patched find_parentage for syntax error

.gitignore

@@ -3,4 +3,5 @@
 .RData
 .Ruserdata
 .positai
-popR.Rproj
+BIBpopA.Rproj
+.DS_Store

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: popR
+Package: BIBpopA
 Title: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species
 Version: 0.1.0
 Authors@R: c(person(given='Josue',
@@ -11,16 +11,16 @@ Authors@R: c(person(given='Josue',
 Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
 Description: Tools for pedigree quality control and genomic breed/line
     composition estimation in diploid and polyploid breeding populations.
-    'popR' provides functions to check and correct common pedigree
+    'BIBpopA' provides functions to check and correct common pedigree
     errors, assign parentage from SNP genotype data using Mendelian error
     rates, validate parent-offspring trios, and estimate genome-wide
     breed or line composition using quadratic programming. Supports both
     diploid and polyploid species. For details on the composition
     estimation methods, see Funkhouser et al. (2017)
     <doi:10.2527/tas2016.0003>.
 License: Apache License (>= 2)
-URL: https://github.com/Breeding-Insight/popR
-BugReports: https://github.com/Breeding-Insight/popR/issues
+URL: https://github.com/Breeding-Insight/BIBpopA
+BugReports: https://github.com/Breeding-Insight/BIBpopA/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Depends: R (>= 4.4.0)

NEWS.md

@@ -1,7 +1,7 @@
-# popR 0.1.0
+# BIBpopA 0.1.0
 
-- Initial release of `popR` as a standalone package.
-- `popR` contains pedigree validation and breed/line composition functions
+- Initial release of `BIBpopA` as a standalone package.
+- `BIBpopA` contains pedigree validation and breed/line composition functions
   previously found in [BIGr](https://github.com/Breeding-Insight/BIGr),
   where they will no longer be maintained going forward.
 - These functions are the backbone of the pedigree and composition modules
@@ -18,4 +18,4 @@
 - `allele_freq_poly()` — computes allele frequencies for diploid and
   polyploid reference populations
 - `solve_composition_poly()` — estimates genome-wide breed/line composition
-  using quadratic programming
+  using quadratic programming

R/check_ped.R

@@ -27,7 +27,7 @@
 #' }
 #'
 #' @examples
-#' ped_file <- system.file("check_ped_test.txt", package = "popR")
+#' ped_file <- system.file("check_ped_test.txt", package = "BIBpopA")
 #' ped_errors <- check_ped(ped.file = ped_file, seed = 101919, verbose = FALSE)
 #'
 #' # Also accepts a data.table directly

R/find_parentage.R

@@ -413,6 +413,7 @@ find_parentage <- function(genotypes_file, parents_file, progeny_file,
                             linetype = "dashed", color = "black", linewidth = 1) +
         ggplot2::scale_x_continuous(breaks = seq(0, 100, by = 5)) +
         ggplot2::scale_y_continuous() +
+        ggplot2::scale_fill_manual(
           values = c("pass"        = "#339900",
                      "high_error"  = "#cc3333",
                      "low_markers" = "#F1C40F",

README.md

@@ -1,34 +1,34 @@
 <!-- badges: start -->
-[![Development Status](https://img.shields.io/badge/status-active%20development-yellow)](https://github.com/Breeding-Insight/popR)
+[![Development Status](https://img.shields.io/badge/status-active%20development-yellow)](https://github.com/Breeding-Insight/BIBpopA)
 [![R](https://img.shields.io/badge/R-%3E%3D%204.4-blue)](https://www.r-project.org/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)
-[![GitHub issues](https://img.shields.io/github/issues/Breeding-Insight/popR)](https://github.com/Breeding-Insight/popR/issues)
-[![GitHub pull requests](https://img.shields.io/github/issues-pr/Breeding-Insight/popR)](https://github.com/Breeding-Insight/popR/pulls)
-[![GitHub Release](https://img.shields.io/github/v/release/Breeding-Insight/popR?include_prereleases)](https://github.com/Breeding-Insight/popR/releases/latest)
-<!-- [![codecov](https://app.codecov.io/gh/Breeding-Insight/popR/graph/badge.svg?token=PJUZMRN1NF)](https://app.codecov.io/gh/Breeding-Insight/popR) -->
+[![GitHub issues](https://img.shields.io/github/issues/Breeding-Insight/BIBpopA)](https://github.com/Breeding-Insight/BIBpopA/issues)
+[![GitHub pull requests](https://img.shields.io/github/issues-pr/Breeding-Insight/BIBpopA)](https://github.com/Breeding-Insight/BIBpopA/pulls)
+[![GitHub Release](https://img.shields.io/github/v/release/Breeding-Insight/BIBpopA?include_prereleases)](https://github.com/Breeding-Insight/BIBpopA/releases/latest)
+<!-- [![codecov](https://app.codecov.io/gh/Breeding-Insight/BIBpopA/graph/badge.svg?token=PJUZMRN1NF)](https://app.codecov.io/gh/Breeding-Insight/BIBpopA) -->
 <!-- badges: end -->
 
-# popR
+# BIBpopA
 
 ### Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species Version 0.1.0
 
-popR is an R package developed by [Breeding Insight](https://breedinginsight.org/) that provides tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. It is designed to help researchers and breeders identify pedigree errors, assign parentage from SNP genotype data, and estimate genome-wide breed or line composition.
+BIBpopA is an R package developed by [Breeding Insight](https://breedinginsight.org/) that provides tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. It is designed to help researchers and breeders identify pedigree errors, assign parentage from SNP genotype data, and estimate genome-wide breed or line composition.
 
 ### Installation
 
-To install the development version of popR, install from GitHub using `remotes`:
+To install the development version of BIBpopA, install from GitHub using `remotes`:
 
 ```R
 install.packages("remotes")
-remotes::install_github("Breeding-Insight/popR", dependencies = TRUE)
-library(popR)
+remotes::install_github("Breeding-Insight/BIBpopA", dependencies = TRUE)
+library(BIBpopA)
 ```
-##### Note: popR is currently in development. Please report any bugs or issues on the GitHub Issues page.
+##### Note: BIBpopA is currently in development. Please report any bugs or issues on the GitHub Issues page.
 
 ### Funding
-popR development is supported by Breeding Insight, a USDA-funded initiative based at the University of Florida - IFAS.
+BIBpopA development is supported by Breeding Insight, a USDA-funded initiative based at the University of Florida - IFAS.
 
 ## Citation
-If you use popR in your research, please cite as:
+If you use BIBpopA in your research, please cite as:
 
-Chinchilla-Vargas, Josue, and Breeding Insight Team. 2025. "popR: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species." https://github.com/Breeding-Insight/popR.
+Chinchilla-Vargas, Josue, and Breeding Insight Team. 2025. "BIBpopA: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species." https://github.com/Breeding-Insight/BIBpopA.

inst/CITATION

@@ -1,6 +1,6 @@
 bibentry(
   bibtype = "Manual",
-  title   = "popR: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species",
+  title   = "BIBpopA: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species",
   author  = c(
     person(given = "Josue",        family = "Chinchilla-Vargas",
            email = "josue.chinchilla@ufl.edu", role = c("cre", "aut")),
@@ -12,5 +12,5 @@ bibentry(
   ),
   year = "2026",
   note = "R package version 0.1.0",
-  url  = "https://github.com/Breeding-Insight/popR"
-)
+  url  = "https://github.com/Breeding-Insight/BIBpopA"
+)

tests/testthat.R

@@ -1,4 +1,4 @@
 library(testthat)
-library(popR)
+library(BIBpopA)
 
-test_check("popR")
+test_check("BIBpopA")

tests/testthat/test-breedtools_poly.R

@@ -3,9 +3,9 @@ context("BreedTools")
 
 test_that("test breedtools poly",{
   #Input variables
-  ref_file <- system.file("test_ref.txt", package="popR")
-  val_file <- system.file("test_test.txt", package="popR")
-  ref_ids <- system.file("ref_ids.txt", package="popR")
+  ref_file <- system.file("test_ref.txt", package="BIBpopA")
+  val_file <- system.file("test_test.txt", package="BIBpopA")
+  ref_ids <- system.file("ref_ids.txt", package="BIBpopA")
 
   #import files
   reference = read.table(ref_file, header = T, row.names = 1, sep = "\t")

tests/testthat/test-check_ped.R

@@ -323,7 +323,7 @@ test_that("no output files are written to disk", {
 # janitor::clean_names() handles any remaining capitalization variants
 # ==============================================================================
 test_that("integration test with bundled fixture file", {
-  ped_file <- system.file("check_ped_test.txt", package = "popR")
+  ped_file <- system.file("check_ped_test.txt", package = "BIBpopA")
   skip_if(ped_file == "", "Bundled fixture file not found; skipping.")
 
   out <- check_ped(ped_file, seed = 101919, verbose = FALSE)