Package: pedprobr 0.9.5

Magnus Dehli Vigeland

pedprobr: Probability Computations on Pedigrees

An implementation of the Elston-Stewart algorithm for calculating pedigree likelihoods given genetic marker data (Elston and Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is extended to allow inbred founders. 'pedprobr' is part of the 'pedsuite', a collection of packages for pedigree analysis in R. In particular, 'pedprobr' depends on 'pedtools' for pedigree manipulations and 'pedmut' for mutation modelling. For more information, see 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).

Authors:Magnus Dehli Vigeland [aut, cre]

pedprobr_0.9.5.tar.gz
pedprobr_0.9.5.zip(r-4.5)pedprobr_0.9.5.zip(r-4.4)pedprobr_0.9.5.zip(r-4.3)
pedprobr_0.9.5.tgz(r-4.5-any)pedprobr_0.9.5.tgz(r-4.4-any)pedprobr_0.9.5.tgz(r-4.3-any)
pedprobr_0.9.5.tar.gz(r-4.5-noble)pedprobr_0.9.5.tar.gz(r-4.4-noble)
pedprobr_0.9.5.tgz(r-4.4-emscripten)pedprobr_0.9.5.tgz(r-4.3-emscripten)
pedprobr.pdf |pedprobr.html
pedprobr/json (API)
NEWS

# Install 'pedprobr' in R:
install.packages('pedprobr', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/magnusdv/pedprobr/issues

On CRAN:

Conda:

5.90 score 4 stars 11 packages 6 scripts 477 downloads 3 mentions 14 exports 11 dependencies

Last updated 14 days agofrom:db9e5ab225. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-winOKMar 19 2025
R-4.5-macOKMar 19 2025
R-4.5-linuxOKMar 19 2025
R-4.4-winOKMar 19 2025
R-4.4-macOKMar 19 2025
R-4.4-linuxOKMar 19 2025
R-4.3-winOKMar 19 2025
R-4.3-macOKMar 19 2025

Exports:allGenotypescheckMerlingenoCombinationshaldaneHWprobkosambilikelihoodlikelihood2likelihoodMerlinlumpAllelesmerlinoneMarkerDistributionsetMutationModeltwoMarkerDistribution

Dependencies:evaluatehighrkinship2knitrlatticeMatrixpedmutpedtoolsquadprogxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Genotype matrixallGenotypes
Genotype combinationsgenoCombinations
Genetic map functionshaldane kosambi
Hardy-Weinberg probabilitiesHWprob
Pedigree likelihoodlikelihood likelihood.list likelihood.ped likelihood2 likelihood2.list likelihood2.ped
Allele lumpinglumpAlleles
Pedigree likelihoods computed by MERLINcheckMerlin likelihoodMerlin merlin
Genotype distribution for a single markeroneMarkerDistribution
Set a mutation modelsetMutationModel
Genotype distribution for two linked markerstwoMarkerDistribution