R Observatory: Metrics for admix version 2.6.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

admix

2.6.1

Package Admix for Admixture (aka Contamination) Models

0packages depend

8.4Kdownloads / year

96.9%test coverage

13/13checks pass

Overview

About

Maintained by Xavier MilhaudFirst published 2021-06-1416 releasesCRAN page ↗GitHub ↗

Implements techniques to estimate the unknown quantities related to two-component admixture models, where the two components can belong to any distribution (note that in the case of multinomial mixtures, the two components must belong to the same family). Estimation methods depend on the assumptions made on the unknown component density; see Bordes and Vandekerkhove (2010) doi:10.3103/S1066530710010023, Patra and Sen (2016) doi:10.1111/rssb.12148, and Milhaud, Pommeret, Salhi, Vandekerkhove (2024) doi:10.3150/23-BEJ1593. In practice, one can estimate both the mixture weight and the unknown component density in a wide variety of frameworks. On top of that, hypothesis tests can be performed in one and two-sample contexts to test the unknown component density (see Milhaud, Pommeret, Salhi and Vandekerkhove (2022) doi:10.1016/j.jspi.2021.05.010, and Milhaud, Pommeret, Salhi, Vandekerkhove (2024) doi:10.3150/23-BEJ1593). Finally, clustering of unknown mixture components is also feasible in a K-sample setting (see Milhaud, Pommeret, Salhi, Vandekerkhove (2024) https://jmlr.org/papers/v25/23-0914.html).

Install

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

install.packages("admix", 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("XavierMilhaud/admix-Rpackage")

Development version from XavierMilhaud/admix-Rpackage. 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-admix

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-admix

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-admix

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

Health

CRAN checks

13OK

Slowest check: 4.8 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.71

96.9%

Coverage · measured lines

100%

Documentation · exports

12

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 338 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 98%
Return-value docs: 96%
References docs: 19%

Downloads

8.4K

CRAN downloads in the past year

Rank #4,893 · ~23/day · ~698/mo

Releases R versions

Daily download trend is not available in this view yet.

36030 days

1.6K90 days

8.4K1 year

Compare downloads with other packages →

Also on510 r2u67 autocran

Repository

GitHub ↗ xaviermilhaud/admix-rpackage

3Stars

0Forks

0Open issues

0Open PRs

0Releases

165Commits

1Contributors

License GPL-3.0 · 165 commits · Last activity 2026-05-29

Stars over time

2025-06-05 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/xaviermilhaud/admix-rpackage on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (12)

base cubature fdrtoolgraphicsIsoMASSorthopolynom pracma Rcpp Rdpackstatsutils

LinkingTo (1)

Rcpp

Suggests (15)

doParallel doRNG evd flexsurv foreach gridExtra knitrlatticelogitnorm plyr reshape2 rmarkdown rmutil mockery testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Xavier Milhaud

Author, Maintainer

Authors (1)

Xavier Milhaud

Author, Maintainer

Contributors (3)

Denys Pommeret

Contributor

Yahia Salhi

Contributor

Pierre Vandekerkhove

Contributor

Package Timeline

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

2.6.1Latest
2026-05-30 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.5.2
2026-01-08 · diff ↗
2.5.1
2025-09-05 · diff ↗
2.4.3
2025-08-21 · diff ↗
2.4.2
2025-07-06 · diff ↗
2.4
2025-05-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.3.4
2025-03-07 · diff ↗
2.3.3
2024-11-08 · diff ↗
2.3.2
2024-11-05 · diff ↗
2.3.1
2024-10-24 · diff ↗
2.1-3
2024-04-25 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1-2
2023-07-13 · diff ↗
2.1-1
2023-07-06 · diff ↗

Show 6 earlier events

R
R 4.3.0 released · 2023-04-21
2.1-0
2023-03-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.4.0
2022-03-24 · diff ↗
0.3.2
2021-06-14
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-14
Total releases: 16 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 2.0 MB / 4 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("admix")

Format

Milhaud, X., Pommeret, D., Salhi, Y., & Vandekerkhove, P. (2026). admix: Package Admix for Admixture (aka Contamination) Models (Version 2.6.1) [Computer software]. https://doi.org/10.32614/CRAN.package.admix

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for admix version 2.6.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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