ipADMIXTURE: Iterative Pruning Population Admixture Inference Framework

A data clustering package based on admixture ratios (Q matrix) of population structure. The framework is based on iterative Pruning procedure that performs data clustering by splitting a given population into subclusters until meeting the condition of stopping criteria the same as ipPCA, iNJclust, and IPCAPS frameworks. The package also provides a function to retrieve phylogeny tree that construct a neighbor-joining tree based on a similar matrix between clusters. By given multiple Q matrices with varying a number of ancestors (K), the framework define a similar value between clusters i,j as a minimum number K* that makes majority of members of two clusters are in the different clusters. This K* reflexes a minimum number of ancestors we need to splitting cluster i,j into different clusters if we assign K* clusters based on maximum admixture ratio of individuals. The publication of this package is at Chainarong Amornbunchornvej, Pongsakorn Wangkumhang, and Sissades Tongsima (2020) <doi:10.1101/2020.03.21.001206>.

Version: 0.1.0
Depends: R (≥ 3.5.0)
Imports: stats, treemap, ape
Suggests: knitr, rmarkdown
Published: 2020-03-26
DOI: 10.32614/CRAN.package.ipADMIXTURE
Author: Chainarong Amornbunchornvej ORCID iD [aut, cre]
Maintainer: Chainarong Amornbunchornvej <grandca at gmail.com>
BugReports: https://github.com/DarkEyes/ipADMIXTURE/issues
License: GPL-3
URL: https://github.com/DarkEyes/ipADMIXTURE
NeedsCompilation: no
Language: en-US
Citation: ipADMIXTURE citation info
Materials: README NEWS
CRAN checks: ipADMIXTURE results


Reference manual: ipADMIXTURE.pdf
Vignettes: ipADMIXTURE_demo


Package source: ipADMIXTURE_0.1.0.tar.gz
Windows binaries: r-devel: ipADMIXTURE_0.1.0.zip, r-release: ipADMIXTURE_0.1.0.zip, r-oldrel: ipADMIXTURE_0.1.0.zip
macOS binaries: r-release (arm64): ipADMIXTURE_0.1.0.tgz, r-oldrel (arm64): ipADMIXTURE_0.1.0.tgz, r-release (x86_64): ipADMIXTURE_0.1.0.tgz, r-oldrel (x86_64): ipADMIXTURE_0.1.0.tgz


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