new EUCAST rules: clinical breakpoints

R/data.R

@@ -186,7 +186,7 @@
 #' Data set with 2000 blood culture isolates of septic patients
 #'
 #' An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
-#' @format A \code{\link{tibble}} with 2,000 observations and 49 variables:
+#' @format A \code{\link{data.frame}} with 2,000 observations and 49 variables:
 #' \describe{
 #'   \item{\code{date}}{date of receipt at the laboratory}
 #'   \item{\code{hospital_id}}{ID of the hospital, from A to D}
@@ -199,7 +199,6 @@
 #'   \item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
 #'   \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
 #' }
-# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
 #' @examples
 #' # ----------- #
 #' # PREPARATION #

R/mic.R

@@ -22,7 +22,7 @@
 #' @rdname as.mic
 #' @param x vector
 #' @param na.rm a logical indicating whether missing values should be removed
-#' @return Ordered factor with new class \code{mic} and new attribute \code{package}
+#' @return Ordered factor with new class \code{mic}
 #' @keywords mic
 #' @export
 #' @importFrom dplyr %>%
@@ -148,11 +148,8 @@ as.mic <- function(x, na.rm = FALSE) {
               list_missing, call. = FALSE)
     }
 
-    x <- factor(x = x,
-                levels = lvls,
-                ordered = TRUE)
+    x <- factor(x, levels = lvls, ordered = TRUE)
     class(x) <- c('mic', 'ordered', 'factor')
-    attr(x, 'package') <- 'AMR'
     x
   }
 }

R/rsi.R

@@ -22,7 +22,7 @@
 #' @rdname as.rsi
 #' @param x vector
 #' @details The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
-#' @return Ordered factor with new class \code{rsi} and new attribute \code{package}
+#' @return Ordered factor with new class \code{rsi}
 #' @keywords rsi
 #' @export
 #' @importFrom dplyr %>%
@@ -81,9 +81,8 @@ as.rsi <- function(x) {
               list_missing, call. = FALSE)
     }
 
-    x <- x %>% factor(levels = c("S", "I", "R"), ordered = TRUE)
+    x <- factor(x, levels = c("S", "I", "R"), ordered = TRUE)
     class(x) <- c('rsi', 'ordered', 'factor')
-    attr(x, 'package') <- 'AMR'
     x
   }
 }