Lizards distribution...\n")
+tryCatch({
+  lizards_df <- data.frame(
+    Time = lizards_bench$time / 1e9,
+    Version = lizards_bench$expr
+  )
+  
+  medians <- aggregate(Time ~ Version, lizards_df, median)
+  
+  png(file.path(plots_dir, "05_lizards_distribution.png"), 
+      width = 800, height = 600, res = 100)
+  
+  p5 <- ggplot(lizards_df, aes(x = Time, fill = Version)) +
+    geom_density(alpha = 0.6) +
+    geom_vline(data = medians,
+               aes(xintercept = Time, color = Version),
+               linetype = "dashed", size = 1) +
+    labs(title = "Execution Time Distribution: Lizards Dataset",
+         subtitle = "Dashed lines show median values",
+         x = "Time (seconds)",
+         y = "Density") +
+    scale_fill_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+    scale_color_manual(values = c("original" = "#E41A1C", "new" = "#4DAF4A")) +
+    theme_minimal(base_size = 12) +
+    theme(legend.position = "top")
+  
+  print(p5)
+  dev.off()
+  cat("Plot 5 saved\n")
+}, error = function(e) {
+  cat("Error in Plot 5:", conditionMessage(e), "\n")
+  dev.off()
+})
+
+cat("\n=== Visualization Complete ===\n")
+cat("All plots saved to:", plots_dir, "\n\n")
+cat("Generated files:\n")
+cat("  01_lizards_comparison.png - Boxplot comparison\n")
+cat("  02_endometrial_comparison.png - Boxplot comparison\n")
+cat("  03_speedup_summary.png - Speedup bar chart\n")
+cat("  04_absolute_timing.png - Absolute time comparison\n")
+cat("  05_lizards_distribution.png - Distribution densities\n")
\ No newline at end of file

From ba3f10ae53d474b31426623deb9f5a9cd5a17b52 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Fri, 14 Nov 2025 11:16:27 +0000
Subject: [PATCH 11/15] Deletion of wrongly added result files before
 .gitignore updated

---
 .../20251110_142635/benchmark_data.RData      | Bin 2082 -> 0 bytes
 .../20251110_142635/benchmark_results.txt     | 165 ------------------
 .../plots/01_lizards_comparison.png           | Bin 581 -> 0 bytes
 .../plots/02_endometrial_comparison.png       | Bin 581 -> 0 bytes
 .../plots/03_speedup_summary.png              | Bin 581 -> 0 bytes
 .../plots/04_absolute_timing.png              | Bin 581 -> 0 bytes
 .../plots/05_lizards_distribution.png         | Bin 581 -> 0 bytes
 .../plots/summary_statistics.csv              |   5 -
 .../results/20251110_142635/test_results.txt  |   3 -
 .../20251110_144218/benchmark_data.RData      | Bin 2111 -> 0 bytes
 .../20251110_144218/benchmark_results.txt     | 165 ------------------
 .../plots/01_lizards_comparison.png           | Bin 581 -> 0 bytes
 .../plots/02_endometrial_comparison.png       | Bin 581 -> 0 bytes
 .../plots/03_speedup_summary.png              | Bin 581 -> 0 bytes
 .../plots/04_absolute_timing.png              | Bin 581 -> 0 bytes
 .../plots/05_lizards_distribution.png         | Bin 581 -> 0 bytes
 .../plots/summary_statistics.csv              |   5 -
 .../results/20251110_144218/test_results.txt  |   3 -
 .../20251110_144957/benchmark_data.RData      | Bin 2129 -> 0 bytes
 .../20251110_144957/benchmark_results.txt     | 164 -----------------
 .../plots/01_lizards_comparison.png           | Bin 581 -> 0 bytes
 .../plots/02_endometrial_comparison.png       | Bin 581 -> 0 bytes
 .../plots/03_speedup_summary.png              | Bin 581 -> 0 bytes
 .../plots/04_absolute_timing.png              | Bin 581 -> 0 bytes
 .../plots/05_lizards_distribution.png         | Bin 581 -> 0 bytes
 .../plots/summary_statistics.csv              |   5 -
 26 files changed, 515 deletions(-)
 delete mode 100644 benchmarks/results/20251110_142635/benchmark_data.RData
 delete mode 100644 benchmarks/results/20251110_142635/benchmark_results.txt
 delete mode 100644 benchmarks/results/20251110_142635/plots/01_lizards_comparison.png
 delete mode 100644 benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png
 delete mode 100644 benchmarks/results/20251110_142635/plots/03_speedup_summary.png
 delete mode 100644 benchmarks/results/20251110_142635/plots/04_absolute_timing.png
 delete mode 100644 benchmarks/results/20251110_142635/plots/05_lizards_distribution.png
 delete mode 100644 benchmarks/results/20251110_142635/plots/summary_statistics.csv
 delete mode 100644 benchmarks/results/20251110_142635/test_results.txt
 delete mode 100644 benchmarks/results/20251110_144218/benchmark_data.RData
 delete mode 100644 benchmarks/results/20251110_144218/benchmark_results.txt
 delete mode 100644 benchmarks/results/20251110_144218/plots/01_lizards_comparison.png
 delete mode 100644 benchmarks/results/20251110_144218/plots/02_endometrial_comparison.png
 delete mode 100644 benchmarks/results/20251110_144218/plots/03_speedup_summary.png
 delete mode 100644 benchmarks/results/20251110_144218/plots/04_absolute_timing.png
 delete mode 100644 benchmarks/results/20251110_144218/plots/05_lizards_distribution.png
 delete mode 100644 benchmarks/results/20251110_144218/plots/summary_statistics.csv
 delete mode 100644 benchmarks/results/20251110_144218/test_results.txt
 delete mode 100644 benchmarks/results/20251110_144957/benchmark_data.RData
 delete mode 100644 benchmarks/results/20251110_144957/benchmark_results.txt
 delete mode 100644 benchmarks/results/20251110_144957/plots/01_lizards_comparison.png
 delete mode 100644 benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png
 delete mode 100644 benchmarks/results/20251110_144957/plots/03_speedup_summary.png
 delete mode 100644 benchmarks/results/20251110_144957/plots/04_absolute_timing.png
 delete mode 100644 benchmarks/results/20251110_144957/plots/05_lizards_distribution.png
 delete mode 100644 benchmarks/results/20251110_144957/plots/summary_statistics.csv

diff --git a/benchmarks/results/20251110_142635/benchmark_data.RData b/benchmarks/results/20251110_142635/benchmark_data.RData
deleted file mode 100644
index 3a83479d688a96d2aafdc6e15a3e237a1045f4dc..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/benchmarks/results/20251110_142635/benchmark_results.txt b/benchmarks/results/20251110_142635/benchmark_results.txt
deleted file mode 100644
index b1f5744..0000000
--- a/benchmarks/results/20251110_142635/benchmark_results.txt
+++ /dev/null
@@ -1,165 +0,0 @@
-====================================================================== 
-BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
-Timestamp: 20251110_142635 
-====================================================================== 
-
-
- ====================================================================== 
-SECTION 1: TEST SUITE EXECUTION
-====================================================================== 
-
-Running test suite for NEW version...
-Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/new 
-
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.9s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 1.1s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.9s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 56ms
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.1s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.8s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.7s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.0s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.3s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 38.4s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 2.2s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.3s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.8s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 41.1s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 14.0s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.6s
-All ok, NA results (113.3s)
-
-Running test suite for ORIGINAL version...
-Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/original 
-
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.8s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 2.4s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.7s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.3s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 83ms
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.7s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.6s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.7s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.4s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.2s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 32.9s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 2.3s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.4s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.7s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 33.3s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.2s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 6.7s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
-All ok, NA results (89.3s)
-
-
-Detailed test results saved to: benchmarks/results/20251110_142635/test_results.txt 
-
- ====================================================================== 
-SECTION 2: MICROBENCHMARK COMPARISON
-(100 evaluations with unit: seconds)
-====================================================================== 
-
-Test: Lizards dataset (small)
-Unit: seconds
-     expr         min         lq       mean    median         uq       max neval
- original 0.007249401 0.01269455 0.01776941 0.0172211 0.02214865 0.0369909   100
-      new 0.006609902 0.01268585 0.01728913 0.0163083 0.02137415 0.0353854   100
-
-
-Speedup factor: 1.055971 x
-
- ====================================================================== 
-SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
-====================================================================== 
-
-Microbenchmark (50 evaluations):
-Unit: seconds
-     expr         min        lq       mean     median        uq       max neval
- original 0.008669302 0.0124377 0.01720837 0.01515210 0.0203757 0.0430905    50
-      new 0.009150701 0.0143091 0.01781808 0.01756955 0.0208440 0.0287275    50
-
-
-Speedup factor: 0.8624068 x
-
- ====================================================================== 
-SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
-Reference: Sterzinger & Kosmidis (2024, Section 8)
-====================================================================== 
-
-Dataset info:
-  Total observations: 2000 
-  Training observations: 1000 
-  Number of features: 140 
-  Dimensionality ratio (kappa): 0.14 
-
-Running single timing test...
-
-Original version timing:
-   user  system elapsed 
-  20.47    0.58   21.79 
-
-New version timing:
-   user  system elapsed 
-  19.33    0.60   20.72 
-
-MultipleFeatures speedup: 1.051641 x
-
-Numerical verification:
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-  Deviance match: TRUE 
-
- ====================================================================== 
-SECTION 5: MDYPL METHOD (MultipleFeatures)
-Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
-====================================================================== 
-
-Testing mdyplFit method with alpha = 1/(1 + kappa)
-  Alpha value: 0.8772 
-
-Original mdyplFit timing:
-   user  system elapsed 
-   0.20    0.03    0.22 
-
-New mdyplFit timing:
-   user  system elapsed 
-   0.25    0.00    0.29 
-
-MDYPL speedup: 0.7586207 x
-
-Numerical verification (MDYPL):
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-
- ====================================================================== 
-SECTION 6: OVERALL SUMMARY
-====================================================================== 
-
-Speedup Summary:
-  Lizards (small)          : 1.06x faster
-  Endometrial (medium)     : 0.86x faster
-  MultipleFeatures (large).elapsed: 1.05x faster
-  MDYPL (large).elapsed    : 0.76x faster
-
-Mean speedup: 0.93 x
-Median speedup: 0.96 x
-
- ====================================================================== 
-BENCHMARKING COMPLETE
-All results saved to: benchmarks/results/20251110_142635 
-====================================================================== 
diff --git a/benchmarks/results/20251110_142635/plots/01_lizards_comparison.png b/benchmarks/results/20251110_142635/plots/01_lizards_comparison.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png b/benchmarks/results/20251110_142635/plots/02_endometrial_comparison.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_142635/plots/04_absolute_timing.png b/benchmarks/results/20251110_142635/plots/04_absolute_timing.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_142635/plots/05_lizards_distribution.png b/benchmarks/results/20251110_142635/plots/05_lizards_distribution.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_142635/plots/summary_statistics.csv b/benchmarks/results/20251110_142635/plots/summary_statistics.csv
deleted file mode 100644
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+++ /dev/null
@@ -1,5 +0,0 @@
-"Dataset","Version","Median","Mean","SD"
-"Lizards","Original",0.0172211005,0.01776941499,0.00652682193196431
-"Lizards","New",0.016308301,0.01728913399,0.00651137518225907
-"Endometrial","Original",0.015152101,0.01720837496,0.0067319175452717
-"Endometrial","New",0.017569551,0.01781808104,0.00452952984679089
diff --git a/benchmarks/results/20251110_142635/test_results.txt b/benchmarks/results/20251110_142635/test_results.txt
deleted file mode 100644
index 8cf4c1d..0000000
--- a/benchmarks/results/20251110_142635/test_results.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Original: NA tests (89.3s)
-New: NA tests (113.3s)
-Speedup: 0.79x faster
diff --git a/benchmarks/results/20251110_144218/benchmark_data.RData b/benchmarks/results/20251110_144218/benchmark_data.RData
deleted file mode 100644
index 76637f1bb1dedd22b1bab241148a13300ee879e8..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/benchmarks/results/20251110_144218/benchmark_results.txt b/benchmarks/results/20251110_144218/benchmark_results.txt
deleted file mode 100644
index 8642dc4..0000000
--- a/benchmarks/results/20251110_144218/benchmark_results.txt
+++ /dev/null
@@ -1,165 +0,0 @@
-====================================================================== 
-BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
-Timestamp: 20251110_144218 
-====================================================================== 
-
-
- ====================================================================== 
-SECTION 1: TEST SUITE EXECUTION
-====================================================================== 
-
-Running test suite for NEW version...
-Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/new 
-
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.7s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.7s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 3.0s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 66ms
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 1.8s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.7s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.8s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.4s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.2s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 36.4s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 1.8s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.3s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 0.7s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 36.0s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 8.3s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
-All ok, NA results (97.8s)
-
-Running test suite for ORIGINAL version...
-Library path: C:/Users/ollie/OneDrive/Desktop/UNI/Project brglm2/benchmark_libs/original 
-
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.3s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 2.0s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.5s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 4.0s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 68ms
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.3s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.1s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 2.6s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.2s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 0.8s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.5s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 0.9s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.1s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.2s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 50.1s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 3.2s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.5s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 1.4s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 58.5s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.2s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 9.9s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.3s
-All ok, NA results (137.4s)
-
-
-Detailed test results saved to: benchmarks/results/20251110_144218/test_results.txt 
-
- ====================================================================== 
-SECTION 2: MICROBENCHMARK COMPARISON
-(100 evaluations with unit: seconds)
-====================================================================== 
-
-Test: Lizards dataset (small)
-Unit: seconds
-     expr         min         lq       mean     median         uq       max neval
- original 0.007330301 0.01378855 0.02005687 0.01725985 0.02418465 0.1216547   100
-      new 0.008511801 0.01436165 0.02051142 0.01865905 0.02408140 0.0660474   100
-
-
-Speedup factor: 0.9250123 x
-
- ====================================================================== 
-SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
-====================================================================== 
-
-Microbenchmark (50 evaluations):
-Unit: seconds
-     expr       min        lq       mean    median        uq       max neval
- original 0.0139655 0.0263821 0.03291419 0.0325623 0.0400453 0.0557061    50
-      new 0.0134326 0.0235499 0.02991951 0.0293484 0.0363481 0.0509676    50
-
-
-Speedup factor: 1.109509 x
-
- ====================================================================== 
-SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
-Reference: Sterzinger & Kosmidis (2024, Section 8)
-====================================================================== 
-
-Dataset info:
-  Total observations: 2000 
-  Training observations: 1000 
-  Number of features: 140 
-  Dimensionality ratio (kappa): 0.14 
-
-Running single timing test...
-
-Original version timing:
-   user  system elapsed 
-  30.63    1.30   35.05 
-
-New version timing:
-   user  system elapsed 
-  31.48    1.72   36.10 
-
-MultipleFeatures speedup: 0.9709141 x
-
-Numerical verification:
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-  Deviance match: TRUE 
-
- ====================================================================== 
-SECTION 5: MDYPL METHOD (MultipleFeatures)
-Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
-====================================================================== 
-
-Testing mdyplFit method with alpha = 1/(1 + kappa)
-  Alpha value: 0.8772 
-
-Original mdyplFit timing:
-   user  system elapsed 
-   0.45    0.03    0.50 
-
-New mdyplFit timing:
-   user  system elapsed 
-   0.45    0.00    0.49 
-
-MDYPL speedup: 1.020408 x
-
-Numerical verification (MDYPL):
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-
- ====================================================================== 
-SECTION 6: OVERALL SUMMARY
-====================================================================== 
-
-Speedup Summary:
-  Lizards (small)          : 0.93x faster
-  Endometrial (medium)     : 1.11x faster
-  MultipleFeatures (large).elapsed: 0.97x faster
-  MDYPL (large).elapsed    : 1.02x faster
-
-Mean speedup: 1.01 x
-Median speedup: 1 x
-
- ====================================================================== 
-BENCHMARKING COMPLETE
-All results saved to: benchmarks/results/20251110_144218 
-====================================================================== 
diff --git a/benchmarks/results/20251110_144218/plots/01_lizards_comparison.png b/benchmarks/results/20251110_144218/plots/01_lizards_comparison.png
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diff --git a/benchmarks/results/20251110_144218/plots/02_endometrial_comparison.png b/benchmarks/results/20251110_144218/plots/02_endometrial_comparison.png
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diff --git a/benchmarks/results/20251110_144218/plots/03_speedup_summary.png b/benchmarks/results/20251110_144218/plots/03_speedup_summary.png
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diff --git a/benchmarks/results/20251110_144218/plots/05_lizards_distribution.png b/benchmarks/results/20251110_144218/plots/05_lizards_distribution.png
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diff --git a/benchmarks/results/20251110_144218/plots/summary_statistics.csv b/benchmarks/results/20251110_144218/plots/summary_statistics.csv
deleted file mode 100644
index ea87d87..0000000
--- a/benchmarks/results/20251110_144218/plots/summary_statistics.csv
+++ /dev/null
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-"Dataset","Version","Median","Mean","SD"
-"Lizards","Original",0.0172598505,0.02005687496,0.0127806048378596
-"Lizards","New",0.0186590505,0.02051141999,0.00995345879697426
-"Endometrial","Original",0.032562301,0.03291419496,0.0106647091686285
-"Endometrial","New",0.029348401,0.02991950706,0.00952642493897422
diff --git a/benchmarks/results/20251110_144218/test_results.txt b/benchmarks/results/20251110_144218/test_results.txt
deleted file mode 100644
index ed74bc5..0000000
--- a/benchmarks/results/20251110_144218/test_results.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-Original: NA tests (137.4s)
-New: NA tests (97.8s)
-Speedup: 1.40x faster
diff --git a/benchmarks/results/20251110_144957/benchmark_data.RData b/benchmarks/results/20251110_144957/benchmark_data.RData
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diff --git a/benchmarks/results/20251110_144957/benchmark_results.txt b/benchmarks/results/20251110_144957/benchmark_results.txt
deleted file mode 100644
index cfbd471..0000000
--- a/benchmarks/results/20251110_144957/benchmark_results.txt
+++ /dev/null
@@ -1,164 +0,0 @@
-====================================================================== 
-BRGLM2 COMPREHENSIVE BENCHMARKING RESULTS
-Timestamp: 20251110_144957 
-====================================================================== 
-
-
- ====================================================================== 
-SECTION 1: TEST SUITE EXECUTION
-====================================================================== 
-
-Running test suite for NEW version...
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.9s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.3s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.9s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 4.9s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 89ms
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.4s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 2.8s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.3s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 1.0s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.3s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.2s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.6s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 1.1s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 6.5s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 1.4s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 2.2s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 1.1s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.2s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.4s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 12.8s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.8s
-NEW: 0/394 tests OK (168.8s)
-
-Running test suite for ORIGINAL version...
-
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    0 tests    
test-binomial.R...............    4 tests OK 0.4s
-
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    0 tests    
test-bracl.R..................    1 tests OK 
test-bracl.R..................    2 tests OK 
test-bracl.R..................    3 tests OK 
test-bracl.R..................    4 tests OK 
test-bracl.R..................    5 tests OK 
test-bracl.R..................    6 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................    7 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   27 tests OK 
test-bracl.R..................   28 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   29 tests OK 
test-bracl.R..................   30 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   31 tests OK 
test-bracl.R..................   32 tests OK 
test-bracl.R..................   33 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   34 tests OK 
test-bracl.R..................   35 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   36 tests OK 
test-bracl.R..................   37 tests OK 
test-bracl.R..................   38 tests OK 
test-bracl.R..................   39 tests OK 
test-bracl.R..................   40 tests OK 
test-bracl.R..................   41 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   42 tests OK 
test-bracl.R..................   43 tests OK 
test-bracl.R..................   44 tests OK 
test-bracl.R..................   45 tests OK 
test-bracl.R..................   46 tests OK 
test-bracl.R..................   47 tests OK 
test-bracl.R..................   48 tests OK 3.0s
-
test-brglmControl.R...........    0 tests    
test-brglmControl.R...........    1 tests OK 
test-brglmControl.R...........    2 tests OK 
test-brglmControl.R...........    3 tests OK 
test-brglmControl.R...........    4 tests OK 
test-brglmControl.R...........    5 tests OK 
test-brglmControl.R...........    6 tests OK 
test-brglmControl.R...........    7 tests OK 
test-brglmControl.R...........    8 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........    9 tests OK 
test-brglmControl.R...........   10 tests OK 
test-brglmControl.R...........   11 tests OK 
test-brglmControl.R...........   12 tests OK 
test-brglmControl.R...........   13 tests OK 
test-brglmControl.R...........   14 tests OK 
test-brglmControl.R...........   15 tests OK 
test-brglmControl.R...........   16 tests OK 
test-brglmControl.R...........   17 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   18 tests OK 
test-brglmControl.R...........   19 tests OK 
test-brglmControl.R...........   20 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   21 tests OK 
test-brglmControl.R...........   22 tests OK 
test-brglmControl.R...........   23 tests OK 
test-brglmControl.R...........   24 tests OK 
test-brglmControl.R...........   25 tests OK 
test-brglmControl.R...........   26 tests OK 
test-brglmControl.R...........   27 tests OK 
test-brglmControl.R...........   28 tests OK 
test-brglmControl.R...........   29 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   30 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   31 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   32 tests OK 
test-brglmControl.R...........   33 tests OK 0.8s
-
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    0 tests    
test-brnp.R...................    1 tests OK 
test-brnp.R...................    2 tests OK 
test-brnp.R...................    3 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    4 tests OK 
test-brnp.R...................    5 tests OK 
test-brnp.R...................    6 tests OK 
test-brnp.R...................    7 tests OK 
test-brnp.R...................    8 tests OK 
test-brnp.R...................    9 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   15 tests OK 
test-brnp.R...................   16 tests OK 
test-brnp.R...................   17 tests OK 
test-brnp.R...................   18 tests OK 7.1s
-
test-checkinfinite.R..........    0 tests    
test-checkinfinite.R..........    1 tests OK 
test-checkinfinite.R..........    2 tests OK 0.4s
-
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    0 tests    
test-correction.R.............    1 tests OK 0.8s
-
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    0 tests    
test-dispersion.R.............    1 tests OK 
test-dispersion.R.............    2 tests OK 0.2s
-
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    0 tests    
test-expo.R...................    6 tests OK 
test-expo.R...................    7 tests OK 
test-expo.R...................    8 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................    9 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   21 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   33 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   45 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   57 tests OK 
test-expo.R...................   62 tests OK 
test-expo.R...................   63 tests OK 3.4s
-
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    0 tests    
test-gamma.R..................    1 tests OK 
test-gamma.R..................    2 tests OK 0.3s
-
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    0 tests    
test-jeffreys.R...............    1 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    2 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............    3 tests OK 
test-jeffreys.R...............   11 tests OK 1.0s
-
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    0 tests    
test-mdyplFit.R...............    1 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    2 tests OK 
test-mdyplFit.R...............    3 tests OK 
test-mdyplFit.R...............    4 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    5 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    6 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............    7 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   41 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   42 tests OK 
test-mdyplFit.R...............   43 tests OK 
test-mdyplFit.R...............   44 tests OK 
test-mdyplFit.R...............   45 tests OK 
test-mdyplFit.R...............   46 tests OK 
test-mdyplFit.R...............   47 tests OK 
test-mdyplFit.R...............   48 tests OK 
test-mdyplFit.R...............   49 tests OK 
test-mdyplFit.R...............   50 tests OK 
test-mdyplFit.R...............   51 tests OK 
test-mdyplFit.R...............   52 tests OK 
test-mdyplFit.R...............   53 tests OK 
test-mdyplFit.R...............   54 tests OK 
test-mdyplFit.R...............   55 tests OK 
test-mdyplFit.R...............   56 tests OK 
test-mdyplFit.R...............   57 tests OK 
test-mdyplFit.R...............   58 tests OK 
test-mdyplFit.R...............   59 tests OK 
test-mdyplFit.R...............   60 tests OK 
test-mdyplFit.R...............   61 tests OK 
test-mdyplFit.R...............   62 tests OK 0.6s
-
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    0 tests    
test-median-binomial.R........    8 tests OK 1.3s
-
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    0 tests    
test-median-dispersion.R......    1 tests OK 0.5s
-
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    0 tests    
test-median-poisson.R.........    1 tests OK 0.5s
-
test-mis.R....................    0 tests    
test-mis.R....................    0 tests    
test-mis.R....................    1 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    2 tests OK 
test-mis.R....................    3 tests OK 
test-mis.R....................    4 tests OK 0.1s
-
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    0 tests    
test-multinom-binom.R.........    1 tests OK 54.4s
-
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    0 tests    
test-multinom.R...............    1 tests OK 
test-multinom.R...............    1 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    2 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    3 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    4 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    5 tests OK 
test-multinom.R...............    6 tests OK 
test-multinom.R...............    7 tests OK 
test-multinom.R...............    8 tests OK 
test-multinom.R...............    9 tests OK 
test-multinom.R...............   10 tests OK 
test-multinom.R...............   11 tests OK 
test-multinom.R...............   12 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   13 tests OK 
test-multinom.R...............   14 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   15 tests OK 
test-multinom.R...............   16 tests OK 
test-multinom.R...............   17 tests OK 
test-multinom.R...............   18 tests OK 
test-multinom.R...............   19 tests OK 
test-multinom.R...............   20 tests OK 
test-multinom.R...............   21 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   22 tests OK 
test-multinom.R...............   23 tests OK 
test-multinom.R...............   24 tests OK 
test-multinom.R...............   25 tests OK 
test-multinom.R...............   26 tests OK 
test-multinom.R...............   27 tests OK 
test-multinom.R...............   28 tests OK 3.0s
-
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    0 tests    
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    1 tests OK 
test-poisson.R................    2 tests OK 0.6s
-
test-print.R..................    0 tests    
test-print.R..................    0 tests    
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   48 tests OK 
test-print.R..................   49 tests OK 
test-print.R..................   50 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   51 tests OK 
test-print.R..................   52 tests OK 
test-print.R..................   53 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   54 tests OK 
test-print.R..................   55 tests OK 
test-print.R..................   56 tests OK 
test-print.R..................   57 tests OK 1.3s
-
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    0 tests    
test-se.R.....................    1 tests OK 
test-se.R.....................    1 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    2 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    6 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    7 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    8 tests OK 
test-se.R.....................    9 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   10 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   14 tests OK 
test-se.R.....................   15 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   16 tests OK 
test-se.R.....................   17 tests OK 
test-se.R.....................   18 tests OK 57.2s
-
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    0 tests    
test-singular.R...............    1 tests OK 
test-singular.R...............    2 tests OK 0.1s
-
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    0 tests    
test-start.R..................    1 tests OK 
test-start.R..................    2 tests OK 0.3s
-
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......    0 tests    
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   16 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   17 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   18 tests OK 
test-summary_mdyplFit.R.......   19 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   20 tests OK 
test-summary_mdyplFit.R.......   21 tests OK 12.2s
-
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    0 tests    
test-transformation.R.........    1 tests OK 
test-transformation.R.........    2 tests OK 
test-transformation.R.........    3 tests OK 0.4s
-ORIGINAL: 0/394 tests OK (150.2s)
-
-Summary:
-  Original: 0/394 tests OK (150.2s)
-  New: 0/394 tests OK (168.8s)
-  Speedup: 0.89x faster
-
-
- ====================================================================== 
-SECTION 2: MICROBENCHMARK COMPARISON
-(100 evaluations with unit: seconds)
-====================================================================== 
-
-Test: Lizards dataset (small)
-Unit: seconds
-     expr       min         lq       mean     median         uq       max neval
- original 0.0187133 0.02525975 0.02957711 0.02941280 0.03280180 0.0476508   100
-      new 0.0199584 0.02579680 0.02939260 0.02859835 0.03194715 0.0505933   100
-
-
-Speedup factor: 1.028479 x
-
- ====================================================================== 
-SECTION 3: ENDOMETRIAL DATASET (PROBIT LINK)
-====================================================================== 
-
-Microbenchmark (50 evaluations):
-Unit: seconds
-     expr       min        lq       mean     median        uq       max neval
- original 0.0260116 0.0341137 0.04680443 0.04065590 0.0510011 0.1197933    50
-      new 0.0276428 0.0368329 0.05011108 0.04384985 0.0529795 0.1234211    50
-
-
-Speedup factor: 0.9271617 x
-
- ====================================================================== 
-SECTION 4: MULTIPLEFEATURES DATASET (HIGH-DIMENSIONAL)
-Reference: Sterzinger & Kosmidis (2024, Section 8)
-====================================================================== 
-
-Dataset info:
-  Total observations: 2000 
-  Training observations: 1000 
-  Number of features: 140 
-  Dimensionality ratio (kappa): 0.14 
-
-Running single timing test...
-
-Original version timing:
-   user  system elapsed 
-  33.13    1.89   38.67 
-
-New version timing:
-   user  system elapsed 
-  33.34    1.32   36.52 
-
-MultipleFeatures speedup: 1.058872 x
-
-Numerical verification:
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-  Deviance match: TRUE 
-
- ====================================================================== 
-SECTION 5: MDYPL METHOD (MultipleFeatures)
-Maximum Diaconis-Ylvisaker Prior Penalized Likelihood
-====================================================================== 
-
-Testing mdyplFit method with alpha = 1/(1 + kappa)
-  Alpha value: 0.8772 
-
-Original mdyplFit timing:
-   user  system elapsed 
-   0.51    0.08    0.66 
-
-New mdyplFit timing:
-   user  system elapsed 
-   0.54    0.00    0.56 
-
-MDYPL speedup: 1.178571 x
-
-Numerical verification (MDYPL):
-  Coefficients match: TRUE 
-  Max coefficient difference: 0 
-
- ====================================================================== 
-SECTION 6: OVERALL SUMMARY
-====================================================================== 
-
-Speedup Summary:
-  Lizards (small)          : 1.03x faster
-  Endometrial (medium)     : 0.93x faster
-  MultipleFeatures (large).elapsed: 1.06x faster
-  MDYPL (large).elapsed    : 1.18x faster
-
-Mean speedup: 1.05 x
-Median speedup: 1.04 x
-
- ====================================================================== 
-BENCHMARKING COMPLETE
-All results saved to: benchmarks/results/20251110_144957 
-====================================================================== 
diff --git a/benchmarks/results/20251110_144957/plots/01_lizards_comparison.png b/benchmarks/results/20251110_144957/plots/01_lizards_comparison.png
deleted file mode 100644
index 7848440833695b218fdcb3a95161ac8a2ccbfd7f..0000000000000000000000000000000000000000
GIT binary patch
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png b/benchmarks/results/20251110_144957/plots/02_endometrial_comparison.png
deleted file mode 100644
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_144957/plots/03_speedup_summary.png b/benchmarks/results/20251110_144957/plots/03_speedup_summary.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_144957/plots/04_absolute_timing.png b/benchmarks/results/20251110_144957/plots/04_absolute_timing.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_144957/plots/05_lizards_distribution.png b/benchmarks/results/20251110_144957/plots/05_lizards_distribution.png
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T``$Dj0Qt(()z4*}Q$iB}(R?6z

diff --git a/benchmarks/results/20251110_144957/plots/summary_statistics.csv b/benchmarks/results/20251110_144957/plots/summary_statistics.csv
deleted file mode 100644
index 752d2e6..0000000
--- a/benchmarks/results/20251110_144957/plots/summary_statistics.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-"Dataset","Version","Median","Mean","SD"
-"Lizards","Original",0.029412801,0.02957711407,0.00609669878307209
-"Lizards","New",0.028598351,0.029392598,0.00532998275559886
-"Endometrial","Original",0.040655901,0.04680443282,0.0205270555333662
-"Endometrial","New",0.043849851,0.05011108294,0.022082500465604

From 2a49294a012d39a5ece3c2bb41842236f074fcb3 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Wed, 26 Nov 2025 12:39:47 +0000
Subject: [PATCH 12/15] Final changes to main_benchmark fixing new replicate
 for MultipleFeatures fits

---
 benchmarks/main_benchmark.R | 66 ++++++++++++++++++++++++-------------
 1 file changed, 44 insertions(+), 22 deletions(-)

diff --git a/benchmarks/main_benchmark.R b/benchmarks/main_benchmark.R
index f064602..9d754cf 100644
--- a/benchmarks/main_benchmark.R
+++ b/benchmarks/main_benchmark.R
@@ -144,34 +144,42 @@ tryCatch({
   cat("Running timing tests...\n\n")
   
   cat("Original version timing:\n")
+  fit_mf_orig <- glm(full_mf_fm, data = MultipleFeatures, 
+                    family = binomial(),
+                    method = brglm2_original, 
+                    subset = training, 
+                    maxit = 200)
+
   time_mf_orig <- system.time({
-  replicate(10, {
-    fit_mf_orig <- glm(full_mf_fm, data = MultipleFeatures, 
-                       family = binomial(),
-                       method = brglm2_original, 
-                       subset = training, 
-                       maxit = 200)
+    replicate(10, {
+      glm(full_mf_fm, data = MultipleFeatures, 
+          family = binomial(),
+          method = brglm2_original, 
+          subset = training, 
+          maxit = 200)
+    })
   })
-})
-
   cat("Average time per run:", time_mf_orig["elapsed"] / 10, "s\n\n")
-  
+
   cat("New version timing:\n")
+  fit_mf_new <- glm(full_mf_fm, data = MultipleFeatures, 
+                    family = binomial(),
+                    method = brglm2_new, 
+                    subset = training, 
+                    maxit = 200)
+
   time_mf_new <- system.time({
-    replicate(10, {  # Change from 10 replications
-      fit_mf_new <- glm(full_mf_fm, data = MultipleFeatures, 
-                        family = binomial(),
-                        method = brglm2_new, 
-                        subset = training, 
-                        maxit = 200)
+    replicate(10, {
+      glm(full_mf_fm, data = MultipleFeatures, 
+          family = binomial(),
+          method = brglm2_new, 
+          subset = training, 
+          maxit = 200)
     })
   })
+  cat("Average time per run:", time_mf_new["elapsed"] / 10, "s\n\n")
 
-  # Divide elapsed time by number of replications for average
-  cat("Average time per run:", time_mf_orig["elapsed"] / 10, "s\n")
-  
-  cat("MultipleFeatures speedup:", 
-      time_mf_orig["elapsed"] / time_mf_new["elapsed"], "x\n")
+  cat("MultipleFeatures speedup:", time_mf_orig["elapsed"] / time_mf_new["elapsed"], "x\n")
   
   # Verify coefficients match
   cat("\nNumerical verification:\n")
@@ -201,9 +209,16 @@ tryCatch({
   cat("  Alpha value:", round(alpha_val, 4), "\n\n")
   
   cat("Original mdyplFit timing:\n")
+  fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
+                         family = binomial(),
+                         method = mdypl_original,
+                         alpha = alpha_val,
+                         subset = training,
+                         maxit = 200)
+
   time_mdypl_orig <- system.time({
     replicate(50, { 
-      fit_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
+      full_mdypl_orig <- glm(full_mf_fm, data = MultipleFeatures,
                             family = binomial(),
                             method = mdypl_original,
                             alpha = alpha_val,
@@ -215,9 +230,16 @@ tryCatch({
   cat("\n")
   
   cat("New mdyplFit timing:\n")
+  fit_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
+                         family = binomial(),
+                         method = mdypl_new,
+                         alpha = alpha_val,
+                         subset = training,
+                         maxit = 200)
+
   time_mdypl_new <- system.time({
     replicate(50, {
-      fit_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
+      full_mdypl_new <- glm(full_mf_fm, data = MultipleFeatures,
                          family = binomial(),
                          method = mdypl_new,
                          alpha = alpha_val,

From ebf1410179dd3c49b9d3b1bcacb89ef171a9a4d7 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Thu, 27 Nov 2025 10:35:51 +0000
Subject: [PATCH 13/15] Helper file implementation with functions: compute_fit,
 estimate_dispersion, adjustment functions (prefix AS_), DD. Tested.

---
 R/brglmFit-helper.R | 367 ++++++++++++++++++++++++++++++++++++++++++++
 R/brglmFit.R        | 329 ++++-----------------------------------
 2 files changed, 397 insertions(+), 299 deletions(-)
 create mode 100644 R/brglmFit-helper.R

diff --git a/R/brglmFit-helper.R b/R/brglmFit-helper.R
new file mode 100644
index 0000000..0f95646
--- /dev/null
+++ b/R/brglmFit-helper.R
@@ -0,0 +1,367 @@
+# Copyright (C) 2016- Ioannis Kosmidis
+
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 or 3 of the License
+#  (at your option).
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  http://www.r-project.org/Licenses/
+
+# Helper functions for brglmFit
+# These are self-contained functions that don't rely on parent scope
+
+#' Compute all quantities needed for a GLM fit
+#'
+#' @param pars Vector of parameters (betas and dispersion)
+#' @param y Response vector
+#' @param x Design matrix
+#' @param weights Observation weights
+#' @param offset Offset vector
+#' @param family GLM family object
+#' @param fixed_totals NULL or grouping vector for fixed totals
+#' @param row_totals NULL or vector of row totals
+#' @param no_dispersion Logical indicating if dispersion is fixed
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param keep Logical vector indicating which observations to keep
+#' @param need_qr Logical indicating if QR decomposition is needed
+#' @param need_hatvalues Logical indicating if hat values are needed
+#'
+#' @return A list of class "brglmFit_quantities" containing all computed quantities
+compute_fit <- function(pars, y, x, weights, offset, family, 
+                        fixed_totals = NULL, row_totals = NULL, 
+                        no_dispersion = FALSE, nobs, nvars, keep,
+                        need_qr = TRUE, need_hatvalues = TRUE) {
+    
+    # Extract Parameters
+    betas <- pars[seq.int(nvars)]
+    dispersion <- pars[nvars + 1]
+    precision <- 1 / dispersion
+
+    # Basic Quantities
+    etas <- drop(x %*% betas + offset)
+    mus <- family$linkinv(etas)
+    mus_unscaled <- mus  # Keep original for gradient computation
+    if (!is.null(fixed_totals)) {
+        mus_totals <- as.vector(tapply(mus, fixed_totals, sum))[fixed_totals]
+        mus <- mus * row_totals / mus_totals  # Scaled version
+        etas <- family$linkfun(mus)  # Update etas to match scaled mus
+    }
+
+    # Mean Quantities
+    d1mus <- family$mu.eta(etas)
+    d2mus <- family$d2mu.deta(etas)
+    varmus <- family$variance(mus)
+    d1varmus <- family$d1variance(mus)
+    working_weights <- weights * d1mus^2 / varmus
+
+    # QR Decomposition and Hat Values (only if needed)
+    qr_decomposition <- R_matrix <- Q_matrix <- hatvalues <- NULL
+    info_beta <- inverse_info_beta <- NULL
+
+    if (need_qr) {
+        wx <- sqrt(working_weights) * x
+        qr_decomposition <- qr(wx)
+        R_matrix <- qr.R(qr_decomposition)
+        
+        # Information Matrices
+        info_beta <- precision * crossprod(R_matrix)
+        inverse_info_beta <- dispersion * chol2inv(R_matrix)
+        
+        # Hat Values (only if needed and we have QR)
+        if (need_hatvalues) {
+            Q_matrix <- qr.Q(qr_decomposition) 
+            hatvalues <- .rowSums(Q_matrix * Q_matrix, nobs, nvars, TRUE)
+        }
+    }
+
+    # Dispersion Quantities (depends on family)
+    if (!no_dispersion) {
+        zetas <- -weights * precision
+        
+        # Derivatives of cumulant function (only for non-zero weights)
+        d1afuns <- d2afuns <- d3afuns <- rep(NA_real_, nobs)
+        d1afuns[keep] <- family$d1afun(zetas[keep])
+        d2afuns[keep] <- family$d2afun(zetas[keep])
+        d3afuns[keep] <- family$d3afun(zetas[keep])
+        
+        # Special case for Gamma family
+        if (family$family == "Gamma") {
+            d1afuns <- d1afuns - 2
+        }
+        
+        # Deviance residuals
+        deviance_residuals <- family$dev.resids(y, mus, weights)
+        Edeviance_residuals <- weights * d1afuns
+        
+        # Information for dispersion parameter
+        info_zeta <- 0.5 * sum(weights^2 * d2afuns, na.rm = TRUE) / dispersion^4
+        inverse_info_zeta <- 1 / info_zeta
+    } else {
+        # Fixed dispersion (binomial, Poisson)
+        zetas <- d1afuns <- d2afuns <- d3afuns <- NA_real_
+        deviance_residuals <- family$dev.resids(y, mus, weights)
+        Edeviance_residuals <- NA_real_
+        info_zeta <- inverse_info_zeta <- NA_real_
+    }
+
+    # Gradient Computation
+    # Use unscaled mus for gradient when fixed_totals is used
+    mus_for_gradient <- if (!is.null(fixed_totals)) mus_unscaled else mus
+    etas_for_gradient <- if (!is.null(fixed_totals)) family$linkfun(mus_unscaled) else etas
+    d1mus_for_gradient <- family$mu.eta(etas_for_gradient)
+    varmus_for_gradient <- family$variance(mus_for_gradient)
+    
+    score_components_beta <- weights * d1mus_for_gradient * (y - mus_for_gradient) / 
+                            varmus_for_gradient * x
+    grad_beta <- precision * .colSums(score_components_beta, nobs, nvars, TRUE)
+    
+    if (!no_dispersion) {
+        grad_zeta <- 0.5 * precision^2 * 
+                    sum(deviance_residuals - Edeviance_residuals, na.rm = TRUE)
+    } else {
+        grad_zeta <- NA_real_
+    }
+
+    # Return all computed quantities as class
+    structure(list(
+        # Parameters
+        betas = betas,
+        dispersion = dispersion,
+        precision = precision,
+        
+        # Basic quantities
+        etas = etas,
+        mus = mus,
+        mus_unscaled = mus_unscaled,  # For gradient with fixed_totals
+        
+        # Mean-related quantities
+        d1mus = d1mus,
+        d2mus = d2mus,
+        varmus = varmus,
+        d1varmus = d1varmus,
+        working_weights = working_weights,
+        
+        # QR decomposition and related
+        qr_decomposition = qr_decomposition,
+        R_matrix = R_matrix,
+        Q_matrix = Q_matrix, 
+        hatvalues = hatvalues,
+        
+        # Information matrices (pre-computed)
+        info_beta = info_beta,
+        inverse_info_beta = inverse_info_beta,
+        
+        # Dispersion-related quantities
+        zetas = zetas,
+        d1afuns = d1afuns,
+        d2afuns = d2afuns,
+        d3afuns = d3afuns,
+        deviance_residuals = deviance_residuals,
+        Edeviance_residuals = Edeviance_residuals,
+        info_zeta = info_zeta,
+        inverse_info_zeta = inverse_info_zeta,
+        
+        # Gradients (pre-computed)
+        grad_beta = grad_beta,
+        grad_zeta = grad_zeta,
+        score_components_beta = score_components_beta,
+        
+        # Metadata
+        has_fixed_totals = !is.null(fixed_totals),
+        no_dispersion = no_dispersion
+    ), class = "brglmFit_quantities")
+}
+
+#' Compute mean bias-reducing adjustment
+#'
+#' @param pars Parameter vector
+#' @param fit Object of class "brglmFit_quantities"
+#' @param level 0 for beta parameters, 1 for dispersion
+#' @param x Design matrix
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param weights Observation weights
+#'
+#' @return Adjustment vector
+AS_mean_adjustment <- function(pars, fit, level = 0, 
+                                       x, nobs, nvars, weights) {
+    if (level == 0) {
+        adj <- .colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
+                   nobs, nvars, TRUE)
+        return(adj)
+    } else {
+        s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+        s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+        return((nvars - 2) / (2 * fit$dispersion) + 
+            s1 / (2 * fit$dispersion^2 * s2))
+    }
+}
+
+#' Compute Jeffreys prior penalty adjustment
+#'
+#' @param pars Parameter vector
+#' @param fit Object of class "brglmFit_quantities"
+#' @param level 0 for beta parameters, 1 for dispersion
+#' @param x Design matrix
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param weights Observation weights
+#' @param a Power of Jeffreys prior (default 0.5)
+#'
+#' @return Adjustment vector
+AS_Jeffreys_adjustment <- function(pars, fit, level = 0, 
+                                           x, nobs, nvars, weights, a = 0.5) {
+    if (level == 0) {
+        return(2 * a * .colSums(0.5 * fit$hatvalues * 
+            (2 * fit$d2mus/fit$d1mus - fit$d1varmus * fit$d1mus / fit$varmus) * x, 
+            nobs, nvars, TRUE))
+    } else {
+        s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+        s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+        return(2 * a * (-(nvars + 4)/(2 * fit$dispersion) + 
+            s1/(2 * fit$dispersion^2 * s2)))
+    }
+}
+
+#' Compute median bias-reducing adjustment
+#'
+#' @param pars Parameter vector
+#' @param fit Object of class "brglmFit_quantities"
+#' @param level 0 for beta parameters, 1 for dispersion
+#' @param x Design matrix
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param weights Observation weights
+#'
+#' @return Adjustment vector
+AS_median_adjustment <- function(pars, fit, level = 0, 
+                                         x, nobs, nvars, weights) {
+    if (level == 0) {
+        info_unscaled <- fit$info_beta / fit$precision
+        inverse_info_unscaled <- fit$inverse_info_beta / fit$dispersion
+
+        b_vector <- numeric(nvars)
+        for (j in seq.int(nvars)) {
+            inverse_info_unscaled_j <- inverse_info_unscaled[j, ]
+            vcov_j <- tcrossprod(inverse_info_unscaled_j) / inverse_info_unscaled_j[j]
+            hats_j <- .rowSums((x %*% vcov_j) * x, nobs, nvars, TRUE) * fit$working_weights
+            b_vector[j] <- inverse_info_unscaled_j %*% .colSums(x * (hats_j * 
+                (fit$d1mus * fit$d1varmus / (6 * fit$varmus) - 0.5 * fit$d2mus/fit$d1mus)), 
+                nobs, nvars, TRUE)
+        }
+        return(.colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
+                   nobs, nvars, TRUE) + 
+           info_unscaled %*% b_vector)
+    } else {
+        s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+        s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+        return(nvars / (2 * fit$dispersion) + 
+            s1 / (6 * fit$dispersion^2 * s2))
+    }
+}
+
+#' Compute mixed bias-reducing adjustment
+#'
+#' @param pars Parameter vector
+#' @param fit Object of class "brglmFit_quantities"
+#' @param level 0 for beta parameters, 1 for dispersion
+#' @param x Design matrix
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param weights Observation weights
+#'
+#' @return Adjustment vector
+AS_mixed_adjustment <- function(pars, fit, level = 0, 
+                                        x, nobs, nvars, weights) {
+    if (level == 0) {
+        return(.colSums(0.5 * fit$hatvalues * fit$d2mus/fit$d1mus * x, 
+                   nobs, nvars, TRUE))
+    } else {
+        s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
+        s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
+        return(nvars / (2 * fit$dispersion) + 
+            s1 / (6 * fit$dispersion^2 * s2))
+    }
+}
+
+#' Estimate the ML of the dispersion parameter for gaussian, gamma and inverse Gaussian
+#' Set the dispersion to 1 if Poisson or binomial
+#' 
+#' @param betas Regression coefficients
+#' @param y Response vector
+#' @param x Design matrix
+#' @param weights Observation weights
+#' @param offset Offset vector
+#' @param family GLM family object
+#' @param fixed_totals NULL or grouping vector for fixed totals
+#' @param row_totals NULL or vector of row totals
+#' @param no_dispersion Logical indicating if dispersion is fixed
+#' @param nobs Number of observations
+#' @param nvars Number of variables
+#' @param keep Logical vector indicating which observations to keep
+#' @param df_residual Residual degrees of freedom
+#' @param control Control parameters
+#' 
+#' @seealso compute_fit
+#'
+#' @return List with dispersion and dispersion_ML
+estimate_dispersion <- function(betas, y, x, weights, offset, family,
+                               fixed_totals, row_totals, no_dispersion,
+                               nobs, nvars, keep, df_residual, control) {
+    if (no_dispersion) {
+        disp <- 1
+        dispML <- 1
+    } else {
+        if (df_residual > 0) {
+            dispFit <- try(uniroot(f = function(phi) {
+                theta <- c(betas, phi)
+                cfit <- compute_fit(pars = theta, 
+                                            y = y, 
+                                            x = x,
+                                            weights = weights,
+                                            offset = offset,
+                                            family = family,
+                                            fixed_totals = fixed_totals,
+                                            row_totals = row_totals,
+                                            no_dispersion = no_dispersion,
+                                            nobs = nobs,
+                                            nvars = nvars,
+                                            keep = keep,
+                                            need_qr = FALSE,
+                                            need_hatvalues = FALSE)
+                cfit$grad_zeta
+            }, lower = .Machine$double.eps, upper = 10000, tol = control$epsilon), silent = FALSE)
+            if (inherits(dispFit, "try-error")) {
+                warning("the ML estimate of the dispersion could not be calculated. An alternative estimate had been used as starting value.")
+                dispML <- NA_real_
+                disp <- NA_real_
+            } else {
+                disp <- dispML <- dispFit$root
+            }
+        } else { ## if the model is saturated dispML is NA_real_
+            disp <- 1 ## A convenient value
+            dispML <- NA_real_
+        }
+    }
+    list(dispersion = disp, dispersion_ML = dispML)
+}
+
+#' Utility function for symbolic differentiation
+#'
+#' @param expr Expression to differentiate
+#' @param name Variable name to differentiate with respect to
+#' @param order Order of derivative
+#'
+#' @return Differentiated expression
+DD <- function(expr, name, order = 1) {
+    if(order < 1) stop("'order' must be >= 1")
+    if(order == 1) D(expr, name)
+    else DD(D(expr, name), name, order - 1)
+}
\ No newline at end of file
diff --git a/R/brglmFit.R b/R/brglmFit.R
index b33ab8d..9be71e4 100644
--- a/R/brglmFit.R
+++ b/R/brglmFit.R
@@ -296,183 +296,6 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         }
     }
 
-    # Always computes everything needed, stores it once, passes it around
-    compute_fit <- function(pars, y, x, weights, offset, family, 
-                            fixed_totals = NULL, row_totals = NULL, 
-                            no_dispersion = FALSE, nobs, nvars, keep,
-                            need_qr = TRUE, need_hatvalues = TRUE) {
-        
-        # Extract Parameters
-        betas <- pars[seq.int(nvars)]
-        dispersion <- pars[nvars + 1]
-        precision <- 1 / dispersion
-
-        # Basic Quantities
-        etas <- drop(x %*% betas + offset)
-        mus <- family$linkinv(etas)
-        mus_unscaled <- mus  # Keep original for gradient computation
-        if (!is.null(fixed_totals)) {
-            mus_totals <- as.vector(tapply(mus, fixed_totals, sum))[fixed_totals]
-            mus <- mus * row_totals / mus_totals  # Scaled version
-            etas <- family$linkfun(mus)  # Update etas to match scaled mus
-        }
-
-        # Mean Quantities
-        d1mus <- family$mu.eta(etas)
-        d2mus <- family$d2mu.deta(etas)
-        varmus <- family$variance(mus)
-        d1varmus <- family$d1variance(mus)
-        working_weights <- weights * d1mus^2 / varmus
-
-        # QR Decomposition and Hat Values (only if needed)
-        qr_decomposition <- R_matrix <- Q_matrix <- hatvalues <- NULL
-        info_beta <- inverse_info_beta <- NULL
-
-        # TODO: Avoid forming full Q? Approximate hat values?
-        if (need_qr) {
-            wx <- sqrt(working_weights) * x
-            qr_decomposition <- qr(wx)
-            R_matrix <- qr.R(qr_decomposition)
-            
-            # Information Matrices
-            info_beta <- precision * crossprod(R_matrix)
-            inverse_info_beta <- dispersion * chol2inv(R_matrix)
-            
-            # Hat Values (only if needed and we have QR)
-            if (need_hatvalues) {
-                Q_matrix <- qr.Q(qr_decomposition) 
-                hatvalues <- .rowSums(Q_matrix * Q_matrix, nobs, nvars, TRUE)
-            }
-        }
-
-        # Dispersion Quantities (dept on family)
-        if (!no_dispersion) {
-            zetas <- -weights * precision
-            
-            # Derivatives of cumulant function (only for non-zero weights)
-            d1afuns <- d2afuns <- d3afuns <- rep(NA_real_, nobs)
-            d1afuns[keep] <- family$d1afun(zetas[keep])
-            d2afuns[keep] <- family$d2afun(zetas[keep])
-            d3afuns[keep] <- family$d3afun(zetas[keep])
-            
-            # Special case for Gamma family
-            if (family$family == "Gamma") {
-                d1afuns <- d1afuns - 2
-            }
-            
-            # Deviance residuals
-            deviance_residuals <- family$dev.resids(y, mus, weights)
-            Edeviance_residuals <- weights * d1afuns
-            
-            # Information for dispersion parameter
-            info_zeta <- 0.5 * sum(weights^2 * d2afuns, na.rm = TRUE) / dispersion^4
-            inverse_info_zeta <- 1 / info_zeta
-        } else {
-            # Fixed dispersion (binomial, Poisson)
-            zetas <- d1afuns <- d2afuns <- d3afuns <- NA_real_
-            deviance_residuals <- family$dev.resids(y, mus, weights)
-            Edeviance_residuals <- NA_real_
-            info_zeta <- inverse_info_zeta <- NA_real_
-        }
-
-        # Gradient Computation
-        # Use unscaled mus for gradient when fixed_totals is used
-        mus_for_gradient <- if (!is.null(fixed_totals)) mus_unscaled else mus
-        etas_for_gradient <- if (!is.null(fixed_totals)) family$linkfun(mus_unscaled) else etas
-        d1mus_for_gradient <- family$mu.eta(etas_for_gradient)
-        varmus_for_gradient <- family$variance(mus_for_gradient)
-        
-        score_components_beta <- weights * d1mus_for_gradient * (y - mus_for_gradient) / 
-                                varmus_for_gradient * x
-        grad_beta <- precision * .colSums(score_components_beta, nobs, nvars, TRUE)
-        
-        if (!no_dispersion) {
-            grad_zeta <- 0.5 * precision^2 * 
-                        sum(deviance_residuals - Edeviance_residuals, na.rm = TRUE)
-        } else {
-            grad_zeta <- NA_real_
-        }
-
-        # Return all computed quantities as class
-        structure(list(
-            # Parameters
-            betas = betas,
-            dispersion = dispersion,
-            precision = precision,
-            
-            # Basic quantities
-            etas = etas,
-            mus = mus,
-            mus_unscaled = mus_unscaled,  # For gradient with fixed_totals
-            
-            # Mean-related quantities
-            d1mus = d1mus,
-            d2mus = d2mus,
-            varmus = varmus,
-            d1varmus = d1varmus,
-            working_weights = working_weights,
-            
-            # QR decomposition and related
-            qr_decomposition = qr_decomposition,
-            R_matrix = R_matrix,
-            Q_matrix = Q_matrix, 
-            hatvalues = hatvalues,
-            
-            # Information matrices (pre-computed)
-            info_beta = info_beta,
-            inverse_info_beta = inverse_info_beta,
-            
-            # Dispersion-related quantities
-            zetas = zetas,
-            d1afuns = d1afuns,
-            d2afuns = d2afuns,
-            d3afuns = d3afuns,
-            deviance_residuals = deviance_residuals,
-            Edeviance_residuals = Edeviance_residuals,
-            info_zeta = info_zeta,
-            inverse_info_zeta = inverse_info_zeta,
-            
-            # Gradients (pre-computed)
-            grad_beta = grad_beta,
-            grad_zeta = grad_zeta,
-            score_components_beta = score_components_beta,
-            
-            # Metadata
-            has_fixed_totals = !is.null(fixed_totals),
-            no_dispersion = no_dispersion
-        ), class = "brglmFit_quantities")
-    }
-
-    gradient <- function(pars, fit, level = 0) {
-        if (level == 0) {
-            return(fit$grad_beta)
-        }
-        else {
-            return(fit$grad_zeta)
-        }
-    }
-
-    information <- function(pars, fit, level = 0, inverse = FALSE) {
-        if (level == 0) {
-            if (inverse) {
-                return(fit$inverse_info_beta)
-            } else {
-                return(fit$info_beta)
-            }
-        }
-        else {
-            if (inverse) {
-                return(fit$inverse_info_zeta)
-            } else {
-                return(fit$info_zeta)
-            }
-        }
-    }
-
-    hat_values <- function(pars, fit = NULL) {
-        return(fit$hatvalues)
-    }
-
     ## FIXME: Redundant function for now
     refit <- function(y, betas_start = NULL) {
         ## Estimate Beta
@@ -486,115 +309,6 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
         betas
     }
 
-    ## Estimate the ML of the dispersion parameter for gaussian, gamma and inverse Gaussian
-    ## Set the dispersion to 1 if Poisson or binomial
-    ## betas is only the regression parameters
-    estimate_dispersion <- function(betas, y) {
-        if (no_dispersion) {
-            disp <- 1
-            dispML <- 1
-        } else {
-            if (df_residual > 0) {
-                dispFit <- try(uniroot(f = function(phi) {
-                    theta <- c(betas, phi)
-                    cfit <- compute_fit(pars = theta, 
-                                                y = y, 
-                                                x = x,
-                                                weights = weights,
-                                                offset = offset,
-                                                family = family,
-                                                fixed_totals = fixed_totals,
-                                                row_totals = row_totals,
-                                                no_dispersion = no_dispersion,
-                                                nobs = nobs,
-                                                nvars = nvars,
-                                                keep = keep,
-                                                need_qr = FALSE,
-                                                need_hatvalues = FALSE)
-                    gradient(theta, level = 1, fit = cfit)
-                }, lower = .Machine$double.eps, upper = 10000, tol = control$epsilon), silent = FALSE)
-                if (inherits(dispFit, "try-error")) {
-                    warning("the ML estimate of the dispersion could not be calculated. An alternative estimate had been used as starting value.")
-                    dispML <- NA_real_
-                    disp <- NA_real_
-                } else {
-                    disp <- dispML <- dispFit$root
-                }
-            } else { ## if the model is saturated dispML is NA_real_
-                disp <- 1 ## A convenient value
-                dispML <- NA_real_
-            }
-        }
-        list(dispersion = disp, dispersion_ML = dispML)
-    }
-
-    AS_mean_adjustment <- function(pars, fit, level = 0) {
-        if (level == 0) {
-            # Zero division already handled by fit computation
-            adj <- .colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
-                       nobs, nvars, TRUE)
-            return(adj)
-        }
-        else {
-            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
-            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
-            return((nvars - 2) / (2 * fit$dispersion) + 
-                s1 / (2 * fit$dispersion^2 * s2))
-        }
-    }
-
-    AS_Jeffreys_adjustment <- function(pars, fit, level = 0, a = 0.5) {
-        if (level == 0) {
-            ## Use only observations with keep = TRUE to ensure that no division with zero takes place
-            return(2 * a * .colSums(0.5 * fit$hatvalues * (2 * fit$d2mus/fit$d1mus - fit$d1varmus * fit$d1mus / fit$varmus) * x, nobs, nvars, TRUE))
-        }
-        else {
-            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
-            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
-            return(2 * a * (-(nvars + 4)/(2 * fit$dispersion) + s1/(2 * fit$dispersion^2 * s2)))
-        }
-    }
-
-    AS_median_adjustment <- function(pars, fit, level = 0) {
-        if (level == 0) {
-            info_unscaled <- fit$info_beta / fit$precision
-            inverse_info_unscaled <- fit$inverse_info_beta / fit$dispersion
-
-            ## TODO: Below fixme? 
-            ## FIXME: There is 1) definitely a better way to do this, 2) no time... 
-            b_vector <- numeric(nvars)
-            for (j in seq.int(nvars)) {
-                inverse_info_unscaled_j <- inverse_info_unscaled[j, ]
-                vcov_j <- tcrossprod(inverse_info_unscaled_j) / inverse_info_unscaled_j[j]
-                hats_j <- .rowSums((x %*% vcov_j) * x, nobs, nvars, TRUE) * fit$working_weights
-                b_vector[j] <- inverse_info_unscaled_j %*% .colSums(x * (hats_j * (fit$d1mus * fit$d1varmus / (6 * fit$varmus) - 0.5 * fit$d2mus/fit$d1mus)), nobs, nvars, TRUE)
-            }
-            return(.colSums(0.5 * fit$hatvalues * fit$d2mus / fit$d1mus * x, 
-                       nobs, nvars, TRUE) + 
-               info_unscaled %*% b_vector)
-        }
-        else {
-            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
-            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
-            return(nvars / (2 * fit$dispersion) + 
-                s1 / (6 * fit$dispersion^2 * s2))
-        }
-    }
-
-    AS_mixed_adjustment <- function(pars, level = 0, fit = NULL) {
-        if (level == 0) {
-            ## Use only observations with keep = TRUE to ensure that no division with zero takes place
-            return(.colSums(0.5 * fit$hatvalues * fit$d2mus/fit$d1mus * x, nobs, nvars, TRUE))
-        }
-        else {
-            s1 <- sum(weights^3 * fit$d3afuns, na.rm = TRUE)
-            s2 <- sum(weights^2 * fit$d2afuns, na.rm = TRUE)
-            return(nvars / (2 * fit$dispersion) + 
-                s1 / (6 * fit$dispersion^2 * s2))
-        }
-    }
-
-
     ## compute_step_components does everything on the scale of the /transformed/ dispersion
     compute_step_components <- function(pars, fit, level = 0) {
 
@@ -602,7 +316,7 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
             # Beta components
             grad <- fit$grad_beta
             inverse_info <- fit$inverse_info_beta
-            adjustment <- adjustment_function(pars, fit = fit, level = 0)
+            adjustment <- adjustment_function(pars, fit = fit, level = 0, x, nobs, nvars, weights)
             
             failed_adjustment <- any(is.na(adjustment))
             failed_inversion <- FALSE  # Already computed successfully
@@ -618,7 +332,7 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                 
                 grad <- fit$grad_zeta / d1zeta
                 inverse_info <- fit$inverse_info_zeta * d1zeta^2
-                adjustment <- adjustment_function(pars, fit = fit, level = 1) / d1zeta - 
+                adjustment <- adjustment_function(pars, fit = fit, level = 1, x, nobs, nvars, weights) / d1zeta - 
                             0.5 * d2zeta / d1zeta^2
 
                 failed_inversion <- !is.finite(inverse_info)
@@ -846,7 +560,20 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
             )
             betas <- coef(tempFit)
             names(betas) <- betas_names
-            dispList <- estimate_dispersion(betas, y = y)
+            dispList <- estimate_dispersion(betas = betas, 
+                                                    y = y, 
+                                                    x = x, 
+                                                    weights = weights, 
+                                                    offset = offset,
+                                                    family = family,
+                                                    fixed_totals = fixed_totals, 
+                                                    row_totals = row_totals,
+                                                    no_dispersion = no_dispersion,
+                                                    nobs = nobs,
+                                                    nvars = nvars,
+                                                    keep = keep, 
+                                                    df_residual = df_residual, 
+                                                    control = control)
             dispersion <- dispList$dispersion
             if (is.na(dispersion)) dispersion <- var(y)/variance(sum(weights * y)/sum(weights))
             dispersion_ML <- dispList$dispersion_ML
@@ -862,7 +589,20 @@ brglmFit <- function(x, y, weights = rep(1, nobs), start = NULL, etastart = NULL
                     betas <- betas_all
                 }
                 ## Estimate dispersion based on current value for betas
-                dispList <- estimate_dispersion(betas, y = y)
+                dispList <- estimate_dispersion(betas = betas, 
+                                                    y = y, 
+                                                    x = x, 
+                                                    weights = weights, 
+                                                    offset = offset,
+                                                    family = family,
+                                                    fixed_totals = fixed_totals, 
+                                                    row_totals = row_totals,
+                                                    no_dispersion = no_dispersion,
+                                                    nobs = nobs,
+                                                    nvars = nvars,
+                                                    keep = keep, 
+                                                    df_residual = df_residual, 
+                                                    control = control)
                 dispersion <- dispList$dispersion
                 if (is.na(dispersion)) dispersion <- var(y)/variance(sum(weights * y)/sum(weights))
                 dispersion_ML <- dispList$dispersion_ML
@@ -1362,15 +1102,6 @@ vcov.brglmFit <- function(object, model = c("mean", "full", "dispersion"), compl
     })
 }
 
-
-DD <- function(expr,name, order = 1) {
-    if(order < 1) stop("'order' must be >= 1")
-    if(order == 1) D(expr,name)
-    else DD(D(expr, name), name, order - 1)
-}
-
-
-
 ## Almost all code in print.summary.brglmFit is from
 ## stats:::print.summary.glm apart from minor modifications
 #' @rdname summary.brglmFit

From 9ae67faf4014d76dba57088411a7f5ac3678a215 Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Tue, 2 Dec 2025 13:14:35 +0000
Subject: [PATCH 14/15] Profiling file inclusion

---
 benchmarks/profiling.R | 55 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 benchmarks/profiling.R

diff --git a/benchmarks/profiling.R b/benchmarks/profiling.R
new file mode 100644
index 0000000..a0b3ba2
--- /dev/null
+++ b/benchmarks/profiling.R
@@ -0,0 +1,55 @@
+# Load required packages
+library(brglm2)
+library(microbenchmark)
+
+# Load the dataset
+data("MultipleFeatures", package = "brglm2")
+
+# Set up the data and formulas (based on the package documentation)
+# Get the fou (Fourier) and kar (Karhunen-Loève) feature names
+vars <- grep("fou|kar", names(MultipleFeatures), value = TRUE)
+
+# Identify training rows
+training <- which(MultipleFeatures$training)
+
+# Center the features on the training set
+MultipleFeatures[training, vars] <- scale(MultipleFeatures[training, vars], 
+                                           scale = FALSE)
+
+# Create the full model formula (predicting digit 7)
+full_mf_fm <- formula(paste("I(digit == 7) ~", paste(vars, collapse = " + ")))
+
+# ===== PROFILING STARTS HERE =====
+
+# 1. Detailed profiling with Rprof 
+print("\n === Rprof Function Timing (ordered by time) ===")
+Rprof("brglm_profile.out", interval = 0.01, memory.profiling = TRUE)
+fit <- glm(full_mf_fm, 
+           data = MultipleFeatures, 
+           family = binomial(),
+           method = brglmFit,
+           subset = training, 
+           maxit = 200)
+Rprof(NULL)
+
+# Get summary showing functions by total time
+prof_summary <- summaryRprof("brglm_profile.out", memory = "both")
+print("Top functions by total time:")
+print(head(prof_summary$by.total, 20))
+print("\nTop functions by self time (excluding called functions):")
+print(head(prof_summary$by.self, 20))
+
+# 2. Visual profiling with profvis
+print("\n === Memory/Time Profiling with profvis ===")
+library(profvis)
+
+p <- profvis({
+  fit <- glm(full_mf_fm, 
+             data = MultipleFeatures, 
+             family = binomial(),
+             method = brglmFit,
+             subset = training, 
+             maxit = 200)
+}, interval = 0.01)  # Smaller interval for more detail
+
+print(p)
\ No newline at end of file

From 1ae9e41f79ca0928d0448261086275a22ff5cf8a Mon Sep 17 00:00:00 2001
From: Ollie <ollie@orcus.co.uk>
Date: Wed, 3 Dec 2025 12:41:41 +0000
Subject: [PATCH 15/15] Complete profiling split into main and fit for more
 specific discovery

---
 benchmarks/fit_profiling.R                   | 198 +++++++++++++++++++
 benchmarks/{profiling.R => main_profiling.R} |   0
 2 files changed, 198 insertions(+)
 create mode 100644 benchmarks/fit_profiling.R
 rename benchmarks/{profiling.R => main_profiling.R} (100%)

diff --git a/benchmarks/fit_profiling.R b/benchmarks/fit_profiling.R
new file mode 100644
index 0000000..1afee9c
--- /dev/null
+++ b/benchmarks/fit_profiling.R
@@ -0,0 +1,198 @@
+# Load required packages
+library(brglm2)
+library(enrichwith)  # Needed for enriching family objects
+library(numDeriv)    # Needed for numerical derivatives
+library(profvis)
+library(microbenchmark)
+
+# Source the helper file to get compute_fit
+# Try different paths depending on where script is run from
+if (file.exists("R/brglmFit-helper.R")) {
+  source("R/brglmFit-helper.R")
+} else if (file.exists("../R/brglmFit-helper.R")) {
+  source("../R/brglmFit-helper.R")
+} else {
+  stop("Cannot find brglmFit-helper.R. Please check your working directory.")
+}
+
+# Verify compute_fit is available
+if (!exists("compute_fit")) {
+  stop("compute_fit function not found after sourcing. Check the helper file.")
+}
+
+cat("compute_fit function loaded successfully\n")
+
+# Load and prepare the dataset (same as your existing script)
+data("MultipleFeatures", package = "brglm2")
+
+vars <- grep("fou|kar", names(MultipleFeatures), value = TRUE)
+training <- which(MultipleFeatures$training)
+MultipleFeatures[training, vars] <- scale(MultipleFeatures[training, vars], 
+                                           scale = FALSE)
+
+# Create the formula and prepare data
+full_mf_fm <- formula(paste("I(digit == 7) ~", paste(vars, collapse = " + ")))
+
+# Prepare inputs for compute_fit (mimicking what brglmFit does)
+train_data <- MultipleFeatures[training, ]
+y <- as.numeric(train_data$digit == 7)
+x <- model.matrix(full_mf_fm, data = train_data)
+weights <- rep(1, length(y))
+offset <- rep(0, length(y))
+
+# Use enrichment approach (matching brglmFit.R line 426)
+family <- enrichwith::enrich(binomial(), with = c("d1afun", "d2afun", "d3afun", "d1variance"))
+
+# Add d2mu.deta if not already present
+if (is.null(family$d2mu.deta)) {
+  mu.eta <- family$mu.eta
+  family$d2mu.deta <- function(eta) {
+    numDeriv::grad(mu.eta, eta)
+  }
+}
+
+# Get dimensions
+nobs <- length(y)
+nvars <- ncol(x)
+keep <- weights > 0
+
+# Get starting values (use a quick ML fit)
+ml_fit <- glm(full_mf_fm, 
+              data = train_data,
+              family = binomial())
+
+# Starting parameter vector
+pars <- c(coef(ml_fit), 1)  # betas + dispersion
+
+# ===== FOCUSED PROFILING OF compute_fit =====
+
+cat("\n=== Profiling compute_fit function ===\n")
+
+# First, test that compute_fit works outside profvis
+cat("\nTesting compute_fit directly...\n")
+test_result <- try({
+  compute_fit(
+    pars = pars,
+    y = y,
+    x = x,
+    weights = weights,
+    offset = offset,
+    family = family,
+    fixed_totals = NULL,
+    row_totals = NULL,
+    no_dispersion = FALSE,
+    nobs = nobs,
+    nvars = nvars,
+    keep = keep,
+    need_qr = TRUE,
+    need_hatvalues = TRUE
+  )
+}, silent = FALSE)
+
+if (inherits(test_result, "try-error")) {
+  cat("\nERROR: compute_fit failed. Error details:\n")
+  print(test_result)
+  stop("Cannot proceed with profiling - compute_fit is not working")
+} else {
+  cat("Success! compute_fit executed without errors.\n")
+  cat("Result class:", class(test_result), "\n")
+}
+
+# 1. Detailed line-by-line profiling with profvis
+cat("\n1. Visual profiling with profvis (check browser/viewer)...\n")
+p <- profvis({
+  for (i in 1:100) {  # Run multiple times to get good sampling
+    fit_result <- compute_fit(
+      pars = pars,
+      y = y,
+      x = x,
+      weights = weights,
+      offset = offset,
+      family = family,
+      fixed_totals = NULL,
+      row_totals = NULL,
+      no_dispersion = FALSE,
+      nobs = nobs,
+      nvars = nvars,
+      keep = keep,
+      need_qr = TRUE,
+      need_hatvalues = TRUE
+    )
+  }
+})
+print(p)
+
+htmlwidgets::saveWidget(p, "fit_profile(03.12.25).html")
+
+# 2. Benchmark different scenarios
+cat("\n2. Benchmarking compute_fit under different conditions...\n")
+
+# Test with QR and hatvalues
+bench_full <- microbenchmark(
+  with_qr_and_hat = compute_fit(
+    pars = pars, y = y, x = x, weights = weights, offset = offset,
+    family = family, fixed_totals = NULL, row_totals = NULL,
+    no_dispersion = FALSE, nobs = nobs, nvars = nvars, keep = keep,
+    need_qr = TRUE, need_hatvalues = TRUE
+  ),
+  with_qr_no_hat = compute_fit(
+    pars = pars, y = y, x = x, weights = weights, offset = offset,
+    family = family, fixed_totals = NULL, row_totals = NULL,
+    no_dispersion = FALSE, nobs = nobs, nvars = nvars, keep = keep,
+    need_qr = TRUE, need_hatvalues = FALSE
+  ),
+  no_qr = compute_fit(
+    pars = pars, y = y, x = x, weights = weights, offset = offset,
+    family = family, fixed_totals = NULL, row_totals = NULL,
+    no_dispersion = FALSE, nobs = nobs, nvars = nvars, keep = keep,
+    need_qr = FALSE, need_hatvalues = FALSE
+  ),
+  times = 50
+)
+print(bench_full)
+
+# 3. Detailed Rprof for function-level timing
+cat("\n3. Function-level profiling with Rprof...\n")
+Rprof("compute_fit_profile.out", interval = 0.001, line.profiling = TRUE)
+for (i in 1:200) {
+  fit_result <- compute_fit(
+    pars = pars, y = y, x = x, weights = weights, offset = offset,
+    family = family, fixed_totals = NULL, row_totals = NULL,
+    no_dispersion = FALSE, nobs = nobs, nvars = nvars, keep = keep,
+    need_qr = TRUE, need_hatvalues = TRUE
+  )
+}
+Rprof(NULL)
+
+prof_summary <- summaryRprof("compute_fit_profile.out", lines = "both")
+cat("\nTop functions by total time:\n")
+print(head(prof_summary$by.total, 20))
+cat("\nTop functions by self time:\n")
+print(head(prof_summary$by.self, 20))
+
+if (!is.null(prof_summary$by.line)) {
+  cat("\nTop lines by total time:\n")
+  print(head(prof_summary$by.line$line.out, 30))
+}
+
+# 4. Memory profiling
+cat("\n4. Memory profiling...\n")
+Rprof("compute_fit_memory.out", memory.profiling = TRUE)
+for (i in 1:100) {
+  fit_result <- compute_fit(
+    pars = pars, y = y, x = x, weights = weights, offset = offset,
+    family = family, fixed_totals = NULL, row_totals = NULL,
+    no_dispersion = FALSE, nobs = nobs, nvars = nvars, keep = keep,
+    need_qr = TRUE, need_hatvalues = TRUE
+  )
+}
+Rprof(NULL)
+
+mem_summary <- summaryRprof("compute_fit_memory.out", memory = "both")
+cat("\nMemory usage by function:\n")
+print(head(mem_summary$by.total, 15))
+
+cat("\n=== Profiling complete ===\n")
+cat("Profile output files created:\n")
+cat("  - compute_fit_profile.out (detailed timing)\n")
+cat("  - compute_fit_memory.out (memory usage)\n")
\ No newline at end of file
diff --git a/benchmarks/profiling.R b/benchmarks/main_profiling.R
similarity index 100%
rename from benchmarks/profiling.R
rename to benchmarks/main_profiling.R