v1.7.0

R/aa_helper_functions.R

@@ -192,7 +192,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
 
   }
   # -- key antibiotics
-  if (type == "keyantibiotics") {
+  if (type %in% c("keyantibiotics", "keyantimicrobials")) {
     if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
       found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
     }
@@ -865,7 +865,7 @@ unique_call_id <- function(entire_session = FALSE) {
     # combination of environment ID (like "0x7fed4ee8c848")
     # and highest system call
     call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
-    if (call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
+    if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
       # unit tests will keep the same call and environment - give them a unique ID
       call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "")
     }
@@ -1122,7 +1122,7 @@ s3_register <- function(generic, class, method = NULL) {
 
 # works exactly like round(), but rounds `round2(44.55, 1)` to 44.6 instead of 44.5
 # and adds decimal zeroes until `digits` is reached when force_zero = TRUE
-round2 <- function(x, digits = 0, force_zero = TRUE) {
+round2 <- function(x, digits = 1, force_zero = TRUE) {
   x <- as.double(x)
   # https://stackoverflow.com/a/12688836/4575331
   val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
@@ -1174,7 +1174,7 @@ percentage <- function(x, digits = NULL, ...) {
     # round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%"
     x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100,
                           scientific = FALSE,
-                          digits = digits,
+                          digits = max(1, digits),
                           nsmall = digits,
                           ...)
     x_formatted <- paste0(x_formatted, "%")

R/ab.R

@@ -50,7 +50,7 @@
 #'
 #' WHONET 2019 software: \url{http://www.whonet.org/software.html}
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso 

R/data.R

@@ -71,7 +71,7 @@
 #'
 #' WHONET 2019 software: <http://www.whonet.org/software.html>
 #'
-#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <http://ec.europa.eu/health/documents/community-register/html/atc.htm>
+#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection WHOCC WHOCC
 #' @inheritSection AMR Read more on Our Website!

R/first_isolate.R

@@ -273,7 +273,7 @@ first_isolate <- function(x = NULL,
   # try to find columns based on type
   # -- mo
   if (is.null(col_mo)) {
-    col_mo <- search_type_in_df(x = x, type = "mo")
+    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
     stop_if(is.null(col_mo), "`col_mo` must be set")
   }
   
@@ -299,7 +299,7 @@ first_isolate <- function(x = NULL,
       x$keyantimicrobials <- all_antimicrobials(x, only_rsi_columns = FALSE)
       col_keyantimicrobials <- "keyantimicrobials"
     } else if (type == "keyantimicrobials" & is.null(col_keyantimicrobials)) {
-      col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantibiotics")
+      col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantimicrobials", info = info)
       if (is.null(col_keyantimicrobials)) {
         # still not found as a column, create it ourselves
         x$keyantimicrobials <- key_antimicrobials(x, only_rsi_columns = FALSE, col_mo = col_mo, ...)
@@ -310,7 +310,7 @@ first_isolate <- function(x = NULL,
   
   # -- date
   if (is.null(col_date)) {
-    col_date <- search_type_in_df(x = x, type = "date")
+    col_date <- search_type_in_df(x = x, type = "date", info = info)
     stop_if(is.null(col_date), "`col_date` must be set")
   }
   
@@ -322,14 +322,14 @@ first_isolate <- function(x = NULL,
       col_patient_id <- "patient_id"
       message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
     } else {
-      col_patient_id <- search_type_in_df(x = x, type = "patient_id")
+      col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
     }
     stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
   }
 
   # -- specimen
   if (is.null(col_specimen) & !is.null(specimen_group)) {
-    col_specimen <- search_type_in_df(x = x, type = "specimen")
+    col_specimen <- search_type_in_df(x = x, type = "specimen", info = info)
   }
   
   # check if columns exist

R/rsi.R

@@ -215,7 +215,6 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
             "ab",
             "Date",
             "POSIXt",
-            "rsi",
             "raw",
             "hms",
             "mic",

R/whocc.R

@@ -28,7 +28,7 @@
 #' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
 #' @section WHOCC:
 #' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
-#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<http://ec.europa.eu/health/documents/community-register/html/atc.htm>). 
+#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>). 
 #'
 #' These have become the gold standard for international drug utilisation monitoring and research.
 #'