Enhance com2links to subset matrices and improve error handling

[smasongarrison]

This pull request introduces several improvements and bug fixes to the BGmisc package, focusing on more robust handling of pedigree matrices, smarter string ID management, and enhanced control over family ID assignment. The most important changes are summarized below:

Robust handling of mismatched pedigree matrix dimensions

• The com2links function now automatically subsets all input matrices to match the smallest matrix by number of columns, ensuring consistent IDs and preventing errors when matrices of different sizes are provided. This includes informative messages and error handling for missing or malformed IDs.
• New tests were added to verify that com2links correctly handles mismatched matrix dimensions, including cases with two or three matrices and different combinations of which matrix is smallest.

Improvements to ID handling and family assignment

• The ID extraction logic in family assignment now detects and warns if coercing IDs to numeric results in NA values, and falls back to using string IDs when necessary, preventing silent data loss.
• The ped2fam and underlying .ped2id functions now have an overwrite argument (default TRUE) that controls whether an existing family ID column in the pedigree is replaced, with appropriate user warnings. [1] [2] [3] [4] [5]

Documentation and metadata updates

• The DESCRIPTION file and NEWS.md were updated to reflect the new version and summarize the main changes. [1] [2]
• Documentation for ped2fam was updated to describe the new overwrite parameter. [1] [2]

Minor tutorial and vignette corrections

• Minor content and formatting corrections were made to the tutorial manuscript vignette. [1] [2]

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[Copilot]

Pull request overview

This PR improves robustness around pedigree-derived relationship matrices and family ID assignment, primarily by subsetting mismatched matrices in com2links and adding an overwrite control to ped2fam.

Changes:

• Update com2links to subset all provided matrices to the smallest (by column count) to prevent dimension mismatches.
• Enhance ped2fam/.ped2id with an overwrite argument and additional warnings around ID coercion.
• Add tests for com2links mismatched-dimension scenarios; update docs/metadata/vignette and NEWS.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
R/makeLinks.R	Implements “subset to smallest matrix” behavior for com2links.
tests/testthat/test-makeLinks.R	Adds regression tests for mismatched matrix dimensions in com2links.
R/segmentPedigree.R	Adds overwrite argument to ped2fam and warning logic for ID coercion.
man/ped2fam.Rd	Documents new overwrite parameter for ped2fam.
NEWS.md	Notes changes for string ID handling and matrix size handling.
DESCRIPTION	Bumps package version.
vignettes/articles/tutorialmanuscript.Xmd	Minor formatting/content edits in tutorial vignette.

[smasongarrison]

@copilot can you make a unit test for the new function (alignPhenToMatrix)?

[Copilot]

@copilot can you make a unit test for the new function (alignPhenToMatrix)?

Added 7 unit tests for alignPhenToMatrix in commit ac2c077, appended to tests/testthat/test-buildmxPedigrees.R. The tests cover:

• Returns a 1-row matrix with correct values
• Subsets to only the requested IDs
• Preserves the order of keep_ids in output columns
• Column names are valid R names (via make.names())
• Returns NA for IDs not present in the pedigree
• Respects a custom personID column name
• Coerces phenotype values to double

No skip_if_not_installed("OpenMx") guard is needed since alignPhenToMatrix is a pure data-preparation utility with no OpenMx dependency.