Fixing the direction of the nodes and checking them

[smasongarrison]

This pull request introduces several improvements and bug fixes related to pedigree data handling, especially around helper functions, ID validation/repair, and graph construction. The most significant changes include new utility functions for duplicate handling and list updates, a fix to ensure parent-child direction in pedigree graphs, and enhancements to column name restoration and validation logic.

New helper functions and utilities:

• Added dropIdenticalDuplicateIDs to efficiently remove identical duplicate rows by ID in pedigree data frames, along with a log of changes. [1] [2]
• Introduced addIfAny, a utility to conditionally add elements to a list, improving code clarity and reducing redundancy. [1] [2]

Pedigree graph construction and validation fixes:

• Fixed the direction of edges in ped2graph so parents point to children, aligning with igraph conventions and biological relationships. This is verified by new tests. [1] [2] [3] [4]
• Updated tests to ensure that all graph edges are correctly oriented from parent to child, preventing regression.

Pedigree data validation and repair enhancements:

• Refactored duplicate ID repair in checkIDs to use the new dropIdenticalDuplicateIDs helper, simplifying logic and improving maintainability.
• Improved parent ID validation in checkParentIDs by using addIfAny and clarifying the logic for detecting single parents.
• Enhanced restoration of original column names after processing with the new restorePedColnames function, ensuring user-supplied names are preserved. [1] [2] [3]

Documentation and housekeeping:

• Added and updated documentation for new helper functions and moved/renamed several files for better organization. [1] [2] [3] [4] [5]
• Updated the NEWS.md file to reflect these changes and improvements.

Exports and minor code cleanups:

• Cleaned up exports in the NAMESPACE, removing now-internal functions from the public API.
• Minor improvements to logical checks and verbosity handling in validation functions.

These changes collectively improve the reliability, maintainability, and clarity of pedigree data processing and graphing in the package.

[codecov]

Codecov Report

❌ Patch coverage is 84.84848% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.32%. Comparing base (fd3b709) to head (a8ef38d).
⚠️ Report is 7 commits behind head on main.

Files with missing lines	Patch %	Lines
R/helpNames.R	77.77%	6 Missing ⚠️
R/helpChecks.R	76.47%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #112      +/-   ##
==========================================
- Coverage   84.38%   84.32%   -0.07%     
==========================================
  Files          27       28       +1     
  Lines        4240     4281      +41     
==========================================
+ Hits         3578     3610      +32     
- Misses        662      671       +9     

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