Add customizable sex coding to checkParentIDs #106

smasongarrison · 2025-12-25T23:38:27Z

Introduced code_male and code_female parameters to checkParentIDs, allowing users to specify custom values for male and female sex coding. Updated documentation and NEWS to reflect this change. Improved handling of missing sex values in checkParentSex.

codecov · 2025-12-26T00:11:16Z

Codecov Report

❌ Patch coverage is 74.46809% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.42%. Comparing base (2e38d01) to head (fb30e5b).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
R/checkSex.R	77.50%	9 Missing ⚠️
R/checkParents.R	57.14%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #106      +/-   ##
==========================================
- Coverage   84.45%   84.42%   -0.03%     
==========================================
  Files          25       25              
  Lines        3957     3982      +25     
==========================================
+ Hits         3342     3362      +20     
- Misses        615      620       +5

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Introduced the 'code_unknown' parameter to checkSex, repairSex, and recodeSex functions, allowing explicit handling and recoding of unknown sex values. Updated documentation to reflect the new parameter and its usage. Should help address R-Computing-Lab/ggpedigree#95

Copilot

Pull request overview

This PR adds customizable sex coding parameters to the checkParentIDs function and related sex-handling functions in the BGmisc package. The changes introduce code_male and code_female parameters to checkParentIDs, and code_unknown parameter to multiple sex-related functions (checkSex, repairSex, recodeSex), allowing users to specify custom values for different sex categories rather than relying solely on inferred values from the pedigree data.

Key changes include:

Added code_male and code_female parameters to checkParentIDs to allow explicit specification of sex codes
Introduced code_unknown parameter to checkSex, repairSex, and recodeSex functions for handling unknown sex values
Enhanced recodeSex function logic to handle unknown sex values with multiple code paths
Improved checkParentSex to handle cases where all parents have missing sex values

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 18 comments.

Show a summary per file

File	Description
R/checkParents.R	Added code_male and code_female parameters to checkParentIDs function; updated logic to use provided sex codes instead of only inferred values
R/checkSex.R	Added code_unknown parameter to checkSex, repairSex, and recodeSex functions; restructured recodeSex logic to handle unknown sex values; improved checkParentSex to handle missing values
man/checkParentIDs.Rd	Added documentation for new code_male and code_female parameters
man/checkSex.Rd	Added documentation for new code_unknown parameter; removed trailing whitespace
man/recodeSex.Rd	Added documentation for code_unknown and recode_unknown parameters; removed trailing whitespace
man/repairSex.Rd	Added code_unknown parameter to function signature and documentation; removed trailing whitespace
NEWS.md	Updated version entry to document sex coding enhancements

Copilot · 2026-01-02T19:46:40Z

man/checkParentIDs.Rd

+\item{code_male}{Value representing male sex}
+
+\item{code_female}{Value representing female sex}


The documentation for code_male and code_female parameters is incomplete. They should specify what they represent (e.g., "The code value used to represent male sex in the 'sex' column" and "The code value used to represent female sex in the 'sex' column").

Suggested change

\item{code_male}{Value representing male sex}

\item{code_female}{Value representing female sex}

\item{code_male}{The code value used to represent male sex in the \code{sex} column of \code{ped}.}

\item{code_female}{The code value used to represent female sex in the \code{sex} column of \code{ped}.}

Copilot · 2026-01-02T19:46:40Z

R/checkParents.R

+                           dadID = "dadID",
+                           code_male = NULL,
+                           code_female = NULL
+                           ) {


The indentation is inconsistent with the closing parenthesis. It should align with the function name or be properly indented.

Suggested change

) {

) {

Copilot · 2026-01-02T19:46:40Z

R/checkSex.R

+        code_male = validation_results$most_frequent_sex_dad,
+        code_female = validation_results$most_frequent_sex_mom,
+        code_unknown = code_unknown
+      )


The indentation for closing parenthesis should be consistent with the opening line or properly aligned. This closing parenthesis should align with the opening function call on line 98.

Copilot · 2026-01-02T19:46:41Z

R/checkSex.R

+    ped$sex_recode[!ped$sex %in% c(code_male, code_female) & !is.na(ped$sex)] <- recode_unknown
+  }
+
+


Empty line here serves no purpose and reduces code readability. Consider removing this blank line.

Suggested change

Copilot · 2026-01-02T19:46:41Z

R/checkParents.R

+                           code_male = NULL,
+                           code_female = NULL
+                           ) {


The new code_male and code_female parameters in checkParentIDs lack test coverage. Tests should verify that when these parameters are provided, they are properly used to set validation_results$male_var and validation_results$female_var instead of inferring them from the data.

R/checkSex.R

R/checkParents.R

Copilot · 2026-01-02T19:46:43Z

R/checkParents.R

+
+
+


Empty lines here serve no purpose and reduce code readability. Consider removing these blank lines.

R/checkParents.R

Copilot · 2026-01-02T19:46:44Z

R/checkSex.R

 recodeSex <- function(
-    ped, verbose = FALSE, code_male = NULL, code_na = NULL, code_female = NULL,
-    recode_male = "M", recode_female = "F", recode_na = NA_character_) {
+  ped, verbose = FALSE, code_male = NULL, code_na = NULL, code_female = NULL,
+  code_unknown = NULL,
+  recode_male = "M",
+  recode_female = "F",
+  recode_unknown = "U",
+  recode_na = NA_character_
+) {
+  if (is.null(code_male) && is.null(code_female)) {
+    if (verbose == TRUE) {
+      warning("Both code male and code female are empty. No recoding was done.")
+    }
+    return(ped)
+  }
+  # First, set any code_na values to NA
  if (!is.null(code_na)) {
    ped$sex[ped$sex == code_na] <- NA
  }
-  # Recode as "F" or "M" based on code_male, preserving NAs
-  if (!is.null(code_male) && !is.null(code_female)) {
-    # Initialize sex_recode as NA, preserving the length of the 'sex' column
-    ped$sex_recode <- recode_na
-    ped$sex_recode[ped$sex == code_female] <- recode_female
-    ped$sex_recode[ped$sex == code_male] <- recode_male
-    # Overwriting temp recode variable
-    ped$sex <- ped$sex_recode
-    ped$sex_recode <- NULL
-  } else if (!is.null(code_male) && is.null(code_female)) {
-    # Initialize sex_recode as NA, preserving the length of the 'sex' column
-    ped$sex_recode <- recode_na
-    ped$sex_recode[ped$sex != code_male & !is.na(ped$sex)] <- recode_female
+
+  # Initialize sex_recode as NA, preserving the length of the 'sex' column
+  ped$sex_recode <- recode_na
+
+
+  if (!is.null(code_male)) {
    ped$sex_recode[ped$sex == code_male] <- recode_male
-    # Overwriting temp recode variable
-    ped$sex <- ped$sex_recode
-    ped$sex_recode <- NULL
-  } else if (is.null(code_male) && !is.null(code_female)) {
-    # Initialize sex_recode as NA, preserving the length of the 'sex' column
-    ped$sex_recode <- recode_na
-    ped$sex_recode[ped$sex != code_female & !is.na(ped$sex)] <- recode_male
+  }
+  if (!is.null(code_female)) {
    ped$sex_recode[ped$sex == code_female] <- recode_female
-    # Overwriting temp recode variable
-    ped$sex <- ped$sex_recode
-    ped$sex_recode <- NULL
-  } else {
-    if (verbose == TRUE) {
-      warning("Both code male and code female are empty. No recoding was done.")
+  }
+
+  # handle unknown codes
+  if (!is.null(code_unknown) && !is.na(code_unknown)) {
+    ped$sex_recode[ped$sex == code_unknown] <- recode_unknown
+  } else if (!is.null(code_unknown) && is.na(code_unknown)) {
+    ped$sex_recode[is.na(ped$sex)] <- recode_unknown
+  } else if (!is.null(code_male) && !is.null(code_female)) {
+    ped$sex_recode[!ped$sex %in% c(code_male, code_female) & !is.na(ped$sex)] <- recode_unknown
+  }
+
+
+  # Handle cases where only one of code
+  # just male
+  if (!is.null(code_male) && is.null(code_female)) {
+    if (!is.null(code_unknown)) {
+      ped$sex_recode[ped$sex != code_male & !is.na(ped$sex) & ped$sex != code_unknown] <- recode_female
+    } else if (is.null(code_unknown)) {
+      ped$sex_recode[ped$sex != code_male & !is.na(ped$sex)] <- recode_female
    }
  }
+  # just female
+  if (is.null(code_male) && !is.null(code_female)) {
+    if (!is.null(code_unknown)) {
+      ped$sex_recode[ped$sex != code_female & !is.na(ped$sex) & ped$sex != code_unknown] <- recode_male
+    } else if (is.null(code_unknown)) {
+      ped$sex_recode[ped$sex != code_female & !is.na(ped$sex)] <- recode_male
+    }
+  }


The new code_unknown parameter and recode_unknown parameter lack test coverage. Tests should verify the behavior when code_unknown is provided, including the edge cases where code_unknown is NA (lines 198-199) and when it needs to infer unknown values from the data (lines 200-201).

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-01-02T20:32:55Z

@smasongarrison I've opened a new pull request, #107, to work on those changes. Once the pull request is ready, I'll request review from you.

Update R/checkParents.R Update R/checkParents.R Co-Authored-By: Copilot <175728472+Copilot@users.noreply.github.com>

…ecodeSex (#107) * Update R/checkParents.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update R/checkParents.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Initial plan * Add comprehensive test coverage for code_unknown and recode_unknown parameters Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> * Address code review feedback: improve documentation and test comments Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> * Remove brittle line number references from test comments Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com> --------- Co-authored-by: Mason Garrison <garrissm@wfu.edu> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: smasongarrison <6001608+smasongarrison@users.noreply.github.com>

smasongarrison force-pushed the dev_main branch from 7cc9405 to d212334 Compare December 26, 2025 00:09

smasongarrison added 2 commits January 2, 2026 12:53

Merge branch 'main' into dev_main

83c5857

smasongarrison force-pushed the dev_main branch from c248db1 to 4060a62 Compare January 2, 2026 18:36

smasongarrison added 2 commits January 2, 2026 14:29

Update checkSex.R

63182ab

Update NEWS.md

f0ae841

smasongarrison requested a review from Copilot January 2, 2026 19:42

Copilot started reviewing on behalf of smasongarrison January 2, 2026 19:42 View session

Copilot AI reviewed Jan 2, 2026

View reviewed changes

Copilot AI mentioned this pull request Jan 2, 2026

Add test coverage for code_unknown and recode_unknown parameters in recodeSex #107

Merged

smasongarrison force-pushed the dev_main branch from adacf1d to 79ab419 Compare January 2, 2026 20:33

Update R/checkSex.R

e37cd10

Update R/checkParents.R Update R/checkParents.R Co-Authored-By: Copilot <175728472+Copilot@users.noreply.github.com>

smasongarrison force-pushed the dev_main branch from 79ab419 to e37cd10 Compare January 2, 2026 20:34

Copilot AI and others added 2 commits January 2, 2026 15:43

docs

fb30e5b

smasongarrison merged commit 90b1bbe into main Jan 2, 2026
14 checks passed

		\item{code_male}{Value representing male sex}

		\item{code_female}{Value representing female sex}

		ped$sex_recode[!ped$sex %in% c(code_male, code_female) & !is.na(ped$sex)] <- recode_unknown
		}

Add customizable sex coding to checkParentIDs #106

Add customizable sex coding to checkParentIDs #106

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codecov bot commented Dec 26, 2025 •

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