misc

R/EUCAST.R

@@ -45,10 +45,10 @@
 #'                 stringsAsFactors = FALSE)
 #' a
 #' 
-#' b <- EUCAST_rules(a)
+#' b <- EUCAST_rules(a, "bactid")
 #' b
 EUCAST_rules <- function(tbl,
-                         col_bactcode = 'bactid',
+                         col_bactcode,
                          info = TRUE,
                          amcl = 'amcl',
                          amik = 'amik',

R/atc.R

@@ -128,7 +128,7 @@ atc_property <- function(atc_code,
 #' Name of an antibiotic
 #'
 #' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{ablist}}.
-#' @param abcode a code or name, like \code{"amox"}, \code{"cftr"} or \code{"J01CA04"}
+#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
 #' @param from,to type to transform from and to. See \code{\link{ablist}} for its column names.
 #' @param textbetween text to put between multiple returned texts
 #' @param tolower return output as lower case with function \code{\link{tolower}}.
@@ -146,7 +146,7 @@ atc_property <- function(atc_code,
 #' abname(c("AMCL", "GENT"))
 #' # "amoxicillin and enzyme inhibitor" "gentamicin" 
 #'
-#' abname("AMCL", to = "trivial")
+#' abname("AMCL", to = "trivial_nl")
 #' # "Amoxicilline/clavulaanzuur"
 #'
 #' abname("AMCL", to = "atc")
@@ -210,7 +210,7 @@ abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ',
           select(to) %>%
           slice(1) %>%
           as.character()
-        if (j > 1 & to %in% c('official', 'trivial')) {
+        if (j > 1 & to %in% c('official', 'trivial_nl')) {
           drug.group[j] <- drug.group[j] %>% tolower()
         }
       }

R/data.R

@@ -26,7 +26,7 @@
 #'   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
 #'   \item{\code{official}}{Official name by the WHO, like \code{"amoxicillin and enzyme inhibitor"}}
 #'   \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
-#'   \item{\code{trivial}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
+#'   \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
 #'   \item{\code{oral_ddd}}{Daily Defined Dose (DDD) according to the WHO, oral treatment}
 #'   \item{\code{oral_units}}{Units of \code{ddd_units}}
 #'   \item{\code{iv_ddd}}{Daily Defined Dose (DDD) according to the WHO, parenteral treatment}

R/rsi_analysis.R

@@ -254,7 +254,8 @@ rsi <- function(ab1, ab2 = NA, interpretation = 'IR', minimum = 30, percent = FA
 #' @examples
 #' \dontrun{
 #' # use it directly:
-#' rsi_predict(tbl[which(first_isolate == TRUE & genus == "Haemophilus"),], col_ab = "amcl", coldate = "date")
+#' rsi_predict(tbl = tbl[which(first_isolate == TRUE & genus == "Haemophilus"),],
+#'             col_ab = "amcl", coldate = "date")
 #'   
 #' # or with dplyr so you can actually read it:
 #' library(dplyr)