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.
| Version: |
1.9.0 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
data.table (≥ 1.14.0), igraph (≥ 1.3.0), Matrix, methods, Rcpp, lattice |
| LinkingTo: |
Rcpp, RcppArmadillo |
| Suggests: |
nadiv (≥ 2.18.0), testthat (≥ 3.0.0), knitr, rmarkdown, devtools, roxygen2, pkgdown |
| Published: |
2026-07-15 |
| DOI: |
10.32614/CRAN.package.visPedigree |
| Author: |
Sheng Luan [aut, cre] |
| Maintainer: |
Sheng Luan <luansheng at gmail.com> |
| BugReports: |
https://github.com/luansheng/visPedigree/issues |
| License: |
GPL-3 |
| URL: |
https://github.com/luansheng/visPedigree,
https://luansheng.github.io/visPedigree/ |
| NeedsCompilation: |
yes |
| Materials: |
README, NEWS |
| CRAN checks: |
visPedigree results |
Documentation:
Downloads:
Reverse dependencies:
Linking:
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