R Observatory: Metrics for CovidMutations version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CovidMutations

0.1.3

Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)

0packages depend

2.7Kdownloads / year

7.4%test coverage

13/13checks pass

Overview

About

Maintained by Shaoqian MaFirst published 2020-09-181 releasesCRAN page ↗GitHub ↗

A feasible framework for mutation analysis and reverse transcription polymerase chain reaction (RT-PCR) assay evaluation of COVID-19, including mutation profile visualization, statistics and mutation ratio of each assay. The mutation ratio is conducive to evaluating the coverage of RT-PCR assays in large-sized samples. Mercatelli, D. and Giorgi, F. M. (2020) doi:10.20944/preprints202004.0529.v1.

Install

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

install.packages("CovidMutations", 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("MSQ-123/CovidMutations")

Development version from MSQ-123/CovidMutations. 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-covidmutations

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-CovidMutations

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-CovidMutations

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

Health

CRAN checks

13OK

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

7.4%

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 215 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 5%

Downloads

2.7K

CRAN downloads in the past year

Rank #13,344 · ~7/day · ~225/mo

Releases R versions

Daily download trend is not available in this view yet.

18630 days

76090 days

2.7K1 year

Compare downloads with other packages →

Also on215 r2u3 autocran52 c2d4u

Repository

GitHub ↗ msq-123/covidmutations

4Stars

2Forks

0Open issues

0Open PRs

0Releases

14Commits

1Contributors

14 commits · Last activity 2020-08-29

Stars over time

2023-01-28 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/msq-123/covidmutations on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (10)

ggplot2 cowplot seqinr stringrgrDevicesgraphicsutilsggpubr dplyr VennDiagram

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Shaoqian Ma

Author, Maintainer

Authors (2)

Shaoqian Ma

Author, Maintainer

Yongyou Zhang

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-09-18
Total releases: 1 / 6 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 3.6
Bundled data: 87 KB / 8 files
Download size: 2.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CovidMutations")

Format

Ma, S., & Zhang, Y. (2020). CovidMutations: Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019) (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.CovidMutations

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 CovidMutations version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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