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dr. M.S. (Matthijs) Berends
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README.md
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# `AMR`
This is an [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR).
### An [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR).
[![logo_rug](man/figures/logo_rug.png)](https://www.rug.nl)[![logo_umcg](man/figures/logo_umcg.png)](https://www.umcg.nl)[![logo_eh1h](man/figures/logo_eh1h.png)](http://www.eurhealth-1health.eu)[![logo_interreg](man/figures/logo_interreg.png)](http://www.eurhealth-1health.eu)
[![logo_rug](man/figures/logo_rug.png)](https://www.rug.nl)[![logo_umcg](man/figures/logo_umcg.png)](https://www.umcg.nl)
This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen)](https://www.rug.nl) and the Medical Microbiology & Infection Prevention department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl). They also maintain this package, see [Authors](#authors).
This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen)](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl). See [Authors](#authors).
## Why this package?
This R package contains functions to make microbiological, epidemiological data analysis easier. It allows the use of some new classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
This R package contains functions to make **microbiological, epidemiological data analysis easier**. It allows the use of some new classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
With `AMR` you can also:
* Create frequency tables with the `freq` function
@ -264,11 +264,14 @@ abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
### Databases included in package
Datasets to work with antibiotics and bacteria properties.
```r
# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
ablist # A tibble: 420 x 12
# Dataset with 2000 random blood culture isolates from anonymised septic patients between 2001 and 2017 in 5 Dutch hospitals
septic_patients # A tibble: 4,000 x 47
# Dataset with ATC antibiotics codes, official names, trade names and DDD's (oral and parenteral)
antibiotics # A tibble: 420 x 18
# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
bactlist # A tibble: 2,507 x 10
microorganisms # A tibble: 2,453 x 12
```
@ -282,6 +285,8 @@ bactlist # A tibble: 2,507 x 10
<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands
[![logo_umcg](man/figures/logo_umcg.png)](https://www.umcg.nl)[![logo_certe](man/figures/logo_certe.png)](https://www.certe.nl)[![logo_eh1h](man/figures/logo_eh1h.png)](http://www.eurhealth-1health.eu)[![logo_interreg](man/figures/logo_interreg.png)](http://www.eurhealth-1health.eu)
## Copyright
[![License](https://img.shields.io/github/license/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/blob/master/LICENSE)