From 6eaf594cb7c04242252a04c373df0c43f60e0d88 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Tue, 1 May 2018 09:57:50 +0200 Subject: [PATCH] update data info --- R/data.R | 6 +++--- README.md | 19 ++++++++++++------- man/antibiotics.Rd | 2 +- man/figures/logo_certe.png | Bin 0 -> 14359 bytes man/microorganisms.Rd | 4 ++-- 5 files changed, 18 insertions(+), 13 deletions(-) create mode 100644 man/figures/logo_certe.png diff --git a/R/data.R b/R/data.R index 9fc7c588..8f6a0291 100644 --- a/R/data.R +++ b/R/data.R @@ -19,7 +19,7 @@ #' 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. -#' @format A data.frame with 420 observations and 16 variables: +#' @format A data.frame with 420 observations and 18 variables: #' \describe{ #' \item{\code{atc}}{ATC code, like \code{J01CR02}} #' \item{\code{molis}}{MOLIS code, like \code{amcl}} @@ -236,8 +236,8 @@ #' Dataset with ~2500 microorganisms #' -#' A dataset containing 2500 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: +#' A dataset containing 2453 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}. +#' @format A data.frame with 2453 observations and 12 variables: #' \describe{ #' \item{\code{bactid}}{ID of microorganism} #' \item{\code{bactsys}}{Bactsyscode of microorganism} diff --git a/README.md b/README.md index a06d280f..ab51253b 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # `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 2 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) diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 73d25ef7..db8cf86e 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -4,7 +4,7 @@ \name{antibiotics} \alias{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{ \item{\code{atc}}{ATC code, like \code{J01CR02}} \item{\code{molis}}{MOLIS code, like \code{amcl}} diff --git a/man/figures/logo_certe.png b/man/figures/logo_certe.png new file mode 100644 index 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