R Observatory: Metrics for pedmut version 0.9.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pedmut

0.9.1Package record

Mutation Models for Pedigree Likelihood Computations

7packages dependsuggested by 1

10.1Kdownloads / year

42.4%test coverage

13/13flavors OK

Overview

About

Maintained by Magnus Dehli VigelandCRAN page ↗GitHub ↗

A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include equal, proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.

Changes in 0.9.1

New features

New output format (format = 4) in getParams(). This produces a list of lists, suitable for programmatic use.

From NEWS.md in the release

Install

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

install.packages("pedmut", 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("magnusdv/pedmut")

Development version from magnusdv/pedmut. 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-pedmut

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-pedmut

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-pedmut

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: 1.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.1

READMEYes · 762 wordsVignettesNoNEWSYes · 100% structured · mentions 0.9.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16 (1 internal)includes a package overview page
Examples that run: 100%14 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 25%

How these are measured

Downloads

10.1K

CRAN downloads in the past year

Rank #4,255 · ~28/day · ~842/mo

Releases R versions

Daily download trend is not available in this view yet.

86830 days

2K90 days

10.1K1 year

Compare downloads with other packages →

Also on211 r2u6 autocran

How downloads are counted

Repository

magnusdv/pedmut ↗Account: magnusdv

3Stars

0Forks

2Open issues

0Open PRs

9Releases

182Commits

2Commit identities

mutation-modelingpedigree-analysispedsuite

182 commits · Last activity 2026-08-30 · 0% stars, 30d · Default branch at 0.9.1.9000, ahead of CRAN 0.9.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 13
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2018-09-11 · 12026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/magnusdv/pedmut on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing pedmut adds 1 package (1 with compiled code, 457 KB of source tarballs). Heaviest: lpSolve 457 KB.

Depends (1)

R >= 4.2.0

Imports (1)

lpSolve

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

15indirect

Imports 7

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

pedtools pedprobr pedbuildr pedFamilias KLINK pedsuite famnesia

Suggests, most downloaded first

mispitools

How these are counted

Code & Tests

People & History

People (2)

Magnus Dehli Vigeland

Author, Maintainer since 0.1.0 (2019)

Thore Egeland

Contributor · added in 0.7.1

Releases (10)

Pick two releases to compare their code metrics.

0.9.1Latest
record
2026-05-17 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.9.0
record
2025-04-29 · diff ↗ ·
added 2 exports
lumpMutSpecial, makeStationary
R
R 4.5.0 released · 2025-04-11
0.8.0
record
2025-04-01 · diff ↗ ·
added 2 exports
adjustRate, makeReversible
R
R 4.4.0 released · 2024-04-24
0.7.1
record
2023-11-05 · diff ↗ ·
added 3 exports
isBounded, mutRate, stepwiseReversible
R
R 4.3.0 released · 2023-04-21
0.6.0
record
2023-04-12 · diff ↗ ·
added 5 exports
findStationary, getParams, isMutationMatrix, isMutationModel, stabilize
0.5.0
record
2023-02-11 · diff ↗ ·
added 2 exports
lumpedModel, sexEqual
0.4.0
record
2022-11-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
record
2021-10-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.0
record
2020-07-30 · diff ↗
R
R 4.0.0 released · 2020-04-24

Show 2 earlier eventsHide 2 earlier events

0.1.0
record
2019-10-01
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-01
Total releases: 10 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Download size: 38 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pedmut")

Format

Vigeland, M. D., & Egeland, T. (2026). pedmut: Mutation Models for Pedigree Likelihood Computations (Version 0.9.1) [Computer software]. https://doi.org/10.32614/CRAN.package.pedmut

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 pedmut version 0.9.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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