Check ped update by josuechinchilla · Pull Request #48 · Breeding-Insight/BIGr

josuechinchilla · 2026-02-26T20:20:15Z

Added options to output graph or list. This makes ready for BIG integration

Copilot

Pull request overview

Updates BIGr’s pedigree QC and imputation concordance utilities, primarily by expanding output/reporting options (including optional plotting) and refreshing the check_ped documentation to match new behaviors.

Changes:

Expanded check_ped reporting (exact duplicates, conflicting IDs) and added interactive/automatic saving behavior.
Added plot and print_result options to imputation_concordance and updated its roxygen docs.
Misc repo metadata changes (RoxygenNote, .Rproj) and an unintended .DS_Store addition.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
`R/check_ped.R`	Adds new checks and introduces interactive prompt + GlobalEnv assignment behavior.
`man/check_ped.Rd`	Updates generated Rd docs for `check_ped` to reflect new outputs.
`R/imputation_concordance.R`	Adds optional plotting/printing and updates roxygen documentation.
`DESCRIPTION`	Bumps `RoxygenNote`.
`BIGr.Rproj`	Adds a `ProjectId` entry.
`.DS_Store`	Adds a macOS Finder artifact (should not be committed).

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Copilot · 2026-02-26T20:26:35Z

BIGr.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 0eeaab63-2615-4da7-b10a-927160fc78a3


Adding a ProjectId to the .Rproj file is usually machine/user-specific and tends to create noisy diffs. Unless there’s a clear need for it, consider omitting this line from version control.

Suggested change

ProjectId: 0eeaab63-2615-4da7-b10a-927160fc78a3

Copilot · 2026-02-26T20:26:35Z

R/check_ped.R

+      assign(corrected_name, data, envir = .GlobalEnv)
+      assign("input_ped_report", input_ped_report, envir = .GlobalEnv)
+      cat(paste0("Saved corrected pedigree as `", corrected_name, "` and report as `input_ped_report`.\n"))


In the interactive save path, the report is always assigned as input_ped_report rather than using the computed report_name. This makes the saved object naming inconsistent with the non-verbose path (which uses report_name). Please make the naming consistent and document it.

Copilot · 2026-02-26T20:26:35Z

R/imputation_concordance.R

+#' @examples
+#' result <- imputation_concordance(
+#'   reference_genos = ref,
+#'   imputed_genos = test,
+#'   snps_2_exclude = snps,


The @examples block uses ref, test, and snps objects that are not defined anywhere in the example. This will fail during package checks when examples are executed. Please either define them in the example (e.g., via system.file() + read.table()) or wrap the block in \dontrun{}.

Copilot · 2026-02-26T20:26:36Z

man/check_ped.Rd

-ped_errors <- check_ped(ped.file = ped_file,
-                        seed = 101919)
+ped_file <- system.file("check_ped_test.txt", package = "BIGr")
+ped_errors <- check_ped(ped.file = ped_file, seed = 101919)


The example runs check_ped() with default verbose = TRUE, but the function now prompts via readline(). Package examples should not require interactive input; please adjust the example to use verbose = FALSE (or ensure prompting is gated behind interactive()).

Suggested change

ped_errors <- check_ped(ped.file = ped_file, seed = 101919)

ped_errors <- check_ped(ped.file = ped_file, seed = 101919, verbose = FALSE)

Copilot · 2026-02-26T20:26:36Z

R/imputation_concordance.R

 #'
-#' @export
+#' @import dplyr
+#' @import ggplot2


The function calls ggplot(), geom_bar(), etc. but the package DESCRIPTION does not list ggplot2 in Imports, and NAMESPACE currently has no ggplot2 imports. As-is, plot = TRUE will error unless ggplot2 happens to be attached by the user. Please add ggplot2 to DESCRIPTION Imports and regenerate NAMESPACE (or fully qualify calls with ggplot2::...).

Suggested change

#' @import ggplot2

Copilot · 2026-02-26T20:26:37Z

R/check_ped.R

    if (sire != "0" && sire != id && !sire %in% data$id) {
      missing_parents <- rbind(missing_parents, data.frame(id = sire, sire = "0", dam = "0", stringsAsFactors = FALSE))
    }
    if (dam != "0" && dam != id && !dam %in% data$id) {
      missing_parents <- rbind(missing_parents, data.frame(id = dam, sire = "0", dam = "0", stringsAsFactors = FALSE))


Building missing_parents via repeated rbind() inside the row loop is quadratic and can be very slow for large pedigrees. Prefer collecting rows in a list and binding once (or use vectorized set operations) to keep runtime reasonable at scale.

Copilot · 2026-02-26T20:26:37Z

R/check_ped.R

+  #### file names ####
+  file_base <- tools::file_path_sans_ext(basename(ped.file))
+  corrected_name <- paste0(file_base, "_corrected")
+  report_name <- paste0(file_base, "_report")


report_name is computed but never used in the verbose = TRUE branch. Either use it for the report object name in both branches or remove it to avoid confusion.

Copilot · 2026-02-26T20:26:37Z

R/check_ped.R

-#' ped_errors <- check_ped(ped.file = ped_file,
-#'                         seed = 101919)
+#' ped_file <- system.file("check_ped_test.txt", package = "BIGr")
+#' ped_errors <- check_ped(ped.file = ped_file, seed = 101919)


The documented example calls check_ped(...) with default verbose = TRUE, but the function now prompts via readline(). Running examples during R CMD check (non-interactive) can error or hang waiting for input. Please update the example to set verbose = FALSE and/or wrap interactive behavior in \dontrun{}/\donttest{}.

Suggested change

#' ped_errors <- check_ped(ped.file = ped_file, seed = 101919)

#' ped_errors <- check_ped(ped.file = ped_file, seed = 101919, verbose = FALSE)

Copilot · 2026-02-26T20:26:37Z

R/check_ped.R

+  repeated_ids_report <- conflicting_ids
+
+  #### check 3: missing parents ####
  for (i in 1:nrow(data)) {


The loop uses for (i in 1:nrow(data)), which behaves incorrectly when nrow(data) == 0 (it iterates over c(1, 0)). Please use seq_len(nrow(data)) to avoid edge-case errors with empty input pedigrees.

Suggested change

for (i in 1:nrow(data)) {

for (i in seq_len(nrow(data))) {

Copilot · 2026-02-26T20:26:37Z

R/check_ped.R

-  missing_parents <- data.frame(id = character(), sire = character(), dam = character(), stringsAsFactors = FALSE)
+    )
+
+  original_data <- data


original_data <- data is never used and can be removed to avoid confusion about whether the function intends to compare/restore against the original input.

Suggested change

original_data <- data

josuechinchilla and others added 3 commits November 4, 2025 16:06

updated check_ped to save corrected dataframe and report

1b761b9

reorganized report and fixed language

743043a

added option to print plot or list to imputation_concordance

82279af

josuechinchilla requested review from Cristianetaniguti and Copilot February 26, 2026 20:20

Copilot started reviewing on behalf of josuechinchilla February 26, 2026 20:20 View session

josuechinchilla requested review from alex-sandercock and removed request for Cristianetaniguti February 26, 2026 20:20

Copilot AI reviewed Feb 26, 2026

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Check ped update#48

Check ped update#48
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		@@ -1,4 +1,5 @@
		Version: 1.0
		ProjectId: 0eeaab63-2615-4da7-b10a-927160fc78a3

	ped_errors <- check_ped(ped.file = ped_file, seed = 101919)
	ped_errors <- check_ped(ped.file = ped_file, seed = 101919, verbose = FALSE)

	#' ped_errors <- check_ped(ped.file = ped_file, seed = 101919)
	#' ped_errors <- check_ped(ped.file = ped_file, seed = 101919, verbose = FALSE)

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