Smarterwithdups

[smasongarrison]

This PR, titled "Smarterwithdups", implements a major overhaul for handling duplicate members in pedigree layouts. Key changes include adjusting visual parameters (e.g. point and label sizes), refactoring duplicate appearance resolution logic with new helper functions, and updating documentation and tests to reflect the revised handling.

[Copilot]

Pull Request Overview

This PR, titled "Smarterwithdups", implements a major overhaul for handling duplicate members in pedigree layouts. Key changes include adjusting visual parameters (e.g. point and label sizes), refactoring duplicate appearance resolution logic with new helper functions, and updating documentation and tests to reflect the revised handling.

Reviewed Changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
vignettes/plots_morecomplexity.xmd	Reduced point size and added a label text size option to fine‑tune plot scales.
vignettes/plots.Rmd	Introduced additional complex plotting examples and removed extra blank lines.
tests/testthat/test-calcCoordinates.R	Updated test to check against the new nested connection structure.
man/ggPedigree.Rd	Adjusted file reference in documentation to match the actual filename.
R/processExtras.R	Updated duplicate handling logic with unique numeric IDs and related operations.
R/calcConnections.R	Standardized naming conventions for identifiers such as parent hashes.
DESCRIPTION	Added required dependencies for string and tibble support.
.Rbuildignore	Updated ignore settings to include files ending with .X

Comments suppressed due to low confidence (3)

tests/testthat/test-calcCoordinates.R:64

• Ensure that the updated test properly validates the new structure of 'conns$connections' after the duplicate handling changes. Confirm that the expected column names match the updated connections output.

expect_true(all(expected_cols %in% names(conns$connections)))

vignettes/plots_morecomplexity.xmd:130

• The new value for 'point_size' is significantly reduced from 3 to .5, and a new 'label_text_size' parameter is introduced. Please verify if these adjustments produce the intended visual outcome for the pedigree plots.

point_size = .5,

man/ggPedigree.Rd:2

• The documentation now references 'R/ggpedigree.R'; please confirm this matches the actual file naming to avoid potential confusion.

% Please edit documentation in R/ggpedigree.R