mirror of
https://github.com/msberends/AMR.git
synced 2025-04-22 17:43:56 +02:00
61 lines
3.6 KiB
Plaintext
61 lines
3.6 KiB
Plaintext
---
|
|
output: github_document
|
|
---
|
|
|
|
<!-- README.md is generated from README.Rmd; please edit that file. -->
|
|
|
|
```{r, include = FALSE}
|
|
knitr::opts_chunk$set(
|
|
collapse = TRUE,
|
|
comment = "#>",
|
|
# fig.path = "man/figures/README-",
|
|
out.width = "100%"
|
|
)
|
|
```
|
|
|
|
# The `AMR` Package for R
|
|
|
|
Please visit our comprehensive package website <https://amr-for-r.org> to read more about this package, including many examples and tutorials.
|
|
|
|
Overview:
|
|
|
|
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
|
|
* Peer-reviewed, used in over 175 countries, available in 20 languages
|
|
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
|
|
* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
|
|
* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$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:
|
|
remotes::install_github("msberends/AMR")
|
|
```
|
|
|
|
----
|
|
|
|
<small>
|
|
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.
|
|
</small>
|