Package: ibdsegments 1.0.1

ibdsegments: Identity by Descent Probability in Pedigrees

Identity by Descent (IBD) distributions in pedigrees. A Hidden Markov Model is used to compute identity coefficients, simulate IBD segments and to derive the distribution of total IBD sharing and segment count across chromosomes. The methods are applied in Kruijver (2025) <doi:10.3390/genes16050492>. The probability that the total IBD sharing is zero can be computed using the method of Donnelly (1983) <doi:10.1016/0040-5809(83)90004-7>.

Authors:Maarten Kruijver [aut, cre]

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ibdsegments_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ibdsegments/json (API)

# Install 'ibdsegments' in R:

install.packages('ibdsegments', repos = c('https://mkruijver.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mkruijver/ibdsegments/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.40 score 5 stars 237 downloads 16 exports 14 dependencies

Last updated from:04e5b58dbe. Checks:11 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	190
linux-devel-x86_64	ERROR	156
source / vignettes	OK	175
linux-release-arm64	ERROR	158
linux-release-x86_64	ERROR	157
macos-release-arm64	ERROR	124
macos-release-x86_64	ERROR	208
macos-oldrel-arm64	ERROR	130
macos-oldrel-x86_64	ERROR	417
windows-devel	ERROR	121
windows-release	ERROR	133
windows-oldrel	ERROR	140
wasm-release	OK	142

Exports:convolve_total_ibd_dists d d_cibd d_ibd E inheritance_pattern inheritance_space multi_ibd_patterns pr_0_total_ibd pr_all_genes_survive r_cibd sd segment_count_dist total_ibd_dist total_ibd_dist_moments var

Dependencies:evaluate expm highr kinship2 knitr lattice lpSolve Matrix pedmut pedtools quadprog Rcpp xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convolve IBD distributions to obtain the distribution of the sum	convolve_total_ibd_dists
Probability function for IBD Distribution Objects	d
Probability density of continuously observed IBD segment lengths for pedigree members	d_cibd
Compute probability of IBD for pedigree members	d_ibd
Expectation for IBD Distribution Objects	E
Inheritance pattern for inheritance vectors	inheritance_pattern
Inheritance space for pedigree	inheritance_space
Compute probabilities of minimal multi-id IBD patterns	multi_ibd_patterns
Probability of no IBD across one or more chromosomes	pr_0_total_ibd
Probability of passing down all autosomal genes to offspring	pr_all_genes_survive
Random generation for IBD on a continuous genome	r_cibd
Standard Deviation for IBD Distribution Objects	sd
Compute probability distribution of IBD segment count	segment_count_dist
Compute probability distribution of total IBD	total_ibd_dist
Compute moments of probability distribution of total IBD	total_ibd_dist_moments
Variance for IBD Distribution Objects	var