R Observatory: Metrics for MADPop version 1.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MADPop

1.1.7Package record

MHC Allele-Based Differencing Between Populations

0packages depend

2.9Kdownloads / year

77.9%test coverage

13/13flavors OK

Overview

About

Maintained by Martin LysyCRAN page ↗GitHub ↗Issues ↗

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.

Install

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

install.packages("MADPop", 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("mlysy/MADPop")

Development version from mlysy/MADPop. 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-madpop

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-MADPop

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-MADPop

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-07-27
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.7

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 1.1.7Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9 (2 internal)includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Bayesian Testing of Equal Genotype Proportions between Multiple Populations HTML

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #13,575 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

30530 days

85590 days

2.9K1 year

Compare downloads with other packages →

Also on348 r2u4 autocran

How downloads are counted

Repository

mlysy/madpop ↗Account: mlysy

1Stars

1Forks

0Open issues

0Open PRs

0Releases

67Commits

2Commit identities

License file reads as GPL-3.0 · 67 commits · Last activity 2024-02-26 · The default branch showed an older version (1.1.6) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 46

Stars over time

2022-08-23 · 12026-07-07 · 1

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mlysy/madpop on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing MADPop adds 48 packages (22 with compiled code, 43 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (2)

R >= 3.4.0rstan

Imports (4)

methodsRcppstatsrstantools

LinkingTo (6)

BH Rcpp RcppEigen rstan StanHeaders RcppParallel (>= 5.0.1)

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Martin Lysy

Maintainer since 1.1 (2017), Author

Peter W.J. Kim

Author

Terin Robinson

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.7Latest
record
2024-02-27 · current release · diff ↗
1.1.6
record
2023-10-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.5
record
2023-04-04 · diff ↗
unarchivedReturned to CRAN
2022-08-22
1.1.4
record
2022-08-22 · diff ↗
archivedRemoved from CRAN
2022-08-17
issues were not corrected in time
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
R
R 3.6.0 released · 2019-04-26
1.1.2
record
2018-11-08 · diff ↗
1.1.1
record
2018-10-27 · diff ↗

Show 4 earlier eventsHide 4 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.1
record
2017-01-18
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-18
Total releases: 7 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Bundled data: 1.2 KB / 1 file
Download size: 106 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MADPop")

Format

Lysy, M., Kim, P. W. J., & Robinson, T. (2024). MADPop: MHC Allele-Based Differencing Between Populations (Version 1.1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.MADPop

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 MADPop version 1.1.7 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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