git update

R/aa_helper_functions.R

@@ -324,7 +324,7 @@ warning_ <- function(...,
 # - adds the function name where the error was thrown
 # - wraps text to never break lines within words
 stop_ <- function(..., call = TRUE) {
-  msg <- word_wrap(..., add_fn = list(), as_note = FALSE)
+  msg <- paste0(c(...), collapse = "")
   if (!isFALSE(call)) {
     if (isTRUE(call)) {
       call <- as.character(sys.call(-1)[1])
@@ -334,6 +334,7 @@ stop_ <- function(..., call = TRUE) {
     }
     msg <- paste0("in ", call, "(): ", msg)
   }
+  msg <- word_wrap(msg, add_fn = list(), as_note = FALSE)
   stop(msg, call. = FALSE)
 }
 
@@ -409,6 +410,7 @@ dataset_UTF8_to_ASCII <- function(df) {
   df
 }
 
+# for eucast_rules() and mdro(), creates markdown output with URLs and names
 create_ab_documentation <- function(ab) {
   ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
   ab <- ab[order(ab_names)]

R/first_isolate.R

@@ -50,7 +50,7 @@
 #' All isolates with a microbial ID of `NA` will be excluded as first isolate.
 #' 
 #' ### Why this is so important
-#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(ref)](https:/pubmed.ncbi.nlm.nih.gov/17304462/). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
+#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(Hindler *et al.* 2007)](https://pubmed.ncbi.nlm.nih.gov/17304462/). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
 #'
 #' ### `filter_*()` shortcuts
 #'
@@ -60,6 +60,7 @@
 #' 
 #' ```
 #'   x[first_isolate(x, ...), ]
+#'   
 #'   x %>% filter(first_isolate(x, ...))
 #' ```
 #'