R Observatory: Metrics for coala version 0.7.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

coala

0.7.2

A Framework for Coalescent Simulation

2packages depend

9Kdownloads / year

73.9%test coverage

13/13checks pass

Overview

About

Maintained by Dirk MetzlerFirst published 2015-07-1415 releasesCRAN page ↗GitHub ↗

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 doi:10.1093/bioinformatics/btw098). It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (https://github.com/pievos101/PopGenome).

Install

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

install.packages("coala", 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("statgenlmu/coala")

Development version from statgenlmu/coala. 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-coala

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-coala

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-coala

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

Health

CRAN checks

13OK

Slowest check: 6.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.71

73.9%

Coverage · measured lines

100%

Documentation · exports

10

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 374 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: 98%
Return-value docs: 57%
References docs: 12%

Downloads

9K

CRAN downloads in the past year

Rank #9,166 · ~25/day · ~752/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

1K90 days

9K1 year

Compare downloads with other packages →

Also on390 r2u16 autocran

Repository

GitHub ↗ statgenlmu/coala

24Stars

4Forks

6Open issues

0Open PRs

17Releases

685Commits

7Contributors

rstatscoalescentsimulationdnapopgenevolution

685 commits · Last activity 2024-03-20 · 0% stars, 30d

Stars over time

2024-11-27 · 232026-07-07 · 24

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/statgenlmu/coala on 2026-08-09.

Continuous integration (2)

Travis CIAppVeyor

Lint, format, editor (2)

lintrRStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (10)

assertthat digestmethodsparallelR6 Rcpp rehh scrmstatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

abc knitr PopGenome phyclust (>= 0.1-16)rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

jaatha jackalope

Code & Tests

People & History

People (3)

Maintainer (1)

Dirk Metzler

Author, Thesis advisor, Maintainer

Authors (2)

Dirk Metzler

Author, Thesis advisor, Maintainer

Paul Staab

Author

Contributors (1)

Jorge E. Amaya Romero

Contributor · added in 0.5.0

Package Timeline

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

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
0.7.2Latest
2024-03-04 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.7.1
2023-01-05 · diff ↗
unarchivedReturned to CRAN
2023-01-05
archivedRemoved from CRAN
2022-12-07
issues were not corrected in time
0.7.0
2022-08-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.6.1
2022-02-14 · diff ↗
unarchivedReturned to CRAN
2022-02-14
archivedRemoved from CRAN
2021-08-01
required archived package 'scrm'
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.6.0
2020-01-19 · diff ↗

Show 15 earlier events

0.5.3
2019-07-09 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.5.2
2017-10-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.5.0
2016-12-29 · diff ↗
0.4.1
2016-08-04 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.4.0
2016-02-06 · diff ↗
0.3.0
2015-12-21 · diff ↗
0.2.1
2015-11-17 · diff ↗
0.2.0
2015-11-11 · diff ↗
0.1.1
2015-07-17 · diff ↗
0.1.0
2015-07-14
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-07-14
Total releases: 15 / 11 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.1.0
Download size: 293 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("coala")

Format

Metzler, D., Amaya Romero, J. E., & Staab, P. (2024). coala: A Framework for Coalescent Simulation (Version 0.7.2) [Computer software]. https://doi.org/10.32614/CRAN.package.coala

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 coala version 0.7.2 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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