R Observatory: Metrics for AMR version 3.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AMR

3.0.1

Antimicrobial Resistance Data Analysis

2packages depend

25.7Kdownloads / year

78.6%test coverage

13/13checks pass

Overview

About

Maintained by Matthijs S. BerendsFirst published 2018-02-2229 releasesCRAN page ↗GitHub ↗

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in doi:10.18637/jss.v104.i03.

Install

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

install.packages("AMR", 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("msberends/AMR")

Development version from msberends/AMR. 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-amr

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-AMR

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-AMR

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

Health

CRAN checks

13OK

Slowest check: 5.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.19

78.6%

Coverage · measured lines

98%

Documentation · exports

0

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
OK2026-07-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-03-13
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-12
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 399 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 92%
Return-value docs: 67%
References docs: 2%

Downloads

25.7K

CRAN downloads in the past year

Rank #3,059 · ~70/day · ~2.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

4.1K90 days

25.7K1 year

Compare downloads with other packages →

Also on305 r2u30 autocran50 c2d4u

Repository

GitHub ↗ msberends/amr

112Stars

24Forks

16Open issues

1Open PRs

2Releases

1,786Commits

8Contributors

rmicrobiologyepidemiologyantimicrobial-dataamrsoftware

1,786 commits · Last activity 2026-08-20 · 0% stars, 30d

Stars over time

2025-07-26 · 1002026-07-07 · 112

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/msberends/amr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

Governance and community (1)

Issue templates

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-02-27

claude

Most recent: claude on 2026-02-27

Evidence

claude: on 2026-02-27 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (0)

none

LinkingTo (0)

none

Suggests (26)

cleaner cli crayon curl data.table dplyr ggplot2 knitr openxlsx parallelly pillar progress readxl recipes rlang rmarkdown rstudioapi rvest skimr testthat tibble tidymodels tidyselect tinytest vctrs xml2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

MIC MIMER

Code & Tests

Datasets

People & History

People (30)

Maintainer (1)

Matthijs S. Berends

Author, Maintainer

Authors (3)

Matthijs S. Berends

Author, Maintainer

Erwin E. A. Hassing

Author, Contributor

Dennis Souverein

Author, Contributor · added in 0.8.0

Contributors (25)

Erwin E. A. Hassing

Author, Contributor

Dennis Souverein

Author, Contributor · added in 0.8.0

Contributor

Contributor

Contributor

Contributor · added in 2.0.0

Judith M. Fonville

Contributor

Jane Hawkey

Contributor

Show 17 more contributors

Eric H. L. C. M. Hazenberg

Contributor

Kathryn Holt

Contributor

Gwen Knight

Contributor · added in 1.4.0

Annick Lenglet

Contributor · added in 0.8.0

Christian F. Luz

Contributor

Bart C. Meijer

Contributor

Dmytro Mykhailenko

Contributor · added in 2.0.0

Anton Mymrikov

Contributor · added in 2.0.0

Andrew P. Norgan

Contributor

Sofia Ny

Contributor · added in 0.9.0

Matthew Saab

Contributor

Jonas Salm

Contributor · added in 2.0.0

Contributor

Contributor

Contributor

Contributor · added in 1.4.0

Anita Williams

Contributor · added in 2.0.0

Other (4)

Casper J. Albers

Thesis advisor

Alex W. Friedrich

Thesis advisor

Corinna Glasner

Thesis advisor · added in 0.3.0

Bhanu N. M. Sinha

Thesis advisor

Listed in earlier versions (41)

Berends

no longer listed · 0.1.0 to 3.0.1

Hassing

no longer listed · 0.1.0 to 3.0.1

Luz

no longer listed · 0.1.0 to 3.0.1

Friedrich

no longer listed · 0.3.0 to 3.0.1

Bhanu Sinha

no longer listed · 0.3.0 to 2.1.1

Sinha

no longer listed · 0.6.0 to 3.0.1

Albers

no longer listed · 0.8.0 to 3.0.1

Fonville

no longer listed · 0.8.0 to 3.0.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.0.1Latest
2025-09-20 · current release · diff ↗
3.0.0
2025-06-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.1.1
2023-10-22 · diff ↗
2.1.0
2023-07-16 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.0
2023-03-12 · diff ↗
1.8.2
2022-09-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.8.1
2022-03-24 · diff ↗
1.8.0
2022-01-07 · diff ↗
1.7.1
2021-06-03 · diff ↗
unarchivedReturned to CRAN
2021-06-03
archivedRemoved from CRAN
2021-05-22
check problems were not corrected in time

Show 29 earlier events

R
R 4.1.0 released · 2021-05-18
1.6.0
2021-03-15 · diff ↗
1.5.0
2021-01-06 · diff ↗
1.4.0
2020-10-08 · diff ↗
1.3.0
2020-07-31 · diff ↗
1.2.0
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
2020-04-15 · diff ↗
1.0.1
2020-02-23 · diff ↗
1.0.0
2020-02-17 · diff ↗
0.9.0
2019-11-29 · diff ↗
0.8.0
2019-10-15 · diff ↗
0.7.1
2019-06-23 · diff ↗
0.7.0
2019-06-03 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.6.1
2019-03-29 · diff ↗
unarchivedReturned to CRAN
2019-03-29
0.6.0
2019-03-27 · diff ↗
archivedRemoved from CRAN
2019-03-27
policy violation Creates '~/.Rhistory_mo'
0.5.0
2018-11-30 · diff ↗
0.4.0
2018-10-01 · diff ↗
unarchivedReturned to CRAN
2018-10-01
archivedRemoved from CRAN
2018-09-28
policy violation Write to clipboard, leaves xsel process running
0.3.0
2018-08-14 · diff ↗
0.2.0
2018-05-03 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.1
2018-03-14 · diff ↗
0.1.0
2018-02-22
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-02-22
Total releases: 29 / 8 yrs
License: GPL-2 | file LICENSE OSI
Minimum R: ≥ 3.0.0
Bundled data: 2.1 MB / 12 files
Download size: 2.7 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("AMR")

Format

Berends, M. S., Albers, C. J., Bolton, L., Cook, A., Couto, N., Dutey-Magni, P., Fonville, J. M., Friedrich, A. W., Glasner, C., Hassing, E. E. A., Hawkey, J., Hazenberg, E. H. L. C. M., Holt, K., Knight, G., Lenglet, A., Luz, C. F., Meijer, B. C., Mykhailenko, D., Mymrikov, A., Norgan, A. P., Ny, S., Saab, M., Salm, J., Sanchez, J., Schade, R. P., Sinha, B. N. M., Souverein, D., Stull, J., Underwood, A., & Williams, A. (2025). AMR: Antimicrobial Resistance Data Analysis (Version 3.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.AMR

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 AMR version 3.0.1 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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