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# `AMR`
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This is an [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR).
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![logo_uni](man/figures/logo_en.png)![logo_umcg](man/figures/logo_umcg.png)
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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). They also maintain this package, see [Authors](#authors).
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## Why this package?
This R package contains functions to make microbiological, epidemiological data analysis easier. It allows the use of some new S3 classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
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AMR can also be predicted for the forthcoming years with the `rsi_predict` function. For use with the `dplyr` package, the `rsi` function can be used in conjunction with `summarise` to calculate the resistance percentages of different antibiotic columns of a table.
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It also contains functions to translate antibiotic codes from the lab (like `"AMOX"`) or the [WHO](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like `"J01CA04"`) to trivial names (like `"amoxicillin"`) and vice versa.
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## How to use it?
```r
# Call it with:
library(AMR)
# For a list of functions:
help(package = "AMR")
```
### Databases included in package
```r
# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
ablist # A tibble: 420 x 12
# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
bactlist # A tibble: 2,507 x 10
```
### New classes
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
```r
# Transform values to new classes
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
```
These functions also try to coerce valid values.
Quick overviews when just printing objects:
```r
mic_data
# Class 'mic': 7 isolates
#
# <NA> 0
#
# <=0.128 1 8 16 >=32
# 1 1 2 2 1
rsi_data
# Class 'rsi': 880 isolates
#
# <NA>: 0
# Sum of S: 474
# Sum of IR: 406
# - Sum of R: 370
# - Sum of I: 36
#
# %S %IR %I %R
# 53.9 46.1 4.1 42.0
```
A plot of `rsi_data`:
```r
plot(rsi_data)
```
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![example](man/figures/rsi_example.png)
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Other epidemiological functions:
```r
# Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns
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EUCAST_rules(...)
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# Determine key antibiotic based on bacteria ID
key_antibiotics(...)
# Check if key antibiotics are equal
key_antibiotics_equal(...)
# Selection of first isolates of any patient
first_isolate(...)
# Calculate resistance levels of antibiotics
rsi(...)
# Predict resistance levels of antibiotics
rsi_predict(...)
# Get name of antibiotic by ATC code
abname(...)
abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
```
## How to get it?
This package is only available here on GitHub, but respects the [CRAN Repository Policy](https://cran.r-project.org/web/packages/policies.html).
*Installation commands:*
```r
library(devtools)
install_github("msberends/AMR")
```
*Working behind a proxy? Then use:*
```r
library(httr)
library(devtools)
set_config(use_proxy("yourproxydomain.com",
8080,
"username",
"password",
"any")) # change "any" to "basic" or "digest" if needed
install_github("msberends/AMR")
reset_config()
```
## Authors
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- [Berends MS](https://github.com/msberends)<sup>1,2</sup>, PhD Student
- [Luz CF](https://github.com/ceefluz)<sup>1</sup>, PhD Student
- [Hassing EEA](https://github.com/erwinhassing)<sup>2</sup>, Data Analyst (contributor)
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<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
<sup>2</sup> Department of Medical, Market and Innovation (MMI), Certe Medische diagnostiek & advies, Groningen, the Netherlands
## Copyright
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
- May be used for commercial purposes
- May be used for private purposes
- May be modified, although:
- Modifications **must** be released under the same license when distributing the package
- Changes made to the code **must** be documented
- May be distributed, although:
- Source code **must** be made available when the package is distributed
- A copy of the license and copyright notice **must** be included with the package.
- Comes with a LIMITATION of liability
- Comes with NO warranty