ipADMIXTURE

0.1.2

Iterative Pruning Population Admixture Inference Framework

0packages depend

6.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Chainarong AmornbunchornvejFirst published 2020-03-262 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ipADMIXTURE", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("DarkEyes/ipADMIXTURE")

Development version from DarkEyes/ipADMIXTURE. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ipadmixture

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ipADMIXTURE

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ipADMIXTURE

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 557 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 0%

Downloads

6.4K

CRAN downloads in the past year

Rank #7,175 · ~18/day · ~536/mo

Releases R versions

Daily download trend is not available in this view yet.

28730 days

1.4K90 days

6.4K1 year

Compare downloads with other packages →

Also on99 r2u1 autocran

Repository

GitHub ↗ darkeyes/ipadmixture

6Stars

1Forks

0Open issues

0Open PRs

0Releases

53Commits

1Contributors

admixturepopulation-structurepopulation-stratificationdata-clustering-algorithmrbioinformatics

License GPL-3.0 · 53 commits · Last activity 2025-05-07 · 0% stars, 30d

Stars over time

2025-03-20 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/darkeyes/ipadmixture on 2026-07-30.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (3)

statstreemap ape

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Chainarong Amornbunchornvej

Author, Maintainer

Authors (1)

Chainarong Amornbunchornvej

Author, Maintainer

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2025-05-06 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
2020-03-26
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-26
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 713 KB / 1 file
Download size: 934 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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