visPedigree - Tidying, Analysis, and Fast Visualization of Animal and Plant
Pedigrees
Provides tools for the analysis and visualization of
animal and plant pedigrees. Analytical methods include
equivalent complete generations, generation intervals,
effective population size (via inbreeding, coancestry, and
demographic approaches), founder and ancestor contributions,
partial inbreeding, genetic diversity indices, and additive
(A), dominance (D), and epistatic (AA) relationship matrices.
Core algorithms — ancestry tracing, topological sorting,
inbreeding coefficients, and matrix construction — are
implemented in C++ ('Rcpp', 'RcppArmadillo') and 'data.table',
scaling to pedigrees with over one million individuals.
Matrix-free pedigree traversals apply additive relationship
matrices or their inverses to vectors and matrices without
materializing dense square matrices. Pedigree graphs are
rendered via 'igraph' with support for compact full-sib family
display; relationship matrices can be visualized as heatmaps.
Supports complex mating systems, including selfing and
pedigrees in which the same individual can appear as both sire
and dam.
