diff --git a/NAMESPACE b/NAMESPACE
index fe4c23d6..c448ff13 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,18 +11,19 @@ export(addLeaves2Alignment)
 export(addLineage)
 export(addName)
 export(addTaxID)
-export(advanced_opts2est_walltime)
 export(alignFasta)
-export(assign_job_queue)
+export(assignJobQueue)
+export(calculateEstimatedWallTimeFromOpts)
+export(calculateProcessRuntime)
 export(cleanClusters)
 export(cleanDomainArchitecture)
 export(cleanGeneDescription)
 export(cleanGenomicContext)
 export(cleanLineage)
 export(cleanSpecies)
-export(combine_files)
-export(combine_full)
-export(combine_ipr)
+export(combineFiles)
+export(combineFullAnalysis)
+export(combineIPR)
 export(condenseRepeatedDomains)
 export(convert2TitleCase)
 export(convertAlignment2FA)
@@ -32,10 +33,10 @@ export(countByColumn)
 export(createFA2Tree)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createLineageLookup)
 export(createRepresentativeAccNum)
 export(createWordCloud2Element)
 export(createWordCloudElement)
-export(create_lineage_lookup)
 export(domain_network)
 export(downloadAssemblySummary)
 export(efetchIPG)
@@ -48,13 +49,13 @@ export(gc_undirected_network)
 export(generateAllAlignments2FA)
 export(generate_msa)
 export(getAccNumFromFA)
+export(getProcessRuntimeWeights)
 export(getTopAccByLinDomArch)
-export(get_proc_medians)
-export(get_proc_weights)
-export(make_opts2procs)
 export(mapAcc2Name)
-export(map_advanced_opts2procs)
+export(mapAdvOption2Process)
+export(mapOption2Process)
 export(msa_pdf)
+export(plotEstimatedWallTimes)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)
 export(plotLineageDA)
@@ -67,7 +68,6 @@ export(plotStackedLineage)
 export(plotSunburst)
 export(plotTreemap)
 export(plotUpSet)
-export(plot_estimated_walltimes)
 export(prepareColumnParams)
 export(prepareSingleColumnParams)
 export(proteinAcc2TaxID)
@@ -97,8 +97,8 @@ export(totalGenContextOrDomArchCounts)
 export(validateCountDF)
 export(wordcloud3)
 export(writeMSA_AA2FA)
-export(write_proc_medians_table)
-export(write_proc_medians_yml)
+export(writeProcessRuntime2TSV)
+export(writeProcessRuntime2YML)
 importFrom(Biostrings,AAStringSet)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,toString)
diff --git a/R/acc2lin.R b/R/acc2lin.R
index bf6fec54..5f25afe2 100644
--- a/R/acc2lin.R
+++ b/R/acc2lin.R
@@ -10,6 +10,7 @@
 #' Sink Reset
 #'
 #' @return No return, but run to close all outstanding `sink()`s
+#'
 #' @export
 #'
 #' @examples
@@ -18,7 +19,7 @@
 #' }
 sinkReset <- function() {
     for (i in seq_len(sink.number())) {
-        sink(NULL)
+      sink(NULL)
     }
 }
 
@@ -56,18 +57,20 @@ addLineage <- function(df, acc_col = "AccNum", assembly_path,
     accessions <- df %>% pull(acc_col)
     lins <- acc2Lineage(accessions, assembly_path, lineagelookup_path, ipgout_path, plan)
 
-    # Drop a lot of the unimportant columns for now? will make merging much easier
-    lins <- lins[, c(
+      # Drop a lot of the unimportant columns for now? 
+      # will make merging much easier
+      lins <- lins[, c(
         "Strand", "Start", "Stop", "Nucleotide Accession", "Source",
         "Id", "Strain"
-    ) := NULL]
-    lins <- unique(lins)
+      ) := NULL]
+      lins <- unique(lins)
 
-    # dup <- lins %>% group_by(Protein) %>% summarize(count = n()) %>% filter(count > 1) %>%
-    #   pull(Protein)
+      # dup <- lins %>% group_by(Protein) %>% 
+      # summarize(count = n()) %>% filter(count > 1) %>%
+      # pull(Protein)
 
-    merged <- merge(df, lins, by.x = acc_col, by.y = "Protein", all.x = TRUE)
-    return(merged)
+      merged <- merge(df, lins, by.x = acc_col, by.y = "Protein", all.x = TRUE)
+      return(merged)
 }
 
 
@@ -107,10 +110,10 @@ acc2Lineage <- function(accessions, assembly_path, lineagelookup_path, ipgout_pa
 
     lins <- IPG2Lineage(accessions, ipgout_path, assembly_path, lineagelookup_path)
 
-    if (tmp_ipg) {
-        unlink(tempdir(), recursive = T)
-    }
-    return(lins)
+  if (tmp_ipg) {
+    unlink(tempdir(), recursive = T)
+  }
+  return(lins)
 }
 
 #' efetchIPG
@@ -118,7 +121,6 @@ acc2Lineage <- function(accessions, assembly_path, lineagelookup_path, ipgout_pa
 #' @author Samuel Chen, Janani Ravi
 #'
 #' @description Perform efetch on the ipg database and write the results to out_path
-#'
 #' @param accnums Character vector containing the accession numbers to query on
 #' the ipg database
 #' @param out_path Path to write the efetch results to
@@ -144,46 +146,52 @@ efetchIPG <- function(accnums, out_path, plan = "sequential", ...) {
             # limit of 10/second w/ key
             l <- length(in_data)
 
-            partitioned <- list()
-            for (i in 1:groups)
-            {
-                partitioned[[i]] <- in_data[seq.int(i, l, groups)]
-            }
-
-            return(partitioned)
-        }
-
-        plan(strategy = plan, .skip = T)
-
-
-        min_groups <- length(accnums) / 200
-        groups <- min(max(min_groups, 15), length(accnums))
-        partitioned_acc <- partition(accnums, groups)
-        sink(out_path)
-
-        a <- future_map(1:length(partitioned_acc), function(x) {
-            # Avoid hitting the rate API limit
-            if (x %% 9 == 0) {
-                Sys.sleep(1)
-            }
-            cat(
-                entrez_fetch(
-                    id = partitioned_acc[[x]],
-                    db = "ipg",
-                    rettype = "xml",
-                    api_key = "YOUR_KEY_HERE" ## Can this be included in public package?
-                )
-            )
-        })
-        sink(NULL)
+      partitioned <- list()
+      for (i in 1:groups){
+        partitioned[[i]] <- in_data[seq.int(i, l, groups)]
+      }
+
+      return(partitioned)
     }
+
+    # Set the future plan strategy
+    plan(strategy = plan, .skip = T)
+
+
+    min_groups <- length(accnums) / 200
+    groups <- min(max(min_groups, 15), length(accnums))
+    partitioned_acc <- partition(accnums, groups)
+
+    # Open the sink to the output path
+    sink(out_path)
+
+    a <- future_map(1:length(partitioned_acc), function(x) {
+      # Avoid hitting the rate API limit
+      if (x %% 9 == 0) {
+        Sys.sleep(1)
+      }
+      cat(
+        entrez_fetch(
+          id = partitioned_acc[[x]],
+          db = "ipg",
+          rettype = "xml",
+          api_key = "YOUR_KEY_HERE" ## Can this be included in public package?
+        )
+      )
+    })
+    sink(NULL)
+
+  }
 }
 
+
+
 #' IPG2Lineage
 #'
 #' @author Samuel Chen, Janani Ravi
 #'
-#' @description Takes the resulting file of an efetch run on the ipg database and
+#' @description Takes the resulting file
+#'              of an efetch run on the ipg database and
 #'
 #' @param accessions Character vector of protein accessions
 #' @param ipg_file Filepath to the file containing results of an efetch run on the
@@ -193,7 +201,7 @@ efetchIPG <- function(accnums, out_path, plan = "sequential", ...) {
 #' This file can be generated using the \link[MolEvolvR]{downloadAssemblySummary} function
 #' @param lineagelookup_path String of the path to the lineage lookup file
 #' (taxid to lineage mapping). This file can be generated using the
-#' "create_lineage_lookup()" function
+#' "createLineageLookup()" function
 #'
 #' @importFrom data.table fread
 #'
@@ -209,8 +217,10 @@ efetchIPG <- function(accnums, out_path, plan = "sequential", ...) {
 IPG2Lineage <- function(accessions, ipg_file, assembly_path, lineagelookup_path, ...) {
     ipg_dt <- fread(ipg_file, sep = "\t", fill = T)
 
+    # Filter the IPG data table to only include the accessions
     ipg_dt <- ipg_dt[Protein %in% accessions]
 
+    # Rename the 'Assembly' column to 'GCA_ID'
     ipg_dt <- setnames(ipg_dt, "Assembly", "GCA_ID")
 
     lins <- GCA2Lineage(prot_data = ipg_dt, assembly_path, lineagelookup_path)
diff --git a/R/assign_job_queue.R b/R/assign_job_queue.R
index bc5253d4..69609417 100644
--- a/R/assign_job_queue.R
+++ b/R/assign_job_queue.R
@@ -3,24 +3,31 @@
 # pipeline.
 # to use this, construct paths like so: file.path(common_root, "path", "to", "file.R")
 # for example, the reference for this file would be:
-# file.path(common_root, "molevol_scripts", "R", "assign_job_queue.R")
+# file.path(common_root, "molevol_scripts", "R", "assignJobQueue.R")
 common_root <- Sys.getenv("COMMON_SRC_ROOT")
 
+#' mapOption2Process
+#' 
+#' @description
 #' Construct list where names (MolEvolvR advanced options) point to processes
 #'
 #' @return list where names (MolEvolvR advanced options) point to processes
 #'
-#' example: list_opts2procs <- make_opts2procs
+#' example: list_opts2procs <- mapOption2Process
 #' @export
-make_opts2procs <- function() {
-    opts2processes <- list(
-        "homology_search" = c("dblast", "dblast_cleanup"),
-        "domain_architecture" = c("iprscan", "ipr2lineage", "ipr2da"),
-        "always" = c("blast_clust", "clust2table") # processes always present agnostic of advanced options
-    )
-    return(opts2processes)
+mapOption2Process <- function() {
+  opts2processes <- list(
+    "homology_search" = c("dblast", "dblast_cleanup"),
+    "domain_architecture" = c("iprscan", "ipr2lineage", "ipr2da"),
+    # processes always present agnostic of advanced options
+    "always" = c("blast_clust", "clust2table")
+  )
+  return(opts2processes)
 }
 
+#' mapAdvOption2Process
+#' 
+#' @description
 #' Use MolEvolvR advanced options to get associated processes
 #'
 #' @param advanced_opts character vector of MolEvolvR advanced options
@@ -30,19 +37,22 @@ make_opts2procs <- function() {
 #'
 #' example:
 #' advanced_opts <- c("homology_search", "domain_architecture")
-#' procs <- map_advanced_opts2procs(advanced_opts)
+#' procs <- mapAdvOption2Process(advanced_opts)
 #' @export
-map_advanced_opts2procs <- function(advanced_opts) {
-    # append 'always' to add procs that always run
-    advanced_opts <- c(advanced_opts, "always")
-    opts2proc <- make_opts2procs()
-    # setup index for opts2proc based on advanced options
-    idx <- which(names(opts2proc) %in% advanced_opts)
-    # extract processes that will run
-    procs <- opts2proc[idx] |> unlist()
-    return(procs)
+mapAdvOption2Process <- function(advanced_opts) {
+  # append 'always' to add procs that always run
+  advanced_opts <- c(advanced_opts, "always")
+  opts2proc <- mapOption2Process()
+  # setup index for opts2proc based on advanced options
+  idx <- which(names(opts2proc) %in% advanced_opts)
+  # extract processes that will run
+  procs <- opts2proc[idx] |> unlist()
+  return(procs)
 }
 
+#' calculateProcessRuntime
+#' 
+#' @description
 #' Scrape MolEvolvR logs and calculate median processes
 #'
 #' @param dir_job_results [chr] path to MolEvolvR job_results
@@ -58,49 +68,54 @@ map_advanced_opts2procs <- function(advanced_opts) {
 #'
 #' 1)
 #' dir_job_results <- "/data/scratch/janani/molevolvr_out"
-#' list_proc_medians <- get_proc_medians(dir_job_results)
+#' list_proc_medians <- calculateProcessRuntime(dir_job_results)
 #'
 #' 2) from outside container environment
 #' common_root <- "/data/molevolvr_transfer/molevolvr_dev"
 #' dir_job_results <- "/data/molevolvr_transfer/molevolvr_dev/job_results"
-#' list_proc_medians <- get_proc_medians(dir_job_results)
+#' list_proc_medians <- calculateProcessRuntime(dir_job_results)
 #' @export
-get_proc_medians <- function(dir_job_results) {
-    source(file.path(common_root, "molevol_scripts", "R", "metrics.R"))
+calculateProcessRuntime <- function(dir_job_results) {
+  source(file.path(common_root, "molevol_scripts", "R", "metrics.R"))
 
-    # aggregate logs from
-    path_log_data <- file.path(common_root, "molevol_scripts", "log_data", "prod_logs.rda")
+  # aggregate logs from
+  path_log_data <- file.path(common_root,
+                              "molevol_scripts", "log_data", "prod_logs.rda")
 
-    # ensure the folder exists to the location
-    if (!dir.exists(path_log_data)) {
-        dir.create(dirname(path_log_data), recursive = TRUE, showWarnings = FALSE)
-    }
+  # ensure the folder exists to the location
+  if (!dir.exists(path_log_data)) {
+    dir.create(dirname(path_log_data),
+                recursive = TRUE, showWarnings = FALSE)
+  }
 
-    # attempt to load pre-generated logdata
-    if (!file.exists(path_log_data)) {
-        logs <- aggregate_logs(dir_job_results, latest_date = Sys.Date() - 60)
-        save(logs, file = path_log_data)
-    } else {
-        load(path_log_data) # loads the logs object
-    }
-    df_log <- logs$df_log
-    procs <- c(
-        "dblast", "dblast_cleanup", "iprscan",
-        "ipr2lineage", "ipr2da", "blast_clust",
-        "clust2table"
-    )
-    list_proc_medians <- df_log |>
-        dplyr::select(dplyr::all_of(procs)) |>
-        dplyr::summarise(
-            dplyr::across(
-                dplyr::everything(),
-                \(x) median(x, na.rm = TRUE)
-            )
-        ) |>
-        as.list()
-    return(list_proc_medians)
+  # attempt to load pre-generated logdata
+  if (!file.exists(path_log_data)) {
+    logs <- aggregate_logs(dir_job_results, latest_date = Sys.Date() - 60)
+    save(logs, file = path_log_data)
+  } else {
+    load(path_log_data) # loads the logs object
+  }
+  df_log <- logs$df_log
+  procs <- c(
+    "dblast", "dblast_cleanup", "iprscan",
+    "ipr2lineage", "ipr2da", "blast_clust",
+    "clust2table"
+  )
+  list_proc_medians <- df_log |>
+    dplyr::select(dplyr::all_of(procs)) |>
+    dplyr::summarise(
+      dplyr::across(
+        dplyr::everything(),
+        \(x) median(x, na.rm = TRUE)
+      )
+    ) |>
+    as.list()
+  return(list_proc_medians)
 }
 
+#' writeProcessRuntime2TSV
+#' 
+#' @description
 #' Write a table of 2 columns: 1) process and 2) median seconds
 #'
 #' @param dir_job_results [chr] path to MolEvolvR job_results
@@ -113,53 +128,61 @@ get_proc_medians <- function(dir_job_results) {
 #'
 #' @return [tbl_df] 2 columns: 1) process and 2) median seconds
 #'
-#' example: write_proc_medians_table(
+#' example: writeProcessRuntime2TSV(
 #'   "/data/scratch/janani/molevolvr_out/",
 #'   "/data/scratch/janani/molevolvr_out/log_tbl.tsv"
 #' )
 #' @export
-write_proc_medians_table <- function(dir_job_results, filepath) {
-    df_proc_medians <- get_proc_medians(dir_job_results) |>
-        tibble::as_tibble() |>
-        tidyr::pivot_longer(
-            dplyr::everything(),
-            names_to = "process",
-            values_to = "median_seconds"
-        ) |>
-        dplyr::arrange(dplyr::desc(median_seconds))
-    readr::write_tsv(df_proc_medians, file = filepath)
-    return(df_proc_medians)
+writeProcessRuntime2TSV <- function(dir_job_results, filepath) {
+  df_proc_medians <- calculateProcessRuntime(dir_job_results) |>
+    tibble::as_tibble() |>
+    tidyr::pivot_longer(
+      dplyr::everything(),
+      names_to = "process",
+      values_to = "median_seconds"
+    ) |>
+    dplyr::arrange(dplyr::desc(median_seconds))
+
+  # Write the resulting tibble to a TSV file
+  readr::write_tsv(df_proc_medians, file = filepath)
+  return(df_proc_medians)
 }
 
+#' writeProcessRuntime2YML
+#' 
+#' @description
 #' Compute median process runtimes, then write a YAML list of the processes and
 #' their median runtimes in seconds to the path specified by 'filepath'.
 #'
 #' The default value of filepath is the value of the env var
-#' MOLEVOLVR_PROC_WEIGHTS, which get_proc_weights() also uses as its default
+#' MOLEVOLVR_PROC_WEIGHTS, which getProcessRuntimeWeights() also uses as its default
 #' read location.
 #'
 #' @param dir_job_results [chr] path to MolEvolvR job_results directory
-#' @param filepath [chr] path to save YAML file; if NULL, uses ./molevol_scripts/log_data/job_proc_weights.yml
+#' @param filepath [chr] path to save YAML file; if NULL, 
+#'                 uses ./molevol_scripts/log_data/job_proc_weights.yml
 #'
 #' @importFrom yaml write_yaml
 #'
 #' @examples
 #' \dontrun{
-#' write_proc_medians_yml(
+#' writeProcessRuntime2YML(
 #'     "/data/scratch/janani/molevolvr_out/",
 #'     "/data/scratch/janani/molevolvr_out/log_tbl.yml"
 #' )
 #' }
 #' @export
-write_proc_medians_yml <- function(dir_job_results, filepath = NULL) {
-    if (is.null(filepath)) {
-        filepath <- file.path(common_root, "molevol_scripts", "log_data", "job_proc_weights.yml")
-    }
-
-    medians <- get_proc_medians(dir_job_results)
-    yaml::write_yaml(medians, filepath)
+writeProcessRuntime2YML <- function(dir_job_results, filepath = NULL) {
+  if (is.null(filepath)) {
+    filepath <- file.path(common_root, "molevol_scripts", "log_data", "job_proc_weights.yml")
+  }
+  medians <- calculateProcessRuntime(dir_job_results)
+  yaml::write_yaml(medians, filepath)
 }
 
+#' getProcessRuntimeWeights
+#' 
+#' @description
 #' Quickly get the runtime weights for MolEvolvR backend processes
 #'
 #' @param dir_job_results [chr] path to MolEvolvR job_results
@@ -170,50 +193,55 @@ write_proc_medians_yml <- function(dir_job_results, filepath = NULL) {
 #'
 #' @return [list] names: processes; values: median runtime (seconds)
 #'
-#' example: get_proc_weights()
+#' example: writeProcessRuntime2YML()
 #' @export
-get_proc_weights <- function(medians_yml_path = NULL) {
-    if (is.null(medians_yml_path)) {
-        medians_yml_path <- file.path(common_root, "molevol_scripts", "log_data", "job_proc_weights.yml")
-    }
+getProcessRuntimeWeights <- function(medians_yml_path = NULL) {
+  if (is.null(medians_yml_path)) {
+    medians_yml_path <- file.path(common_root,
+                                  "molevol_scripts",
+                                  "log_data",
+                                  "job_proc_weights.yml")
+  }
 
-    proc_weights <- tryCatch(
-        {
-            # attempt to read the weights from the YAML file produced by
-            # write_proc_medians_yml()
-            if (stringr::str_trim(medians_yml_path) == "") {
-                stop(
-                    stringr::str_glue("medians_yml_path is empty ({medians_yml_path}), returning default weights")
-                )
-            }
+  proc_weights <- tryCatch({
+    # attempt to read the weights from the YAML file produced by
+    # writeProcessRuntime2YML()
+    if (stringr::str_trim(medians_yml_path) == "") {
+      stop(
+        stringr::str_glue("medians_yml_path is empty 
+                          ({medians_yml_path}), returning default weights")
+      )
+    }
 
-            proc_weights <- yaml::read_yaml(medians_yml_path)
-        },
-        # to avoid fatal errors in reading the proc weights yaml,
-        # some median process runtimes have been hardcoded based on
-        # the result of get_proc_medians() from Jan 2024
-        error = function(cond) {
-            proc_weights <- list(
-                "dblast" = 2810,
-                "iprscan" = 1016,
-                "dblast_cleanup" = 79,
-                "ipr2lineage" = 18,
-                "ipr2da" = 12,
-                "blast_clust" = 2,
-                "clust2table" = 2
-            )
-            proc_weights
-        }
+    proc_weights <- yaml::read_yaml(medians_yml_path)
+  },
+  # to avoid fatal errors in reading the proc weights yaml,
+  # some median process runtimes have been hardcoded based on
+  # the result of calculateProcessRuntime() from Jan 2024
+  error = function(cond) {
+    proc_weights <- list(
+      "dblast" = 2810,
+      "iprscan" = 1016,
+      "dblast_cleanup" = 79,
+      "ipr2lineage" = 18,
+      "ipr2da" = 12,
+      "blast_clust" = 2,
+      "clust2table" = 2
     )
+    proc_weights
+  })
 
-    return(proc_weights)
+  return(proc_weights)
 }
 
+#' calculateEstimatedWallTimeFromOpts
+#' 
+#' @description
 #' Given MolEvolvR advanced options and number of inputs,
 #' calculate the total estimated walltime for the job
 #'
 #' @param advanced_opts character vector of MolEvolvR advanced options
-#' (see make_opts2procs for the options)
+#' (see mapOption2Process for the options)
 #' @param n_inputs total number of input proteins
 #'
 #' @importFrom dplyr if_else
@@ -221,70 +249,88 @@ get_proc_weights <- function(medians_yml_path = NULL) {
 #'
 #' @return total estimated number of seconds a job will process (walltime)
 #'
-#' example: advanced_opts2est_walltime(c("homology_search", "domain_architecture"), n_inputs = 3, n_hits = 50L)
+#' example: calculateEstimatedWallTimeFromOpts	(c("homology_search",
+#'                                       "domain_architecture"),
+#'                                       n_inputs = 3, n_hits = 50L)
 #' @export
-advanced_opts2est_walltime <- function(advanced_opts, n_inputs = 1L, n_hits = NULL, verbose = FALSE) {
-    # to calculate est walltime for a homology search job, the number of hits
-    # must be provided
-    validation_fail <- is.null(n_hits) && "homology_search" %in% advanced_opts
-    stopifnot(!validation_fail)
+calculateEstimatedWallTimeFromOpts	 <- function(advanced_opts,
+                                                  n_inputs = 1L,
+                                                  n_hits = NULL,
+                                                  verbose = FALSE) {
+  # to calculate est walltime for a homology search job, the number of hits
+  # must be provided
+  validation_fail <- is.null(n_hits) && "homology_search" %in% advanced_opts
+  stopifnot(!validation_fail)
 
-    proc_weights <- get_proc_weights()
-    # sort process weights by names and convert to vec
-    proc_weights <- proc_weights[order(names(proc_weights))] |> unlist()
-    all_procs <- names(proc_weights) |> sort()
-    # get processes from advanced options and sort by names
-    procs_from_opts <- map_advanced_opts2procs(advanced_opts)
-    procs_from_opts <- sort(procs_from_opts)
-    # binary encode: yes proc will run (1); else 0
-    binary_proc_vec <- dplyr::if_else(all_procs %in% procs_from_opts, 1L, 0L)
-    # dot product of weights and procs to run; scaled by the number of inputs
-    est_walltime <- (n_inputs * (binary_proc_vec %*% proc_weights)) |>
-        as.numeric()
-    # calculate the additional processes to run for the homologous hits
-    if ("homology_search" %in% advanced_opts) {
-        opts2procs <- make_opts2procs()
-        # exclude the homology search processes for the homologous hits
-        procs2exclude_for_homologs <- opts2procs[["homology_search"]]
-        procs_homologs <- procs_from_opts[!(procs_from_opts %in% procs2exclude_for_homologs)]
-        binary_proc_vec_homolog <- dplyr::if_else(all_procs %in% procs_homologs, 1L, 0L)
-        # add the estimated walltime for processes run on the homologous hits
-        est_walltime <- est_walltime +
-            (n_hits * (binary_proc_vec_homolog %*% proc_weights) |> as.numeric())
-    }
-    if (verbose) {
-        msg <- stringr::str_glue(
-            "warnings from advanced_opts2est_walltime():\n",
-            "\tn_inputs={n_inputs}\n",
-            "\tn_hits={ifelse(is.null(n_hits), 'null', n_hits)}\n",
-            "\test_walltime={est_walltime}\n\n"
-        )
-        cat(file = stderr(), msg)
-    }
-    return(est_walltime)
+  # Get process weights
+  proc_weights <- writeProcessRuntime2YML()
+
+  # sort process weights by names and convert to vec
+  proc_weights <- proc_weights[order(names(proc_weights))] |> unlist()
+  all_procs <- names(proc_weights) |> sort()
+  # get processes from advanced options and sort by names
+  procs_from_opts <- mapAdvOption2Process(advanced_opts)
+  procs_from_opts <- sort(procs_from_opts)
+  # binary encode: yes proc will run (1); else 0
+  binary_proc_vec <- dplyr::if_else(all_procs %in% procs_from_opts, 1L, 0L)
+  # dot product of weights and procs to run; scaled by the number of inputs
+  est_walltime <- (n_inputs * (binary_proc_vec %*% proc_weights)) |>
+    as.numeric()
+  # calculate the additional processes to run for the homologous hits
+  if ("homology_search" %in% advanced_opts) {
+    opts2procs <- mapOption2Process()
+    # exclude the homology search processes for the homologous hits
+    procs2exclude_for_homologs <- opts2procs[["homology_search"]]
+    procs_homologs <- procs_from_opts[!(procs_from_opts 
+                                        %in% procs2exclude_for_homologs)]
+    binary_proc_vec_homolog <- dplyr::if_else(all_procs 
+                                              %in% procs_homologs, 1L, 0L)
+    # add the estimated walltime for processes run on the homologous hits
+    est_walltime <- est_walltime +
+      (n_hits * (binary_proc_vec_homolog
+                  %*% proc_weights) |> as.numeric())
+  }
+  if (verbose) {
+    msg <- stringr::str_glue(
+      "warnings from calculateEstimatedWallTimeFromOpts	():\n",
+      "\tn_inputs={n_inputs}\n",
+      "\tn_hits={ifelse(is.null(n_hits), 'null', n_hits)}\n",
+      "\test_walltime={est_walltime}\n\n"
+    )
+    cat(file = stderr(), msg)
+  }
+  return(est_walltime)
 }
 
+
+#' assignJobQueue
+#' 
+#' @description
 #' Decision function to assign job queue
 #'
 #' @param t_sec_estimate estimated number of seconds a job will process
-#' (from advanced_opts2est_walltime())
+#' (from calculateEstimatedWallTimeFromOpts	())
 #' @param t_long threshold value that defines the lower bound for assigning a
 #' job to the "long queue"
 #'
 #' @return a string of "short" or "long"
 #'
 #' example:
-#' advanced_opts2est_walltime(c("homology_search", "domain_architecture"), 3) |>
-#'   assign_job_queue()
+#' calculateEstimatedWallTimeFromOpts	(c("homology_search",
+#'                                         "domain_architecture"), 3) |>
+#'   assignJobQueue()
 #' @export
-assign_job_queue <- function(
-        t_sec_estimate,
-        t_cutoff = 21600 # 6 hours
-    ) {
-    queue <- ifelse(t_sec_estimate > t_cutoff, "long", "short")
-    return(queue)
+assignJobQueue <- function(
+  t_sec_estimate,
+  t_cutoff = 21600 # 6 hours
+) {
+  queue <- ifelse(t_sec_estimate > t_cutoff, "long", "short")
+  return(queue)
 }
 
+#' plotEstimatedWallTimes
+#' 
+#' @description
 #' Plot the estimated runtimes for different advanced options and number
 #' of inputs
 #'
@@ -297,81 +343,88 @@ assign_job_queue <- function(
 #' @return line plot object
 #'
 #' example:
-#' p <- plot_estimated_walltimes()
-#' ggplot2::ggsave(filename = "/data/molevolvr_transfer/molevolvr_dev/molevol_scripts/docs/estimate_walltimes.png", plot = p)
+#' p <- plotEstimatedWallTimes()
+#' ggplot2::ggsave(filename = "/data/molevolvr_transfer/molevolvr_
+#'                 dev/molevol_scripts/docs/estimate_walltimes.png", plot = p)
 #' @export
-plot_estimated_walltimes <- function() {
-    opts <- make_opts2procs() |> names()
+plotEstimatedWallTimes <- function() {
+    opts <- mapOption2Process() |> names()
     # get all possible submission permutations (powerset)
     get_powerset <- function(vec) {
-        # generate powerset (do not include empty set)
-        n <- length(vec)
-        indices <- 1:n
-        powerset <- lapply(1:n, function(x) combn(indices, x, simplify = FALSE))
-        powerset <- unlist(powerset, recursive = FALSE)
-        powerset <- lapply(powerset, function(index) vec[index])
-        powerset
+      # generate powerset (do not include empty set)
+      n <- length(vec)
+      indices <- 1:n
+      powerset <- lapply(1:n, function(x) combn(indices, x, simplify = FALSE))
+      powerset <- unlist(powerset, recursive = FALSE)
+      powerset <- lapply(powerset, function(index) vec[index])
+      powerset
     }
     opts_power_set <- get_powerset(opts)
     est_walltimes <- list()
     for (i in 1:20) {
-        est_walltimes <- append(
-            x = est_walltimes,
-            values = sapply(
-                opts_power_set,
-                FUN = function(advanced_opts) {
-                    # for simplicity, assume the default number of homologus hits (100)
-                    n_hits <- if ("homology_search" %in% advanced_opts) {
-                        100
-                    } else {
-                        NULL
-                    }
-                    est_walltime <- advanced_opts2est_walltime(
-                        advanced_opts,
-                        n_inputs = i,
-                        n_hits = n_hits,
-                        verbose = TRUE
-                    )
-                    names(est_walltime) <- paste0(advanced_opts, collapse = "_")
-                    est_walltime
-                }
+      est_walltimes <- append(
+        x = est_walltimes,
+        values = sapply(
+          opts_power_set,
+          FUN = function(advanced_opts) {
+            # for simplicity, assume the default number of homologus hits (100)
+            n_hits <- if ("homology_search" %in% advanced_opts) {
+              100
+            } else {
+                NULL
+              }
+            est_walltime <- calculateEstimatedWallTimeFromOpts	(
+              advanced_opts,
+              n_inputs = i,
+              n_hits = n_hits,
+              verbose = TRUE
             )
+            names(est_walltime) <- paste0(advanced_opts, collapse = "_")
+            est_walltime
+          }
         )
+      )
     }
     # concat all results to their unique names
     est_walltimes <- tapply(
-        unlist(
-            est_walltimes,
-            use.names = FALSE
-        ),
-        rep(
-            names(est_walltimes),
-            lengths(est_walltimes)
-        ),
-        FUN = c
+      unlist(
+        est_walltimes,
+        use.names = FALSE
+      ),
+      rep(
+        names(est_walltimes),
+        lengths(est_walltimes)
+      ),
+      FUN = c
     )
     df_walltimes <- est_walltimes |>
-        unlist() |>
-        matrix(nrow = length(est_walltimes[[1]]), ncol = length(names(est_walltimes)))
+      unlist() |>
+      matrix(nrow = length(est_walltimes[[1]]),
+             ncol = length(names(est_walltimes)))
     colnames(df_walltimes) <- names(est_walltimes)
     df_walltimes <- df_walltimes |> tibble::as_tibble()
     # rm always col or powerset outcome without the "always" processes
     col_idx_keep <- grep(pattern = "always$", x = names(df_walltimes))
     df_walltimes <- df_walltimes |>
-        dplyr::select(col_idx_keep)
+      dplyr::select(col_idx_keep)
     # bind n_inputs
     df_walltimes <- df_walltimes |>
-        dplyr::mutate(n_inputs = 1:20)
-    df_walltimes <- tidyr::gather(df_walltimes, key = "advanced_opts", value = "est_walltime", -n_inputs)
+      dplyr::mutate(n_inputs = 1:20)
+    df_walltimes <- tidyr::gather(df_walltimes,
+                                  key = "advanced_opts",
+                                  value = "est_walltime",
+                                  n_inputs)
     # sec to hrs
     df_walltimes <- df_walltimes |>
-        dplyr::mutate(est_walltime = est_walltime / 3600)
-    p <- ggplot2::ggplot(df_walltimes, ggplot2::aes(x = n_inputs, y = est_walltime, color = advanced_opts)) +
-        ggplot2::geom_line() +
-        ggplot2::labs(
-            title = "MolEvolvR estimated runtimes",
-            x = "Number of inputs",
-            y = "Estimated walltime (hours)"
-        )
+      dplyr::mutate(est_walltime = est_walltime / 3600)
+    p <- ggplot2::ggplot(df_walltimes, ggplot2::aes(x = n_inputs, 
+                                                    y = est_walltime, 
+                                                    color = advanced_opts)) +
+      ggplot2::geom_line() +
+      ggplot2::labs(
+        title = "MolEvolvR estimated runtimes",
+        x = "Number of inputs",
+        y = "Estimated walltime (hours)"
+      )
     return(p)
 }
diff --git a/R/blastWrappers.R b/R/blastWrappers.R
index 552b1ff6..9b55f3ee 100755
--- a/R/blastWrappers.R
+++ b/R/blastWrappers.R
@@ -18,25 +18,28 @@
 #'
 #' @examples
 run_deltablast <- function(deltablast_path, db_search_path,
-    db = "refseq", query, evalue = "1e-5",
-    out, num_alignments, num_threads = 1) {
-    start <- Sys.time()
+                           db = "refseq", query, evalue = "1e-5",
+                           out, num_alignments, num_threads = 1) {
 
-    system(paste0("export BLASTDB=/", db_search_path))
+  start <- Sys.time()
 
-    system2(
-        command = deltablast_path,
-        args = c(
-            "-db", db,
-            "-query", query,
-            "-evalue", evalue,
-            "-out", out,
-            "-num_threads", num_threads,
-            "-num_alignments", num_alignments
-            #   ,"-outfmt", outfmt
-        )
+
+  system(paste0("export BLASTDB=/", db_search_path))
+
+  system2(
+    command = deltablast_path,
+    args = c(
+      "-db", db,
+      "-query", query,
+      "-evalue", evalue,
+      "-out", out,
+      "-num_threads", num_threads,
+      "-num_alignments", num_alignments
+      #   ,"-outfmt", outfmt
     )
-    print(Sys.time() - start)
+  )
+  print(Sys.time() - start)
+
 }
 
 
@@ -55,20 +58,21 @@ run_deltablast <- function(deltablast_path, db_search_path,
 #'
 #' @examples
 run_rpsblast <- function(rpsblast_path, db_search_path,
-    db = "refseq", query, evalue = "1e-5",
-    out, num_threads = 1) {
-    start <- Sys.time()
-    system(paste0("export BLASTDB=/", db_search_path))
-    system2(
-        command = rpsblast_path,
-        args = c(
-            "-db", db,
-            "-query", query,
-            "-evalue", evalue,
-            "-out", out,
-            "-num_threads", num_threads
-            #                  , "-outfmt", outfmt
-        )
+                         db = "refseq", query, evalue = "1e-5",
+                         out, num_threads = 1) {
+
+  start <- Sys.time()
+  system(paste0("export BLASTDB=/", db_search_path))
+
+  system2(
+    command = rpsblast_path,
+    args = c(
+      "-db", db,
+      "-query", query,
+      "-evalue", evalue,
+      "-out", out,
+      "-num_threads", num_threads
     )
-    print(Sys.time() - start)
+  )
+  print(Sys.time() - start)
 }
diff --git a/R/clean_clust_file.R b/R/clean_clust_file.R
index d3f813e5..87dcde70 100755
--- a/R/clean_clust_file.R
+++ b/R/clean_clust_file.R
@@ -55,9 +55,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' clean_clust_file("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
+#' cleanClusterFile("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
 #' }
-clean_clust_file <- function(path, writepath = NULL, query) {
+cleanClusterFile <- function(path, writepath = NULL, query) {
     # ?? does the following line need to be changed to read_lines()?
     prot <- read_tsv(path, col_names = F)
 
diff --git a/R/combine_analysis.R b/R/combine_analysis.R
index bb3b3ce2..55e36925 100755
--- a/R/combine_analysis.R
+++ b/R/combine_analysis.R
@@ -17,9 +17,9 @@
 #' @export
 #'
 #' @examples
-combine_full <- function(inpath, ret = FALSE) {
+combineFullAnalysis <- function(inpath, ret = FALSE) {
     ## Combining full_analysis files
-    full_combnd <- combine_files(inpath,
+    full_combnd <- combineFiles(inpath,
         pattern = "*.full_analysis.tsv", skip = 0,
         col_names = T
     )
@@ -44,9 +44,9 @@ combine_full <- function(inpath, ret = FALSE) {
 #' @export
 #'
 #' @examples
-combine_ipr <- function(inpath, ret = FALSE) {
+combineIPR <- function(inpath, ret = FALSE) {
     ## Combining clean ipr files
-    ipr_combnd <- combine_files(inpath,
+    ipr_combnd <- combineFiles(inpath,
         pattern = "*.iprscan_cln.tsv", skip = 0,
         col_names = T
     )
diff --git a/R/combine_files.R b/R/combine_files.R
index 76c5fa09..455ddd53 100755
--- a/R/combine_files.R
+++ b/R/combine_files.R
@@ -38,7 +38,7 @@
 #' @export
 #'
 #' @examples
-combine_files <- function(inpath = c("../molevol_data/project_data/phage_defense/"),
+combineFiles <- function(inpath = c("../molevol_data/project_data/phage_defense/"),
     pattern = "*full_analysis.tsv",
     delim = "\t", skip = 0,
     col_names = T) {
@@ -67,7 +67,7 @@ combine_files <- function(inpath = c("../molevol_data/project_data/phage_defense
 ## Sample Runs ##
 #################
 # ## Combining full_analysis files
-# full_combnd <- combine_files(inpath,
+# full_combnd <- combineFiles(inpath,
 #                             pattern="*full_analysis.txt", skip=0,
 #                             col_names=T)
 #
@@ -75,7 +75,7 @@ combine_files <- function(inpath = c("../molevol_data/project_data/phage_defense
 #           path="../molevol_data/project_data/slps/full_combined.tsv")
 #
 # ## Combining clean files
-# cln_combnd <- combine_files(inpath,
+# cln_combnd <- combineFiles(inpath,
 #                             pattern="^.*cln.txt", skip=0,
 #                             col_names=T)
 #
@@ -86,14 +86,14 @@ combine_files <- function(inpath = c("../molevol_data/project_data/phage_defense
 # ## Less helpful examples!
 # ## Combining BLAST files
 # ## Likely makes no sense since clustering is done per query
-# cl_blast_combnd <- combine_files(inpath,
+# cl_blast_combnd <- combineFiles(inpath,
 #                                  pattern="^.*refseq.1e-5.txt", skip=0,
 #                                  col_names=cl_blast_colnames) %>%
 #   select(-PcPositive, -ClusterID)
 #
 # ## Combining IPR files
 # ## Likely makes no sense since there may be repeated AccNum from indiv. files!
-# ipr_combnd <- combine_files(inpath,
+# ipr_combnd <- combineFiles(inpath,
 #                             pattern="*iprscan.lins*",  skip=0,
 #                             col_names=ipr_colnames)
 #
diff --git a/R/create_lineage_lookup.R b/R/create_lineage_lookup.R
index e7374df3..2408c5e6 100644
--- a/R/create_lineage_lookup.R
+++ b/R/create_lineage_lookup.R
@@ -3,6 +3,9 @@
 # library(biomartr)
 
 
+#' createLineageLookup
+#' 
+#' @description
 #' Create a look up table that goes from TaxID, to Lineage
 #'
 #' @author Samuel Chen
@@ -26,9 +29,9 @@
 #' @export
 #'
 #' @examples
-create_lineage_lookup <- function(lineage_file = here("data/rankedlineage.dmp"),
+createLineageLookup <- function(lineage_file = here("data/rankedlineage.dmp"),
     outfile, taxonomic_rank = "phylum") {
-    shorten_NA <- function(Lineage) {
+    .shortenNA <- function(Lineage) {
         first_NA <- str_locate(Lineage, "NA")[1]
         if (is.na(first_NA)) {
             # No NAs
@@ -92,7 +95,7 @@ create_lineage_lookup <- function(lineage_file = here("data/rankedlineage.dmp"),
     # Takes a while (2million rows after all)
     rankedLinsCombined <- rankedLins %>%
         unite(col = "Lineage", all_of(combined_taxonomy), sep = ">") %>%
-        mutate(Lineage = unlist(map(Lineage, shorten_NA)))
+        mutate(Lineage = unlist(map(Lineage, .shortenNA)))
 
 
 
@@ -101,7 +104,7 @@ create_lineage_lookup <- function(lineage_file = here("data/rankedlineage.dmp"),
 
 
 
-#' CreateLineageLookup <- function(assembly_path, updateAssembly = FALSE, file_type = "tsv")
+#' createLineageLookup <- function(assembly_path, updateAssembly = FALSE, file_type = "tsv")
 #' {
 #'   #' Create a look up table that goes from GCA_ID, to TaxID, to Lineage
 #'   #' @author Samuel Chen
diff --git a/R/lineage.R b/R/lineage.R
index d14246d7..ef4fe586 100644
--- a/R/lineage.R
+++ b/R/lineage.R
@@ -77,7 +77,7 @@ downloadAssemblySummary <- function(outpath,
 #' This file can be generated using the "downloadAssemblySummary()" function
 #' @param lineagelookup_path String of the path to the lineage lookup file
 #' (taxid to lineage mapping). This file can be generated using the
-#' "create_lineage_lookup()" function
+#' "createLineageLookup()" function
 #' @param acc_col
 #'
 #' @importFrom dplyr pull
@@ -309,7 +309,7 @@ efetchIPG <- function(accessions, out_path, plan = "multicore") {
 #' @param genbank_assembly_path
 #' @param lineagelookup_path String of the path to the lineage lookup file
 #' (taxid to lineage mapping). This file can be generated using the
-#' "create_lineage_lookup()" function
+#' "createLineageLookup()" function
 #'
 #' @importFrom data.table fread setnames
 #'
diff --git a/R/msa.R b/R/msa.R
index e56cc32c..0b1b6e34 100644
--- a/R/msa.R
+++ b/R/msa.R
@@ -197,21 +197,21 @@ msa_pdf <- function(fasta_path, out_path = NULL,
 #'
 #' @examples
 generate_msa <- function(fa_file = "", outfile = "") {
-    prot_aa <- readAAStringSet(
-        path = fa_file,
-        format = "fasta"
-    )
-    prot_aa
+  prot_aa <- readAAStringSet(
+    fa_file,
+    format = "fasta"
+  )
+  prot_aa
 
-    ## Install kalign ?rMSA_INSTALL
-    ## Messed up! Reimplement from kalign.R
-    ## https://github.com/mhahsler/rMSA/blob/master/R/kalign.R
+  ## Install kalign ?rMSA_INSTALL
+  ## Messed up! Reimplement from kalign.R
+  ## https://github.com/mhahsler/rMSA/blob/master/R/kalign.R
 
-    # source("scripts/c2r.R")
+  # source("scripts/c2r.R")
 
-    ## align the sequences
-    al <- kalign(prot_aa) # !! won't work!
-    al
+  ## align the sequences
+  al <- kalign(prot_aa) # !! won't work!
+  al
 }
 
 ############################
diff --git a/man/GCA2Lineage.Rd b/man/GCA2Lineage.Rd
index 9ec0ce56..9a2a7a30 100644
--- a/man/GCA2Lineage.Rd
+++ b/man/GCA2Lineage.Rd
@@ -19,7 +19,7 @@ This file can be generated using the "downloadAssemblySummary()" function}
 
 \item{lineagelookup_path}{String of the path to the lineage lookup file
 (taxid to lineage mapping). This file can be generated using the
-"create_lineage_lookup()" function}
+"createLineageLookup()" function}
 
 \item{acc_col}{}
 }
diff --git a/man/IPG2Lineage.Rd b/man/IPG2Lineage.Rd
index 282d5cbf..118812ab 100644
--- a/man/IPG2Lineage.Rd
+++ b/man/IPG2Lineage.Rd
@@ -29,7 +29,7 @@ file}
 
 \item{lineagelookup_path}{String of the path to the lineage lookup file
 (taxid to lineage mapping). This file can be generated using the
-"create_lineage_lookup()" function}
+"createLineageLookup()" function}
 
 \item{assembly_path}{String of the path to the assembly_summary path
 This file can be generated using the \link[MolEvolvR]{downloadAssemblySummary} function}
@@ -39,7 +39,8 @@ A \code{data.table} with the lineage information for the provided protein
 accessions.
 }
 \description{
-Takes the resulting file of an efetch run on the ipg database and
+Takes the resulting file
+of an efetch run on the ipg database and
 
 Takes the resulting file of an efetch run on the ipg database and
 append lineage, and taxid columns
diff --git a/man/assign_job_queue.Rd b/man/assignJobQueue.Rd
similarity index 58%
rename from man/assign_job_queue.Rd
rename to man/assignJobQueue.Rd
index ceb6fa77..de646a82 100644
--- a/man/assign_job_queue.Rd
+++ b/man/assignJobQueue.Rd
@@ -1,14 +1,14 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{assign_job_queue}
-\alias{assign_job_queue}
-\title{Decision function to assign job queue}
+\name{assignJobQueue}
+\alias{assignJobQueue}
+\title{assignJobQueue}
 \usage{
-assign_job_queue(t_sec_estimate, t_cutoff = 21600)
+assignJobQueue(t_sec_estimate, t_cutoff = 21600)
 }
 \arguments{
 \item{t_sec_estimate}{estimated number of seconds a job will process
-(from advanced_opts2est_walltime())}
+(from calculateEstimatedWallTimeFromOpts    ())}
 
 \item{t_long}{threshold value that defines the lower bound for assigning a
 job to the "long queue"}
@@ -17,8 +17,9 @@ job to the "long queue"}
 a string of "short" or "long"
 
 example:
-advanced_opts2est_walltime(c("homology_search", "domain_architecture"), 3) |>
-assign_job_queue()
+calculateEstimatedWallTimeFromOpts	(c("homology_search",
+"domain_architecture"), 3) |>
+assignJobQueue()
 }
 \description{
 Decision function to assign job queue
diff --git a/man/advanced_opts2est_walltime.Rd b/man/calculateEstimatedWallTimeFromOpts.Rd
similarity index 58%
rename from man/advanced_opts2est_walltime.Rd
rename to man/calculateEstimatedWallTimeFromOpts.Rd
index ea4b29e6..d5361001 100644
--- a/man/advanced_opts2est_walltime.Rd
+++ b/man/calculateEstimatedWallTimeFromOpts.Rd
@@ -1,11 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{advanced_opts2est_walltime}
-\alias{advanced_opts2est_walltime}
-\title{Given MolEvolvR advanced options and number of inputs,
-calculate the total estimated walltime for the job}
+\name{calculateEstimatedWallTimeFromOpts}
+\alias{calculateEstimatedWallTimeFromOpts}
+\title{calculateEstimatedWallTimeFromOpts}
 \usage{
-advanced_opts2est_walltime(
+calculateEstimatedWallTimeFromOpts(
   advanced_opts,
   n_inputs = 1L,
   n_hits = NULL,
@@ -14,14 +13,16 @@ advanced_opts2est_walltime(
 }
 \arguments{
 \item{advanced_opts}{character vector of MolEvolvR advanced options
-(see make_opts2procs for the options)}
+(see mapOption2Process for the options)}
 
 \item{n_inputs}{total number of input proteins}
 }
 \value{
 total estimated number of seconds a job will process (walltime)
 
-example: advanced_opts2est_walltime(c("homology_search", "domain_architecture"), n_inputs = 3, n_hits = 50L)
+example: calculateEstimatedWallTimeFromOpts	(c("homology_search",
+"domain_architecture"),
+n_inputs = 3, n_hits = 50L)
 }
 \description{
 Given MolEvolvR advanced options and number of inputs,
diff --git a/man/get_proc_medians.Rd b/man/calculateProcessRuntime.Rd
similarity index 72%
rename from man/get_proc_medians.Rd
rename to man/calculateProcessRuntime.Rd
index b6db0b56..579ea2b6 100644
--- a/man/get_proc_medians.Rd
+++ b/man/calculateProcessRuntime.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{get_proc_medians}
-\alias{get_proc_medians}
-\title{Scrape MolEvolvR logs and calculate median processes}
+\name{calculateProcessRuntime}
+\alias{calculateProcessRuntime}
+\title{calculateProcessRuntime}
 \usage{
-get_proc_medians(dir_job_results)
+calculateProcessRuntime(dir_job_results)
 }
 \arguments{
 \item{dir_job_results}{\link{chr} path to MolEvolvR job_results
@@ -21,12 +21,12 @@ examples:
 }
 
 dir_job_results <- "/data/scratch/janani/molevolvr_out"
-list_proc_medians <- get_proc_medians(dir_job_results)
+list_proc_medians <- calculateProcessRuntime(dir_job_results)
 \enumerate{
 \item from outside container environment
 common_root <- "/data/molevolvr_transfer/molevolvr_dev"
 dir_job_results <- "/data/molevolvr_transfer/molevolvr_dev/job_results"
-list_proc_medians <- get_proc_medians(dir_job_results)
+list_proc_medians <- calculateProcessRuntime(dir_job_results)
 }
 }
 \description{
diff --git a/man/clean_clust_file.Rd b/man/cleanClusterFile.Rd
similarity index 82%
rename from man/clean_clust_file.Rd
rename to man/cleanClusterFile.Rd
index bba3072e..d2818662 100644
--- a/man/clean_clust_file.Rd
+++ b/man/cleanClusterFile.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/clean_clust_file.R
-\name{clean_clust_file}
-\alias{clean_clust_file}
+\name{cleanClusterFile}
+\alias{cleanClusterFile}
 \title{Clean Cluster File}
 \usage{
-clean_clust_file(path, writepath = NULL, query)
+cleanClusterFile(path, writepath = NULL, query)
 }
 \arguments{
 \item{path}{A character to the path of the cluster file to be cleaned}
@@ -24,6 +24,6 @@ This function reads a space-separated cluster file and converts it to a cleaned
 }
 \examples{
 \dontrun{
-clean_clust_file("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
+cleanClusterFile("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
 }
 }
diff --git a/man/combine_files.Rd b/man/combineFiles.Rd
similarity index 92%
rename from man/combine_files.Rd
rename to man/combineFiles.Rd
index 4126eb9e..3b56b923 100644
--- a/man/combine_files.Rd
+++ b/man/combineFiles.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/combine_files.R
-\name{combine_files}
-\alias{combine_files}
+\name{combineFiles}
+\alias{combineFiles}
 \title{Download the combined assembly summaries of genbank and refseq}
 \usage{
-combine_files(
+combineFiles(
   inpath = c("../molevol_data/project_data/phage_defense/"),
   pattern = "*full_analysis.tsv",
   delim = "\\t",
diff --git a/man/combine_full.Rd b/man/combineFullAnalysis.Rd
similarity index 69%
rename from man/combine_full.Rd
rename to man/combineFullAnalysis.Rd
index f4e6597b..35925e86 100644
--- a/man/combine_full.Rd
+++ b/man/combineFullAnalysis.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/combine_analysis.R
-\name{combine_full}
-\alias{combine_full}
+\name{combineFullAnalysis}
+\alias{combineFullAnalysis}
 \title{Combining full_analysis files}
 \usage{
-combine_full(inpath, ret = FALSE)
+combineFullAnalysis(inpath, ret = FALSE)
 }
 \arguments{
 \item{ret}{}
diff --git a/man/combine_ipr.Rd b/man/combineIPR.Rd
similarity index 74%
rename from man/combine_ipr.Rd
rename to man/combineIPR.Rd
index 52aa3057..035c4274 100644
--- a/man/combine_ipr.Rd
+++ b/man/combineIPR.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/combine_analysis.R
-\name{combine_ipr}
-\alias{combine_ipr}
+\name{combineIPR}
+\alias{combineIPR}
 \title{Combining clean ipr files}
 \usage{
-combine_ipr(inpath, ret = FALSE)
+combineIPR(inpath, ret = FALSE)
 }
 \arguments{
 \item{ret}{}
diff --git a/man/create_lineage_lookup.Rd b/man/createLineageLookup.Rd
similarity index 85%
rename from man/create_lineage_lookup.Rd
rename to man/createLineageLookup.Rd
index 51670f35..132019ce 100644
--- a/man/create_lineage_lookup.Rd
+++ b/man/createLineageLookup.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/create_lineage_lookup.R
-\name{create_lineage_lookup}
-\alias{create_lineage_lookup}
-\title{Create a look up table that goes from TaxID, to Lineage}
+\name{createLineageLookup}
+\alias{createLineageLookup}
+\title{createLineageLookup}
 \usage{
-create_lineage_lookup(
+createLineageLookup(
   lineage_file = here("data/rankedlineage.dmp"),
   outfile,
   taxonomic_rank = "phylum"
diff --git a/man/get_proc_weights.Rd b/man/getProcessRuntimeWeights.Rd
similarity index 64%
rename from man/get_proc_weights.Rd
rename to man/getProcessRuntimeWeights.Rd
index 0f4beb57..de0e2ea6 100644
--- a/man/get_proc_weights.Rd
+++ b/man/getProcessRuntimeWeights.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{get_proc_weights}
-\alias{get_proc_weights}
-\title{Quickly get the runtime weights for MolEvolvR backend processes}
+\name{getProcessRuntimeWeights}
+\alias{getProcessRuntimeWeights}
+\title{getProcessRuntimeWeights}
 \usage{
-get_proc_weights(medians_yml_path = NULL)
+getProcessRuntimeWeights(medians_yml_path = NULL)
 }
 \arguments{
 \item{dir_job_results}{\link{chr} path to MolEvolvR job_results
@@ -13,7 +13,7 @@ directory}
 \value{
 \link{list} names: processes; values: median runtime (seconds)
 
-example: get_proc_weights()
+example: writeProcessRuntime2YML()
 }
 \description{
 Quickly get the runtime weights for MolEvolvR backend processes
diff --git a/man/map_advanced_opts2procs.Rd b/man/mapAdvOption2Process.Rd
similarity index 66%
rename from man/map_advanced_opts2procs.Rd
rename to man/mapAdvOption2Process.Rd
index 631708b4..6a210a20 100644
--- a/man/map_advanced_opts2procs.Rd
+++ b/man/mapAdvOption2Process.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{map_advanced_opts2procs}
-\alias{map_advanced_opts2procs}
-\title{Use MolEvolvR advanced options to get associated processes}
+\name{mapAdvOption2Process}
+\alias{mapAdvOption2Process}
+\title{mapAdvOption2Process}
 \usage{
-map_advanced_opts2procs(advanced_opts)
+mapAdvOption2Process(advanced_opts)
 }
 \arguments{
 \item{advanced_opts}{character vector of MolEvolvR advanced options}
@@ -15,7 +15,7 @@ the advanced options
 
 example:
 advanced_opts <- c("homology_search", "domain_architecture")
-procs <- map_advanced_opts2procs(advanced_opts)
+procs <- mapAdvOption2Process(advanced_opts)
 }
 \description{
 Use MolEvolvR advanced options to get associated processes
diff --git a/man/make_opts2procs.Rd b/man/mapOption2Process.Rd
similarity index 58%
rename from man/make_opts2procs.Rd
rename to man/mapOption2Process.Rd
index 07e208b2..9645617b 100644
--- a/man/make_opts2procs.Rd
+++ b/man/mapOption2Process.Rd
@@ -1,15 +1,15 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{make_opts2procs}
-\alias{make_opts2procs}
-\title{Construct list where names (MolEvolvR advanced options) point to processes}
+\name{mapOption2Process}
+\alias{mapOption2Process}
+\title{mapOption2Process}
 \usage{
-make_opts2procs()
+mapOption2Process()
 }
 \value{
 list where names (MolEvolvR advanced options) point to processes
 
-example: list_opts2procs <- make_opts2procs
+example: list_opts2procs <- mapOption2Process
 }
 \description{
 Construct list where names (MolEvolvR advanced options) point to processes
diff --git a/man/plotEstimatedWallTimes.Rd b/man/plotEstimatedWallTimes.Rd
new file mode 100644
index 00000000..36b0ecd5
--- /dev/null
+++ b/man/plotEstimatedWallTimes.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assign_job_queue.R
+\name{plotEstimatedWallTimes}
+\alias{plotEstimatedWallTimes}
+\title{plotEstimatedWallTimes}
+\usage{
+plotEstimatedWallTimes()
+}
+\value{
+line plot object
+
+example:
+p <- plotEstimatedWallTimes()
+ggplot2::ggsave(filename = "/data/molevolvr_transfer/molevolvr_
+dev/molevol_scripts/docs/estimate_walltimes.png", plot = p)
+}
+\description{
+Plot the estimated runtimes for different advanced options and number
+of inputs
+
+this function was just for fun; very, very messy code
+}
diff --git a/man/plot_estimated_walltimes.Rd b/man/plot_estimated_walltimes.Rd
deleted file mode 100644
index 3669e0e0..00000000
--- a/man/plot_estimated_walltimes.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/assign_job_queue.R
-\name{plot_estimated_walltimes}
-\alias{plot_estimated_walltimes}
-\title{Plot the estimated runtimes for different advanced options and number
-of inputs}
-\usage{
-plot_estimated_walltimes()
-}
-\value{
-line plot object
-
-example:
-p <- plot_estimated_walltimes()
-ggplot2::ggsave(filename = "/data/molevolvr_transfer/molevolvr_dev/molevol_scripts/docs/estimate_walltimes.png", plot = p)
-}
-\description{
-this function was just for fun; very, very messy code
-}
diff --git a/man/write_proc_medians_table.Rd b/man/writeProcessRuntime2TSV.Rd
similarity index 67%
rename from man/write_proc_medians_table.Rd
rename to man/writeProcessRuntime2TSV.Rd
index 2ae7a97b..0e045a5c 100644
--- a/man/write_proc_medians_table.Rd
+++ b/man/writeProcessRuntime2TSV.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{write_proc_medians_table}
-\alias{write_proc_medians_table}
-\title{Write a table of 2 columns: 1) process and 2) median seconds}
+\name{writeProcessRuntime2TSV}
+\alias{writeProcessRuntime2TSV}
+\title{writeProcessRuntime2TSV}
 \usage{
-write_proc_medians_table(dir_job_results, filepath)
+writeProcessRuntime2TSV(dir_job_results, filepath)
 }
 \arguments{
 \item{dir_job_results}{\link{chr} path to MolEvolvR job_results}
@@ -14,7 +14,7 @@ write_proc_medians_table(dir_job_results, filepath)
 \value{
 \link{tbl_df} 2 columns: 1) process and 2) median seconds
 
-example: write_proc_medians_table(
+example: writeProcessRuntime2TSV(
 "/data/scratch/janani/molevolvr_out/",
 "/data/scratch/janani/molevolvr_out/log_tbl.tsv"
 )
diff --git a/man/write_proc_medians_yml.Rd b/man/writeProcessRuntime2YML.Rd
similarity index 50%
rename from man/write_proc_medians_yml.Rd
rename to man/writeProcessRuntime2YML.Rd
index a3d8ee5f..5e0a05a4 100644
--- a/man/write_proc_medians_yml.Rd
+++ b/man/writeProcessRuntime2YML.Rd
@@ -1,25 +1,28 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/assign_job_queue.R
-\name{write_proc_medians_yml}
-\alias{write_proc_medians_yml}
-\title{Compute median process runtimes, then write a YAML list of the processes and
-their median runtimes in seconds to the path specified by 'filepath'.}
+\name{writeProcessRuntime2YML}
+\alias{writeProcessRuntime2YML}
+\title{writeProcessRuntime2YML}
 \usage{
-write_proc_medians_yml(dir_job_results, filepath = NULL)
+writeProcessRuntime2YML(dir_job_results, filepath = NULL)
 }
 \arguments{
 \item{dir_job_results}{\link{chr} path to MolEvolvR job_results directory}
 
-\item{filepath}{\link{chr} path to save YAML file; if NULL, uses ./molevol_scripts/log_data/job_proc_weights.yml}
+\item{filepath}{\link{chr} path to save YAML file; if NULL,
+uses ./molevol_scripts/log_data/job_proc_weights.yml}
 }
 \description{
+Compute median process runtimes, then write a YAML list of the processes and
+their median runtimes in seconds to the path specified by 'filepath'.
+
 The default value of filepath is the value of the env var
-MOLEVOLVR_PROC_WEIGHTS, which get_proc_weights() also uses as its default
+MOLEVOLVR_PROC_WEIGHTS, which getProcessRuntimeWeights() also uses as its default
 read location.
 }
 \examples{
 \dontrun{
-write_proc_medians_yml(
+writeProcessRuntime2YML(
     "/data/scratch/janani/molevolvr_out/",
     "/data/scratch/janani/molevolvr_out/log_tbl.yml"
 )