visPedigree: a comprehensive R package for tidying, analyzing, and visualizing breeding pedigrees.

MOTIVATION: Pedigrees support relatedness control, mate allocation, inbreeding monitoring, and diversity assessment, but large breeding populations are often curated, analyzed, and visualized using separate tools and data structures. This fragmentation complicates routine analysis and reporting, particularly in high-fecundity systems with extensive full-sib structure, irregular pedigree depth, and repeated cohort-based evaluation.

RESULTS

We present visPedigree, a software package for large breeding pedigrees built around a new tidyped object model. It integrates pedigree standardization, structural validation, candidate-centered tracing, pedigree statistics, inbreeding and partial inbreeding analysis, founder- and ancestor-based diversity summaries, effective population size estimation, relationship matrices, and scalable visualization. The package also provides Shannon/Hill-based diversity measures, the pedhalflife() temporal diagnostic, and compact visualization of full-sib-dominated subsets. In a giant freshwater prawn pedigree, it produced an interpretable ancestry overview and quantified recent diversity erosion. Simulated benchmarks showed that representative workflows completed within seconds for pedigrees containing up to one million individuals on a standard laptop.

AVAILABILITY AND IMPLEMENTATION: visPedigree is implemented in the R language and is freely available at https://cran.r-project.org/package=visPedigree, with documentation at https://luansheng.github.io/visPedigree/.