From 40a36939fce1ffbb7cd42d304e0e4679438ca1fa Mon Sep 17 00:00:00 2001 From: "josue.chinchilla" Date: Fri, 5 Jun 2026 16:29:37 -0400 Subject: [PATCH 1/3] patched find_parentage for syntax error --- .DS_Store | Bin 10244 -> 10244 bytes .gitignore | 3 ++- R/find_parentage.R | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.DS_Store b/.DS_Store index d587ad5ffa5f0658818cfda5b4422fec399c94fc..ece4fd8875f3ecd36ce90baac191d65860438373 100644 GIT binary patch delta 31 mcmZn(XbIThA;8Em*;C*pJ0k-F10zGwW=9DZ=FPPt?ZNAE2onGR diff --git a/.gitignore b/.gitignore index 2460510..43db397 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,5 @@ .RData .Ruserdata .positai -popR.Rproj \ No newline at end of file +popR.Rproj +.DS_Store diff --git a/R/find_parentage.R b/R/find_parentage.R index 00cc461..351661c 100644 --- a/R/find_parentage.R +++ b/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", From d80fd4dbfa6768bf8c32d42196f44d28e5f359c0 Mon Sep 17 00:00:00 2001 From: Josue Chinchilla-Vargas Date: Mon, 8 Jun 2026 06:54:20 -0400 Subject: [PATCH 2/3] Delete popR.Rproj --- popR.Rproj | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 popR.Rproj diff --git a/popR.Rproj b/popR.Rproj deleted file mode 100644 index eaa6b81..0000000 --- a/popR.Rproj +++ /dev/null @@ -1,18 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: Default -SaveWorkspace: Default -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd,collate,namespace From b18c3d268ecbeb79593e0ec548ab3232af4eee74 Mon Sep 17 00:00:00 2001 From: "josue.chinchilla" Date: Mon, 8 Jun 2026 06:57:44 -0400 Subject: [PATCH 3/3] Changed name to BIGpopA --- .DS_Store | Bin 10244 -> 10244 bytes .gitignore | 2 +- BIGpopA.Rproj | 18 +++++++++++++++++ DESCRIPTION | 8 ++++---- NEWS.md | 8 ++++---- R/check_ped.R | 2 +- README.md | 28 +++++++++++++------------- inst/CITATION | 6 +++--- man/check_ped.Rd | 2 +- tests/testthat.R | 4 ++-- tests/testthat/test-breedtools_poly.R | 6 +++--- tests/testthat/test-check_ped.R | 2 +- 12 files changed, 52 insertions(+), 34 deletions(-) create mode 100644 BIGpopA.Rproj diff --git a/.DS_Store b/.DS_Store index ece4fd8875f3ecd36ce90baac191d65860438373..271d66eeceebfc647f37f0443c9326ba21320233 100644 GIT binary patch delta 25 fcmZn(XbIS0B*@MH1dI$pn;j)wm^asov 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 @@ -19,8 +19,8 @@ Description: Tools for pedigree quality control and genomic breed/line estimation methods, see Funkhouser et al. (2017) . 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) diff --git a/NEWS.md b/NEWS.md index 81be29d..b8f97a3 100644 --- a/NEWS.md +++ b/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 \ No newline at end of file + using quadratic programming diff --git a/R/check_ped.R b/R/check_ped.R index 6e686b8..d433334 100644 --- a/R/check_ped.R +++ b/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 diff --git a/README.md b/README.md index 8935927..9427159 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,34 @@ -[![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) - +[![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) + -# 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. diff --git a/inst/CITATION b/inst/CITATION index 2fa128a..9f77a26 100644 --- a/inst/CITATION +++ b/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" -) \ No newline at end of file + url = "https://github.com/Breeding-Insight/BIBpopA" +) diff --git a/man/check_ped.Rd b/man/check_ped.Rd index ec320d1..c0dbaef 100644 --- a/man/check_ped.Rd +++ b/man/check_ped.Rd @@ -46,7 +46,7 @@ roles are corrected when their respective arguments are TRUE. Cycles are reported only and must be resolved manually. } \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 diff --git a/tests/testthat.R b/tests/testthat.R index 6c7e66a..0245373 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ library(testthat) -library(popR) +library(BIBpopA) -test_check("popR") +test_check("BIBpopA") diff --git a/tests/testthat/test-breedtools_poly.R b/tests/testthat/test-breedtools_poly.R index 503b4ec..06ca0a6 100644 --- a/tests/testthat/test-breedtools_poly.R +++ b/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") diff --git a/tests/testthat/test-check_ped.R b/tests/testthat/test-check_ped.R index 5be6469..b84fb20 100644 --- a/tests/testthat/test-check_ped.R +++ b/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)