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

7
man/antibiotics.Rd
View File

@@ -4,9 +4,10 @@
\name{antibiotics}
\alias{antibiotics}
\title{Data set with ~500 antibiotics}
\format{A \code{\link{data.frame}} with 488 observations and 16 variables:
\format{A \code{\link{data.frame}} with 488 observations and 17 variables:
\describe{
\item{\code{atc}}{ATC code, like \code{J01CR02}}
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical), like \code{J01CR02}}
\item{\code{ears_net}}{EARS-Net code (European Antimicrobial Resistance Surveillance Network), like \code{AMC}}
\item{\code{certe}}{Certe code, like \code{amcl}}
\item{\code{umcg}}{UMCG code, like \code{AMCL}}
\item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
@@ -26,6 +27,8 @@
\source{
- World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
Table antibiotic coding EARSS (from WHONET 5.3): \url{http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf}
EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}

12
man/guess_ab_col.Rd
View File

@@ -14,7 +14,7 @@ guess_ab_col(tbl = NULL, col = NULL, verbose = FALSE)
\item{verbose}{a logical to indicate whether additional info should be printed}
}
\description{
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
}
\section{Read more on our website!}{
@@ -34,4 +34,14 @@ guess_ab_col(df, "J01AA07") # ATC code of Tetracycline
guess_ab_col(df, "J01AA07", verbose = TRUE)
# using column `tetr` for col "J01AA07"
# [1] "tetr"
# WHONET codes
df <- data.frame(AMP_ND10 = "R",
AMC_ED20 = "S")
guess_ab_col(df, "ampicillin")
# [1] "AMP_ND10"
guess_ab_col(df, "J01CR02")
# [1] "AMC_ED20"
guess_ab_col(df, as.atc("augmentin"))
# [1] "AMC_ED20"
}