---
title: "Welcome to the `AMR` package"
output: 
  rmarkdown::html_vignette:
    toc: true
    toc_depth: 3
vignette: >
  %\VignetteIndexEntry{Welcome to the `AMR` package}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r setup, include = FALSE, results = 'markup'}
knitr::opts_chunk$set(
  warning = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.width = 7.5,
  fig.height = 5
)
```

Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: <https://amr-for-r.org>.

----

The `AMR` package is a peer-reviewed, [free and open-source](https://amr-for-r.org/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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. We are a team of [many different researchers](https://amr-for-r.org/authors.html) from around the globe to make this a successful and durable project!

This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).

After installing this package, R knows [**`r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species**](https://amr-for-r.org/reference/microorganisms.html) (updated June 2024) and all [**`r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from 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)))` are included, even with epidemiological cut-off (ECOFF) values. It 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).

The `AMR` package is available in `r AMR:::vector_and(vapply(FUN.VALUE = character(1), AMR:::LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.

This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:

  * Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature ([LPSN]((https://lpsn.dsmz.de))) and the Global Biodiversity Information Facility ([GBIF](https://www.gbif.org)) ([manual](https://amr-for-r.org/reference/mo_property.html))
  * Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline ([manual](https://amr-for-r.org/reference/as.sir.html))
  * Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records ([manual](https://amr-for-r.org/reference/ab_from_text.html))
  * Determining first isolates to be used for AMR data analysis ([manual](https://amr-for-r.org/reference/first_isolate.html))
  * Calculating antimicrobial resistance ([tutorial](https://amr-for-r.org/articles/AMR.html))
  * Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) ([tutorial](https://amr-for-r.org/articles/MDR.html))
  * Calculating (empirical) susceptibility of both mono therapy and combination therapies ([tutorial](https://amr-for-r.org/articles/AMR.html))
  * Apply AMR functions in predictive modelling ([tutorial](https://amr-for-r.org/articles/AMR_with_tidymodels.html))
  * Getting properties for any microorganism (like Gram stain, species, genus or family) ([manual](https://amr-for-r.org/reference/mo_property.html))
  * Getting properties for any antimicrobial (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) ([manual](https://amr-for-r.org/reference/ab_property.html))
  * Plotting antimicrobial resistance ([tutorial](https://amr-for-r.org/articles/AMR.html))
  * Applying EUCAST expert rules ([manual](https://amr-for-r.org/reference/eucast_rules.html))
  * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](https://amr-for-r.org/reference/mo_property.html))
  * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](https://amr-for-r.org/reference/ab_property.html))
  * Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to SIR ([link](https://amr-for-r.org/articles/datasets.html))
  * Principal component analysis for AMR ([tutorial](https://amr-for-r.org/articles/PCA.html))
  
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit [our website for direct download links](https://amr-for-r.org/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).

----

<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>
