Check_ped update

[josuechinchilla]

This pull request refactors and enhances the check_ped pedigree quality-checking function, improves its documentation, and updates project metadata. The changes make the function more robust, user-friendly, and better documented, with clearer outputs and error reporting.

Pedigree checking improvements:

• Refactored the check_ped function to detect and optionally correct five classes of pedigree errors: exact duplicate rows, repeated IDs with conflicting parents, IDs appearing as both sire and dam, missing parents (added as founders), and pedigree cycles (dependencies). The function now outputs a comprehensive report and optionally saves corrected dataframes interactively. [1] [2] [3]

Documentation updates:

• Revised the Roxygen and Rd documentation for check_ped to clearly describe its behavior, inputs, outputs, and usage examples, reflecting the new error types and interactive saving feature.

Project metadata:

• Updated the RoxygenNote version in DESCRIPTION to 7.3.3, reflecting regenerated documentation.
• Added a ProjectId field to BIGr.Rproj for project tracking.