* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed
* Function `guess_bactid` to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
* Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
* Function `MDRO` to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. Suggest your own via [this link](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E). Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
@ -9,7 +10,6 @@
@@ -9,7 +10,6 @@
* New print format for tibbles and data.tables
#### Changed
* Support for old R versions, only R-3.0.0 (April 2013) or later is needed
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange
#' @return A vector to add to table, see Examples.
#' @source Methodology of this function is based on: "M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition", 2014, Clinical and Laboratory Standards Institute. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @examples
#' # septic_patients is a dataset available in the AMR package
@ -8,12 +8,15 @@ This R package was created for academic research by PhD students of the Faculty
@@ -8,12 +8,15 @@ This R package was created for academic research by PhD students of the Faculty
## 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).
With AMR you can also apply EUCAST rules to isolates, identify first isolates of every patient, 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"`), or predict antimicrobial resistance for the nextcoming years with the `rsi_predict` function.
With `AMR` you can also:
* Conduct AMR analysis with the `rsi()` function, that can also be used with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table.
* Predict antimicrobial resistance for the nextcoming years with the `rsi_predict()` function
* Apply [EUCAST rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) with the `EUCAST_rules()` function
* Identify first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute) with the `first_isolate()` function
* 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"`) with the `abname()` function
With the `MDRO` function (abbreviation of mutli-drug resistant organisms), you can check your isolates for exceptional resistance with country-specific guidelines. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
For regular AMR analysis, the `rsi` function can be used. This function als works with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table.
This package contains an example data set `septic_patients`, consisting of 2000 isolates from anonymised septic patients between 2001 and 2017.
## How to get it?
@ -32,7 +35,7 @@ This package is available on CRAN and also here on GitHub.
@@ -32,7 +35,7 @@ This package is available on CRAN and also here on GitHub.
- `install.packages("AMR")`
- <imgsrc="https://exploratory.io/favicon.ico"alt="Exploratory favicon"height="20px"> In [Exploratory.io](https://exploratory.io):
- (Exploratory.io costs $40/month, but is free for students and teachers; if you have an `@umcg.nl` or `@rug.nl` email address, [click here to enroll](https://exploratory.io/plan?plan=Community))
- (Exploratory.io costs $40/month but the somewhat limited Community Plan is free for students and teachers, [click here to enroll](https://exploratory.io/plan?plan=Community))
- Start the software and log in
- Click on your username at the right hand side top
- Click on `R Packages`
@ -276,7 +279,7 @@ bactlist # A tibble: 2,507 x 10
@@ -276,7 +279,7 @@ bactlist # A tibble: 2,507 x 10
<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
<sup>2</sup>Certe Medical Diagnostics & Advice, Groningen, the Netherlands
@ -287,6 +290,8 @@ This R package is licensed under the [GNU General Public License (GPL) v2.0](htt
@@ -287,6 +290,8 @@ This R package is licensed under the [GNU General Public License (GPL) v2.0](htt
- May be used for private purposes
- May **not** be used for patent purposes
- May be modified, although:
- Modifications **must** be released under the same license when distributing the package
Methodology of this function is based on: "M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition", 2014, Clinical and Laboratory Standards Institute. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.