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typo in examples
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NEWS
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NEWS
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@ -3,6 +3,7 @@
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- Edited column names to comply with GLIMS, the laboratory information system
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- Added more valid MIC values
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- Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
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- Added barplots for `rsi` and `mic` classes
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## 0.1.0
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- First submission to CRAN.
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22
R/EUCAST.R
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R/EUCAST.R
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@ -20,7 +20,7 @@
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#'
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#' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
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#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param col_bactcode column name of the bacteria ID in \code{tbl} - should also be present in \code{bactlist$bactid}, see \code{\link{bactlist}}.
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#' @param col_bactcode column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{bactlist$bactid}, see \code{\link{bactlist}}
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#' @param info print progress
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#' @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.
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#' @param ... parameters that are passed on to \code{EUCAST_rules}
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@ -36,19 +36,23 @@
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#' EUCAST Expert Rules Version 3.1: \cr
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#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
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#' @examples
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#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
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#' vanc = "-",
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#' amox = "-",
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#' coli = "-",
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#' cfta = "-",
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#' cfur = "-",
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#' a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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#' "ENCFAE", # Enterococcus faecalis
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#' "ESCCOL", # Escherichia coli
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#' "KLEPNE", # Klebsiella pneumoniae
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#' "PSEAER"), # Pseudomonas aeruginosa
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#' vanc = "-", # Vancomycin
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#' amox = "-", # Amoxicillin
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#' coli = "-", # Colistin
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#' cfta = "-", # Ceftazidime
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#' cfur = "-", # Cefuroxime
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#' stringsAsFactors = FALSE)
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#' a
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#'
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#' b <- EUCAST_rules(a, "bactid")
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#' b <- EUCAST_rules(a)
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#' b
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EUCAST_rules <- function(tbl,
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col_bactcode,
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col_bactcode = 'bactid',
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info = TRUE,
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amcl = 'amcl',
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amik = 'amik',
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@ -48,7 +48,7 @@ help(package = "AMR")
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This is also called *interpretive reading*.
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```r
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before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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"ENCFAE" # Enterococcus faecalis
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"ENCFAE", # Enterococcus faecalis
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"ESCCOL", # Escherichia coli
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"KLEPNE", # Klebsiella pneumoniae
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"PSEAER"), # Pseudomonas aeruginosa
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