(v0.7.1.9063) septic_patients -> example_isolates

R/first_isolate.R

@@ -79,12 +79,12 @@
 #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
-#' # See ?septic_patients.
+#' # `example_isolates` is a dataset available in the AMR package.
+#' # See ?example_isolates.
 #'
 #' library(dplyr)
 #' # Filter on first isolates:
-#' septic_patients %>%
+#' example_isolates %>%
 #'   mutate(first_isolate = first_isolate(.,
 #'                                        col_date = "date",
 #'                                        col_patient_id = "patient_id",
@@ -92,19 +92,19 @@
 #'   filter(first_isolate == TRUE)
 #'
 #' # Which can be shortened to:
-#' septic_patients %>%
+#' example_isolates %>%
 #'   filter_first_isolate()
 #' # or for first weighted isolates:
-#' septic_patients %>%
+#' example_isolates %>%
 #'   filter_first_weighted_isolate()
 #' 
 #' # Now let's see if first isolates matter:
-#' A <- septic_patients %>%
+#' A <- example_isolates %>%
 #'   group_by(hospital_id) %>%
 #'   summarise(count = n_rsi(GEN),            # gentamicin availability
 #'             resistance = portion_IR(GEN))  # gentamicin resistance
 #'
-#' B <- septic_patients %>%
+#' B <- example_isolates %>%
 #'   filter_first_weighted_isolate() %>%      # the 1st isolate filter
 #'   group_by(hospital_id) %>%
 #'   summarise(count = n_rsi(GEN),            # gentamicin availability