R Observatory: Metrics for AMRsurveilR version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AMRsurveilR

0.1.0Package record

Antimicrobial Resistance Surveillance, Epidemiology and Risk Analysis

0packages depend

649downloads / year

95.3%test coverage

13/13flavors OK

Overview

About

Maintained by Vinodhkumar Obli RajendranCRAN page ↗

Provides tools for antimicrobial resistance surveillance, epidemiological analysis, temporal trend detection, early warning detection, spatial cluster identification, and risk factor analysis. The package supports analysis of antimicrobial resistance patterns, resistance to multiple antimicrobial classes, temporal surveillance, and spatial epidemiology for applications in veterinary, medical, and One Health research. Antimicrobial resistance surveillance approaches are informed by guidelines from WHO (2023) https://www.who.int/publications/i/item/9789240076600 and WOAH (2024) https://www.woah.org/fileadmin/Home/eng/Health_standards/tahc/2024/en_chapitre_antibio_harmonisation.htm. Statistical methods include cumulative sum (CUSUM) monitoring (Page, 1954) doi:10.1093/biomet/41.1-2.100, exponentially weighted moving average (EWMA) monitoring (Roberts, 1959) doi:10.1080/00401706.1959.10489860, Local Moran's I spatial analysis (Anselin, 1995) doi:10.1111/j.1538-4632.1995.tb00338.x, and multidrug- and extensively drug-resistant classification (Magiorakos et al., 2012) doi:10.1111/j.1469-0691.2011.03570.x.

Install

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

install.packages("AMRsurveilR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-amrsurveilr

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-AMRsurveilR

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-AMRsurveilR

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: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK5 OK2026-09-13

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12
Examples that run: 100%8 run in a plain check
Exported functions with examples: 73%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

649

CRAN downloads in the past year

Rank #19,731 · ~2/day · ~54/mo

Releases R versions

Daily download trend is not available in this view yet.

58230 days

64990 days

6491 year

Compare downloads with other packages →

Also on8 r2u25 autocran

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing AMRsurveilR adds 38 packages (23 with compiled code, 45 MB of source tarballs). Heaviest: sf 9.3 MB, ggplot2 6.0 MB, spdep 4.5 MB.

Depends (1)

R >= 4.1.0

Imports (6)

dplyr ggplot2 rlang sf spdepstats

LinkingTo (0)

none

Suggests (2)

covr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Vinodhkumar Obli Rajendran

Author, Maintainer since 0.1.0 (2026)

Keerthi Aaradhana

Author

Releases (1)

0.1.0Latest
record
first seen 2026-09-12 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First seen: 2026-09-12
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.5 KB / 1 file
Download size: 17 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AMRsurveilR")

Format

Obli Rajendran, V., & Aaradhana, K. (2026). AMRsurveilR: Antimicrobial Resistance Surveillance, Epidemiology and Risk Analysis (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.AMRsurveilR

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 AMRsurveilR version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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