fixes

R/globals.R

@@ -58,6 +58,7 @@ globalVariables(c(".",
                   "Pasted",
                   "patient_id",
                   "prevalence",
+                  "psae",
                   "R",
                   "ref",
                   "real_first_isolate",

R/mdro.R

@@ -329,11 +329,6 @@ MDRO <- function(tbl,
       & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
       & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
     ), 'MDRO'] <- 4
-    a <<- tbl[which(
-      tbl$family == 'Enterobacteriaceae'
-      & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
-      & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
-    ), ]
     tbl[which(
       tbl$family == 'Enterobacteriaceae'
       & rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1

R/resistance_predict.R

@@ -67,13 +67,7 @@
 #'   # get bacteria properties like genus and species
 #'   left_join_microorganisms("mo") %>%
 #'   # calculate first isolates
-#'   mutate(first_isolate =
-#'            first_isolate(.,
-#'                          "date",
-#'                          "patient_id",
-#'                          "mo",
-#'                          col_specimen = NA,
-#'                          col_icu = NA)) %>%
+#'   mutate(first_isolate = first_isolate(.)) %>%
 #'   # filter on first E. coli isolates
 #'   filter(genus == "Escherichia",
 #'          species == "coli",