R Observatory: Metrics for scrm version 1.7.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scrm

1.7.5

Simulating the Evolution of Biological Sequences

3packages depend

9.8Kdownloads / year

64.6%test coverage

13/13checks pass

Overview

About

Maintained by Dirk MetzlerFirst published 2014-10-2112 releasesCRAN page ↗GitHub ↗

A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution, see Staab et al. (2015) doi:10.1093/bioinformatics/btu861. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.

Install

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

install.packages("scrm", 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("scrm/scrm-r")

Development version from scrm/scrm-r. 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-scrm

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-scrm

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-scrm

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

Health

CRAN checks

13OK

Slowest check: 4.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 2.29

64.6%

Coverage · measured lines

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-04
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 · 203 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

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

Downloads

9.8K

CRAN downloads in the past year

Rank #7,711 · ~27/day · ~813/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

1.1K90 days

9.8K1 year

Compare downloads with other packages →

Also on396 r2u15 autocran4.1K conda_forge741 bioconda

Repository

GitHub ↗ scrm/scrm-r

8Stars

2Forks

0Open issues

0Open PRs

10Releases

191Commits

7Contributors

191 commits · Last activity 2024-01-02

Stars over time

2023-01-07 · 82026-07-07 · 8

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/scrm/scrm-r on 2026-08-16.

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

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (4)

ape knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

coala poolHelper jackalope

Code & Tests

People & History

People (4)

Maintainer (1)

Dirk Metzler

Author, Maintainer, Copyright holder, Thesis advisor

Authors (4)

Dirk Metzler

Author, Maintainer, Copyright holder, Thesis advisor

Gerton Lunter

Author, Copyright holder, Thesis advisor

Zhu Sha

Author, Copyright holder

Paul Staab

Author, Copyright holder

Copyright holders (4)

Dirk Metzler

Author, Maintainer, Copyright holder, Thesis advisor

Gerton Lunter

Author, Copyright holder, Thesis advisor

Zhu Sha

Author, Copyright holder

Paul Staab

Author, Copyright holder

Package Timeline

12 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
1.7.5Latest
2024-01-08 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.7.4-0
2022-02-14 · diff ↗
unarchivedReturned to CRAN
2022-02-14
archivedRemoved from CRAN
2021-08-01
check problems were not corrected despite multiple reminders
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
1.7.3-1
2018-11-19 · diff ↗
1.7.2-4
2018-06-30 · diff ↗
1.7.2-3
2018-06-18 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 11 earlier events

1.7.2-1
2017-12-08 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.7.2-0
2016-12-11 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.6.0-2
2015-06-07 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.5.0-1
2015-04-11 · diff ↗
1.3-3
2014-11-18 · diff ↗
1.3-2
2014-10-22 · diff ↗
1.3-1
2014-10-21
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-10-21
Total releases: 12 / 12 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Download size: 85 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scrm")

Format

Metzler, D., Lunter, G., Sha, Z., & Staab, P. (2024). scrm: Simulating the Evolution of Biological Sequences (Version 1.7.5) [Computer software]. https://doi.org/10.32614/CRAN.package.scrm

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 scrm version 1.7.5 [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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