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dr. M.S. (Matthijs) Berends 2018-05-01 09:57:50 +02:00
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R/data.R
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#' Dataset with 420 antibiotics #' Dataset with 420 antibiotics
#' #'
#' A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source. #' A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source.
#' @format A data.frame with 420 observations and 16 variables: #' @format A data.frame with 420 observations and 18 variables:
#' \describe{ #' \describe{
#' \item{\code{atc}}{ATC code, like \code{J01CR02}} #' \item{\code{atc}}{ATC code, like \code{J01CR02}}
#' \item{\code{molis}}{MOLIS code, like \code{amcl}} #' \item{\code{molis}}{MOLIS code, like \code{amcl}}
@ -236,8 +236,8 @@
#' Dataset with ~2500 microorganisms #' Dataset with ~2500 microorganisms
#' #'
#' A dataset containing 2500 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}. #' A dataset containing 2453 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
#' @format A data.frame with 2507 observations and 12 variables: #' @format A data.frame with 2453 observations and 12 variables:
#' \describe{ #' \describe{
#' \item{\code{bactid}}{ID of microorganism} #' \item{\code{bactid}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism} #' \item{\code{bactsys}}{Bactsyscode of microorganism}

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README.md
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# `AMR` # `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? ## 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: With `AMR` you can also:
* Create frequency tables with the `freq` function * Create frequency tables with the `freq` function
@ -264,11 +264,14 @@ abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
### Databases included in package ### Databases included in package
Datasets to work with antibiotics and bacteria properties. Datasets to work with antibiotics and bacteria properties.
```r ```r
# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral) # Dataset with 2000 random blood culture isolates from anonymised septic patients between 2001 and 2017 in 5 Dutch hospitals
ablist # A tibble: 420 x 12 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 # 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 <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 ## Copyright
[![License](https://img.shields.io/github/license/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/blob/master/LICENSE) [![License](https://img.shields.io/github/license/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/blob/master/LICENSE)

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man/antibiotics.Rd
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\name{antibiotics} \name{antibiotics}
\alias{antibiotics} \alias{antibiotics}
\title{Dataset with 420 antibiotics} \title{Dataset with 420 antibiotics}
\format{A data.frame with 420 observations and 16 variables: \format{A data.frame with 420 observations and 18 variables:
\describe{ \describe{
\item{\code{atc}}{ATC code, like \code{J01CR02}} \item{\code{atc}}{ATC code, like \code{J01CR02}}
\item{\code{molis}}{MOLIS code, like \code{amcl}} \item{\code{molis}}{MOLIS code, like \code{amcl}}

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man/microorganisms.Rd
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\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Dataset with ~2500 microorganisms} \title{Dataset with ~2500 microorganisms}
\format{A data.frame with 2507 observations and 12 variables: \format{A data.frame with 2453 observations and 12 variables:
\describe{ \describe{
\item{\code{bactid}}{ID of microorganism} \item{\code{bactid}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism} \item{\code{bactsys}}{Bactsyscode of microorganism}
@ -26,7 +26,7 @@ MOLIS (LIS of Certe) - \url{https://www.certe.nl}
microorganisms microorganisms
} }
\description{ \description{
A dataset containing 2500 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}. A dataset containing 2453 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
} }
\seealso{ \seealso{
\code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}} \code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}