diff --git a/NEWS b/NEWS index 42405a48..f80f18eb 100644 --- a/NEWS +++ b/NEWS @@ -3,6 +3,7 @@ - Edited column names to comply with GLIMS, the laboratory information system - Added more valid MIC values - Renamed 'Daily Defined Dose' to 'Defined Daily Dose' +- Added barplots for `rsi` and `mic` classes ## 0.1.0 - First submission to CRAN. diff --git a/R/EUCAST.R b/R/EUCAST.R index 3b6a3dfa..54f525f9 100644 --- a/R/EUCAST.R +++ b/R/EUCAST.R @@ -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}. #' @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 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} @@ -36,19 +36,23 @@ #' EUCAST Expert Rules Version 3.1: \cr #' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance} #' @examples -#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"), -#' vanc = "-", -#' amox = "-", -#' coli = "-", -#' cfta = "-", -#' cfur = "-", +#' a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus +#' "ENCFAE", # Enterococcus faecalis +#' "ESCCOL", # Escherichia coli +#' "KLEPNE", # Klebsiella pneumoniae +#' "PSEAER"), # Pseudomonas aeruginosa +#' vanc = "-", # Vancomycin +#' amox = "-", # Amoxicillin +#' coli = "-", # Colistin +#' cfta = "-", # Ceftazidime +#' cfur = "-", # Cefuroxime #' stringsAsFactors = FALSE) #' a #' -#' b <- EUCAST_rules(a, "bactid") +#' b <- EUCAST_rules(a) #' b EUCAST_rules <- function(tbl, - col_bactcode, + col_bactcode = 'bactid', info = TRUE, amcl = 'amcl', amik = 'amik', diff --git a/README.md b/README.md index 3258613f..b896be2a 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ help(package = "AMR") This is also called *interpretive reading*. ```r before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus - "ENCFAE" # Enterococcus faecalis + "ENCFAE", # Enterococcus faecalis "ESCCOL", # Escherichia coli "KLEPNE", # Klebsiella pneumoniae "PSEAER"), # Pseudomonas aeruginosa