Package: MADPop 1.1.6

MADPop: MHC Allele-Based Differencing Between Populations

Tools for the analysis of population differences using the Major Histocompatibility Complex (MHC) genotypes of samples having a variable number of alleles (1-4) recorded for each individual. A hierarchical Dirichlet-Multinomial model on the genotype counts is used to pool small samples from multiple populations for pairwise tests of equality. Bayesian inference is implemented via the 'rstan' package. Bootstrapped and posterior p-values are provided for chi-squared and likelihood ratio tests of equal genotype probabilities.

Authors:Martin Lysy [cre, aut], Peter W.J. Kim [aut], Terin Robinson [ctb]

MADPop_1.1.6.tar.gz
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MADPop.pdf |MADPop.html✨
MADPop/json (API)
NEWS

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

Bug tracker:https://github.com/mlysy/madpop/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • fish215 - Genotypes of lake trout from Ontario, Canada

On CRAN:

Conda:

cpp

3.70 score 1 stars 8 scripts 319 downloads 5 exports 47 dependencies

Last updated from:d40d77b12f. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK285
linux-devel-x86_64OK276
source / vignettesOK326
linux-release-arm64OK262
linux-release-x86_64OK282
macos-release-arm64OK230
macos-release-x86_64OK427
macos-oldrel-arm64OK145
macos-oldrel-x86_64OK389
windows-develOK297
windows-releaseOK296
windows-oldrelOK284
wasm-releaseFAIL163

Exports:chi2.stathUM.postLRT.statUM.eqtestUM.suff

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Bayesian Testing of Equal Genotype Proportions between Multiple Populations

Martin Lysy, Wookjung P. Kim, Terin Robinson

Rendered fromMADPop-quicktut.Rmdusingknitr::rmarkdownon Apr 14 2026.

Last update: 2022-08-19
Started: 2016-12-18