replaced bactid by mo

R/resistance_predict.R

@@ -65,13 +65,13 @@
 #' library(dplyr)
 #' septic_patients %>%
 #'   # get bacteria properties like genus and species
-#'   left_join_microorganisms("bactid") %>%
+#'   left_join_microorganisms("mo") %>%
 #'   # calculate first isolates
 #'   mutate(first_isolate =
 #'            first_isolate(.,
 #'                          "date",
 #'                          "patient_id",
-#'                          "bactid",
+#'                          "mo",
 #'                          col_specimen = NA,
 #'                          col_icu = NA)) %>%
 #'   # filter on first E. coli isolates
@@ -89,7 +89,7 @@
 #' if (!require(ggplot2)) {
 #'
 #'   data <- septic_patients %>%
-#'     filter(bactid == "ESCCOL") %>%
+#'     filter(mo == "ESCCOL") %>%
 #'     resistance_predict(col_ab = "amox",
 #'                       col_date = "date",
 #'                       info = FALSE,