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AMR
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typo in examples

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dr. M.S. (Matthijs) Berends 2018-03-13 14:40:52 +01:00
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3 changed files with 15 additions and 10 deletions
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1
NEWS
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@ -3,6 +3,7 @@
- Edited column names to comply with GLIMS, the laboratory information system - Edited column names to comply with GLIMS, the laboratory information system
- Added more valid MIC values - Added more valid MIC values
- Renamed 'Daily Defined Dose' to 'Defined Daily Dose' - Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
- Added barplots for `rsi` and `mic` classes
## 0.1.0 ## 0.1.0
- First submission to CRAN. - First submission to CRAN.

22
R/EUCAST.R
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@ -20,7 +20,7 @@
#' #'
#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. #' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl} #' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_bactcode column name of the bacteria ID in \code{tbl} - should also be present in \code{bactlist$bactid}, see \code{\link{bactlist}}. #' @param col_bactcode column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{bactlist$bactid}, see \code{\link{bactlist}}
#' @param info print progress #' @param info print progress
#' @param amcl,amik,amox,ampi,azit,aztr,cefa,cfra,cfep,cfot,cfox,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mino,moxi,nali,neom,neti,nitr,novo,norf,oflo,peni,pita,poly,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column names of antibiotics. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing column will be skipped. #' @param amcl,amik,amox,ampi,azit,aztr,cefa,cfra,cfep,cfot,cfox,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mino,moxi,nali,neom,neti,nitr,novo,norf,oflo,peni,pita,poly,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column names of antibiotics. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing column will be skipped.
#' @param ... parameters that are passed on to \code{EUCAST_rules} #' @param ... parameters that are passed on to \code{EUCAST_rules}
@ -36,19 +36,23 @@
#' EUCAST Expert Rules Version 3.1: \cr #' EUCAST Expert Rules Version 3.1: \cr
#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance} #' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
#' @examples #' @examples
#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"), #' a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
#' vanc = "-", #' "ENCFAE", # Enterococcus faecalis
#' amox = "-", #' "ESCCOL", # Escherichia coli
#' coli = "-", #' "KLEPNE", # Klebsiella pneumoniae
#' cfta = "-", #' "PSEAER"), # Pseudomonas aeruginosa
#' cfur = "-", #' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin
#' coli = "-", # Colistin
#' cfta = "-", # Ceftazidime
#' cfur = "-", # Cefuroxime
#' stringsAsFactors = FALSE) #' stringsAsFactors = FALSE)
#' a #' a
#' #'
#' b <- EUCAST_rules(a, "bactid") #' b <- EUCAST_rules(a)
#' b #' b
EUCAST_rules <- function(tbl, EUCAST_rules <- function(tbl,
col_bactcode, col_bactcode = 'bactid',
info = TRUE, info = TRUE,
amcl = 'amcl', amcl = 'amcl',
amik = 'amik', amik = 'amik',

2
README.md
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@ -48,7 +48,7 @@ help(package = "AMR")
This is also called *interpretive reading*. This is also called *interpretive reading*.
```r ```r
before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
"ENCFAE" # Enterococcus faecalis "ENCFAE", # Enterococcus faecalis
"ESCCOL", # Escherichia coli "ESCCOL", # Escherichia coli
"KLEPNE", # Klebsiella pneumoniae "KLEPNE", # Klebsiella pneumoniae
"PSEAER"), # Pseudomonas aeruginosa "PSEAER"), # Pseudomonas aeruginosa