visPedigree

1.9.0

Tidying, Analysis, and Fast Visualization of Animal and Plant Pedigrees

1packages depend

2.8Kdownloads / year

83.8%test coverage

13/13checks pass

Overview

About

Maintained by Sheng LuanFirst published 2026-01-214 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("visPedigree", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("luansheng/visPedigree")

Development version from luansheng/visPedigree. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-vispedigree

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-visPedigree

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-visPedigree

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 8.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.50

83.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 363 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 61%
Documented parameters: 100%
Return-value docs: 100%
References docs: 9%

Downloads

2.8K

CRAN downloads in the past year

Rank #6,729 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

36730 days

1.5K90 days

2.8K1 year

Compare downloads with other packages →

Also on237 r2u33 autocran

Repository

GitHub ↗ luansheng/vispedigree

20Stars

10Forks

0Open issues

0Open PRs

0Releases

428Commits

2Contributors

License GPL-3.0 · 428 commits · Last activity 2026-07-14 · +5.3% stars, 30d

Stars over time

2025-03-08 · 162026-07-07 · 20

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/luansheng/vispedigree on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

renvMakefile

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practices

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (6)

data.table igraphMatrixmethodsRcpplattice

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (7)

nadiv testthat knitr rmarkdown devtools roxygen2 pkgdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

MoBPS

Code & Tests

Code Composition

R 13,782 (66%)Rd 3,019 (15%)Vignettes 2,501 (12%)C++ 1,450 (7%)

Code characteristics

Object systems

S322

Cyclomatic complexity: 5.0 median / 86 max
Test cases: 251 / 0.50 per code line

Test coverage

Line coverage

84%

Expression

83.1%

Tests / Examples

83.8% / 44% ex

Functions

161 27 exported

Complexity

8.9 avg / 86 max

Call network

161 nodes / 181 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

161 functions

Function	Cyclo	Coverage
as.vector.pedmat	1	0%
plot.tidyped	1	0%
print.pedcontrib	7	0%
print.pedstats	3	0%
print.summary.tidyped	31	0%
summary.pedmat	1	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
half_founder_ped	data.frame	600 × 4	–
small_ped	data.frame	19 × 3	–

People & History

People (1)

Maintainer (1)

Sheng Luan

Author, Maintainer

Authors (1)

Sheng Luan

Author, Maintainer

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

1.9.0Latest
2026-07-15 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.8.1
2026-03-30 · diff ↗
1.0.1
2026-02-23 · diff ↗
0.7.1
2026-01-21
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-21
Total releases: 4 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 500 KB / 8 files
Download size: 4.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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