(v1.1.0.9017) as.ab() update, added ab_url()

R/ab.R

@@ -216,7 +216,7 @@ as.ab <- function(x, ...) {
     # replace multiple same characters to single one with '+', like "ll" -> "l+"
     x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
     # replace spaces and slashes with a possibility on both
-    x_spelling <- gsub("[ /]", "( |/)", x_spelling)
+    x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling)
   
     # try if name starts with it
     found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab

R/ab_property.R

@@ -31,6 +31,8 @@
 #' @param units a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples
 #' @param ... other parameters passed on to [as.ab()]
 #' @details All output will be [translate]d where possible.
+#' 
+#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.
 #' @inheritSection as.ab Source
 #' @rdname ab_property
 #' @name ab_property
@@ -52,6 +54,7 @@
 #' ab_group("AMX")      # "Beta-lactams/penicillins"
 #' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
 #' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
+#' ab_url("AMX")        # link to the official WHO page
 #'
 #' # smart lowercase tranformation
 #' ab_name(x = c("AMC", "PLB"))  # "Amoxicillin/clavulanic acid" "Polymyxin B"
@@ -183,6 +186,31 @@ ab_info <- function(x, language = get_locale(), ...) {
                                   units = ab_ddd(x, administration = "iv", units = TRUE))))
 }
 
+
+#' @rdname ab_property
+#' @export
+ab_url <- function(x, open = FALSE, ...) {
+  ab <- as.ab(x = x, ... = ...)
+  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no")
+  u[is.na(ab_atc(ab))] <- NA_character_
+  names(u) <- ab_name(ab)
+  
+  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))]
+  if (length(NAs) > 0) {
+    warning("No ATC code available for ", paste0(NAs, collapse = ", "), ".")
+  }
+  
+  if (open == TRUE) {
+    if (length(u) > 1 & !is.na(u[1L])) {
+      warning("only the first URL will be opened, as `browseURL()` only suports one string.")
+    }
+    if (!is.na(u[1L])) {
+      utils::browseURL(u[1L])
+    }
+  }
+  u
+}
+
 #' @rdname ab_property
 #' @export
 ab_property <- function(x, property = "name", language = get_locale(), ...) {
@@ -217,8 +245,7 @@ ab_validate <- function(x, property, ...) {
   } else if (property %like% "ddd") {
     return(as.double(x))
   } else {
-    # return "(input)" for NAs
-    x[is.na(x) & !is.na(x_bak)] <- paste0("(", x_bak[is.na(x) & !is.na(x_bak)], ")")
+    x[is.na(x) & !is.na(x_bak)] <- NA
     return(x)
   }
 }

R/lifecycle.R

@@ -20,37 +20,31 @@
 # ==================================================================== #
 
 ###############
-# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add another dependency for such an easy job?
+# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add a package dependency for such an easy job??
 ###############
 
 #' Lifecycles of functions in the `AMR` package
 #' @name lifecycle
 #' @rdname lifecycle
-#' @description Our functions are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
+#' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
 #' 
 #' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
-#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of our functions. 
+#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of the functions. 
 #' @section Experimental lifecycle:
 #' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN, since they have not yet matured enough.
+#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 #' @section Maturing lifecycle:
 #' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 #' @section Stable lifecycle:
 #' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 #' 
-#' If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+#' If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 #' @section Retired lifecycle:
 #' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
-#' @section Archived lifecycle:
-#' \if{html}{\figure{lifecycle_archived.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **archived**. The development of an archived function has ended, and it is no longer available in future package versions.
-#' @section Dormant lifecycle:
-#' \if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **dormant**. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
+#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
 #' @section Questioning lifecycle:
 #' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our `AMR` package at all.
+#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. This function might be no longer be optimal approach, or is it questionable whether this function should be in this `AMR` package at all.
 NULL