Data

Tools

Indexes

Applications

Experiments

Open Source Science

AMR

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 https://doi.org/10.18637/jss.v104.i03.

https://github.com/msberends/amr

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.9%) to scientific vocabulary

Keywords

amr antimicrobial-data epidemiology microbiology r software
Last synced: 6 months ago · JSON representation

Repository

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 https://doi.org/10.18637/jss.v104.i03.

Basic Info
  • Host: GitHub
  • Owner: msberends
  • License: other
  • Language: R
  • Default Branch: main
  • Homepage: https://amr-for-r.org
  • Size: 1.43 GB
Statistics
  • Stars: 101
  • Watchers: 7
  • Forks: 21
  • Open Issues: 10
  • Releases: 3
Topics
amr antimicrobial-data epidemiology microbiology r software
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  # fig.path = "man/figures/README-",
  out.width = "100%"
)
AMR:::reset_all_thrown_messages()
```

# The `AMR` Package for R

Please visit our comprehensive package website  to read more about this package, including many examples and tutorials.

Overview:

* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* Peer-reviewed, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antimicrobial class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
* 100% free of costs and dependencies, highly suitable for places with **limited resources**

----

The `AMR` package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.

The `AMR` package supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the [University Medical Center Groningen](https://www.umcg.nl).

----

### How to get this package

To install the latest 'release' version from CRAN:

```{r, eval = FALSE}
install.packages("AMR")
```

To install the latest 'beta' version:

```{r, eval = FALSE}
install.packages("AMR", repos = "beta.amr-for-r.org")
```

If this does not work, try to install directly from GitHub using the `remotes` package:

```{r, eval = FALSE}
remotes::install_github("msberends/AMR")
```

----


This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://amr-for-r.org/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.

Owner

  • Name: Dr. Matthijs Berends
  • Login: msberends
  • Kind: user
  • Location: Northern Netherlands
  • Company: Certe / University Medical Center Groningen

Medical epidemiologist/microbiologist at @certe-medical-epidemiology, the @rijksuniversiteit-groningen and the University Medical Center Groningen

GitHub Events

Total
  • Create event: 6
  • Release event: 1
  • Issues event: 78
  • Watch event: 15
  • Delete event: 6
  • Issue comment event: 62
  • Push event: 395
  • Pull request review event: 2
  • Pull request event: 7
  • Gollum event: 5
  • Fork event: 8
Last Year
  • Create event: 6
  • Release event: 1
  • Issues event: 78
  • Watch event: 15
  • Delete event: 6
  • Issue comment event: 62
  • Push event: 395
  • Pull request review event: 2
  • Pull request event: 7
  • Gollum event: 5
  • Fork event: 8

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 1,539
  • Total Committers: 7
  • Avg Commits per committer: 219.857
  • Development Distribution Score (DDS): 0.005
Past Year
  • Commits: 176
  • Committers: 2
  • Avg Commits per committer: 88.0
  • Development Distribution Score (DDS): 0.006
Top Committers
Name Email Commits
Matthijs S. Berends m****s@u****l 1,532
ceefluz c****z@u****l 2
Emil Rossing e****l@r****g 1
Edwin van Leeuwen e****l@t****o 1
Christian Luz 3****z 1
Anton Mymrikov a****v@g****m 1
uscloud u****d@u****l 1
Committer Domains (Top 20 + Academic)
umcg.nl: 2 uscloud.uscloud.nl: 1 gxpcluster.com: 1 tuta.io: 1 rossing.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 176
  • Total pull requests: 19
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 6 days
  • Total issue authors: 44
  • Total pull request authors: 5
  • Average comments per issue: 2.53
  • Average comments per pull request: 0.79
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 53
  • Pull requests: 8
  • Average time to close issues: 15 days
  • Average time to close pull requests: 7 days
  • Issue authors: 19
  • Pull request authors: 3
  • Average comments per issue: 0.89
  • Average comments per pull request: 1.38
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • msberends (78)
  • jukkiebah (11)
  • theanita1 (9)
  • samueljpearce (6)
  • iDudeRPS (6)
  • andrewjmc (6)
  • send2dan (5)
  • remcv (5)
  • ConnorChato (4)
  • antunderwood (4)
  • fire-bot (3)
  • elisa-sosa (2)
  • erwinhassing (2)
  • peterdutey (2)
  • mvrcwest (2)
Pull Request Authors
  • msberends (12)
  • thomsonn (2)
  • BlackEdder (2)
  • r0ssing (2)
  • gxpcluster (1)
Top Labels
Issue Labels
enhancement (76) bug (75) waiting for us (4) question/suggestion (4) NOT IMPLEMENTED FOR NOW (3) documentation (3) requires thinking (2) duplicate (1) waiting for others (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 2
  • Total downloads:
    • cran 1,791 last-month
    • pypi 2,355 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 7
    (may contain duplicates)
  • Total versions: 184
  • Total maintainers: 2
cran.r-project.org: AMR

Antimicrobial Resistance Data Analysis

  • Versions: 28
  • Dependent Packages: 1
  • Dependent Repositories: 7
  • Downloads: 1,791 Last month
  • Docker Downloads: 21,613
Rankings
Docker downloads count: 0.6%
Stargazers count: 5.0%
Forks count: 6.3%
Average: 10.4%
Downloads: 10.5%
Dependent repos count: 11.1%
Dependent packages count: 28.7%
Maintainers (1)
m.s.berends@umcg.nl
Last synced: 6 months ago
pypi.org: amr

A Python wrapper for the AMR R package

  • Versions: 156
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,355 Last month
Rankings
Dependent packages count: 10.2%
Average: 33.8%
Dependent repos count: 57.4%
Maintainers (1)
msberends
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • cleaner * enhances
  • ggplot2 * enhances
  • skimr * enhances
  • tidyselect * enhances
  • curl * suggests
  • dplyr * suggests
  • ggtext * suggests
  • knitr * suggests
  • progress * suggests
  • readxl * suggests
  • rmarkdown * suggests
  • rvest * suggests
  • tinytest * suggests
  • xml2 * suggests
.github/workflows/check-current-testthat.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/check-old-tinytest.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/codecovr.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/lintr.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/website.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/publish-to-pypi.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/renew-gpt-training-data.yml actions
  • actions/checkout v4 composite