Package: AdmixPoly 1.0.0

AdmixPoly: Global and Local Admixture Inference in Polyploids

Provides functions to perform global (genome-wide) and local admixture inference from bi- and multi-allelic marker dosages (discrete or continuous) in polyploid species.

Authors:Simon Rio [aut, cre], Tristan Mary-Huard [aut], Franck Gauthier [aut]

AdmixPoly_1.0.0.tar.gz
AdmixPoly_1.0.0.zip(r-4.7)AdmixPoly_1.0.0.zip(r-4.6)AdmixPoly_1.0.0.zip(r-4.5)
AdmixPoly_1.0.0.tgz(r-4.6-x86_64)AdmixPoly_1.0.0.tgz(r-4.6-arm64)AdmixPoly_1.0.0.tgz(r-4.5-x86_64)AdmixPoly_1.0.0.tgz(r-4.5-arm64)
AdmixPoly_1.0.0.tar.gz(r-4.7-arm64)AdmixPoly_1.0.0.tar.gz(r-4.7-x86_64)AdmixPoly_1.0.0.tar.gz(r-4.6-arm64)AdmixPoly_1.0.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
AdmixPoly/json (API)

# Install 'AdmixPoly' in R:

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblas cpp openmp

2.70 score 7 exports 34 dependencies

Last updated from:bf647eb5dd. Checks:12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	203
linux-devel-x86_64	OK	240
source / vignettes	OK	299
linux-release-arm64	OK	219
linux-release-x86_64	OK	239
macos-release-arm64	OK	223
macos-release-x86_64	OK	274
macos-oldrel-arm64	OK	202
macos-oldrel-x86_64	OK	336
windows-devel	OK	203
windows-release	OK	174
windows-oldrel	OK	210
wasm-release	FAIL	130

Exports:AdmixGlobal AdmixLocal GlobalPlot LocalPlot ReadHPA ReadVCF SimulatePop

Dependencies:cli cpp11 data.table dplyr farver generics ggplot2 glue gtable isoband labeling lattice lifecycle magrittr Matrix pillar pkgconfig purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

AdmixPoly-vignette

Simon Rio

Rendered fromAdmixPoly-vignette.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-06-08
Started: 2026-06-08

Citation

Readme and manuals

Help Manual

Help page	Topics
AdmixPoly: Global and Local Admixture Inference in Polyploids	AdmixPoly-package AdmixPoly
Expectation-Maximization algorithm for global (genome-wide) admixture inference	AdmixGlobal
Forward-Backward algorithm for local admixture inference	AdmixLocal
Calculate the log-likelihood	ComputeLogLik
Plot global admixture proportions	GlobalPlot
Plot local ancestry dosages	LocalPlot
Read Haplotype Presence-Absence (HPA) file	ReadHPA
Read VCF file	ReadVCF
Simulate an admixed polyploid population characterized for multi-allelic markers	SimulatePop
Update Prop and Freq parameters for EM step	UpdateParam