P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-02 23:44:09 +02:00
Code Releases Activity

WHONET/EARS-Net support

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-01-29 00:06:50 +01:00
parent f6336fdd89
commit 6aae206320
83 changed files with 1428 additions and 633 deletions
Download Patch File Download Diff File Expand all files Collapse all files

39
index.md
View File

@@ -4,7 +4,7 @@
----
`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.
We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but **not** patent) purposes under the terms of the GNU General Public Licence version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full licence [here](./LICENSE-text.html).
@@ -48,7 +48,7 @@ Developers
* Software developers
* Web application / Shiny developers
### Get this package
## Get this package
This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:
@@ -58,11 +58,34 @@ install.packages("AMR")
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
### Get started
The latest and unpublished development version can be installed with (precaution: may be unstable):
```r
install.packages("devtools")
devtools::install_gitlab("msberends/AMR")
```
## Get started
To find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
### Short introduction
## Short introduction
#### WHONET / EARS-Net
<img src="./whonet.png">
We support data (exported files) from WHONET. The `AMR` package contains a data set `antibiotics` which also contains all EARS-Net antibiotic abbreviations. Furthermore, when using WHONET data as input for analysis all input parameters will be set automatically.
Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).
#### Antimicrobial reference data
<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
This package contains **all ~500 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
#### Microbial (taxonomic) reference data
@@ -74,14 +97,6 @@ All ~20,000 (sub)species from **the taxonomic kingdoms Bacteria, Fungi and Proto
Read more about the data from ITIS [in our manual](./reference/ITIS.html).
#### Antimicrobial reference data
<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
This package contains **all ~500 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
#### Overview of functions
The `AMR` package basically does four important things: