fix clipboard on linux

R/data.R

@@ -42,7 +42,7 @@
 #' @seealso \code{\link{microorganisms}}
 # last two columns created with:
 # antibiotics %>%
-#   mutate(useful_gramnegative = 
+#   mutate(useful_gramnegative =
 #            if_else(
 #              atc_group1 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
 #                atc_group2 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
@@ -116,39 +116,39 @@
 #' # ----------- #
 #' # PREPARATION #
 #' # ----------- #
-#' 
+#'
 #' # Save this example dataset to an object, so we can edit it:
 #' my_data <- septic_patients
-#' 
+#'
 #' # load the dplyr package to make data science A LOT easier
 #' library(dplyr)
-#' 
+#'
 #' # Add first isolates to our dataset:
-#' my_data <- my_data %>% 
-#'   mutate(first_isolates = first_isolate(my_data, date, patient_id, bactid))
-#' 
+#' my_data <- my_data %>%
+#'   mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
+#'
 #' # -------- #
 #' # ANALYSIS #
 #' # -------- #
-#' 
-#' # 1. Get the amoxicillin resistance percentages 
+#'
+#' # 1. Get the amoxicillin resistance percentages
 #' #    of E. coli, divided by hospital:
-#' 
+#'
 #' my_data %>%
 #'   filter(bactid == "ESCCOL",
-#'          first_isolates == TRUE) %>% 
-#'   group_by(hospital_id) %>% 
+#'          first_isolates == TRUE) %>%
+#'   group_by(hospital_id) %>%
 #'   summarise(n = n(),
 #'             amoxicillin_resistance = rsi(amox))
-#'   
-#'   
-#' # 2. Get the amoxicillin/clavulanic acid resistance 
+#'
+#'
+#' # 2. Get the amoxicillin/clavulanic acid resistance
 #' #    percentages of E. coli, trend over the years:
-#' 
-#' my_data %>% 
+#'
+#' my_data %>%
 #'   filter(bactid == guess_bactid("E. coli"),
-#'          first_isolates == TRUE) %>% 
-#'   group_by(year = format(date, "%Y")) %>% 
+#'          first_isolates == TRUE) %>%
+#'   group_by(year = format(date, "%Y")) %>%
 #'   summarise(n = n(),
 #'             amoxclav_resistance = rsi(amcl, minimum = 20))
 "septic_patients"