documentation fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9011
+Version: 1.8.2.9012
 Date: 2022-10-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9011
+# AMR 1.8.2.9012
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

R/ab_property.R

@@ -458,7 +458,7 @@ ab_validate <- function(x, property, ...) {
   } else {
     # try to catch an error when inputting an invalid argument
     # so the 'call.' can be set to FALSE
-    tryCatch(x[1L] %in% AMR::antibiotics[1, property, drop = TRUE],
+    tryCatch(x[1L] %in% AB_lookup[1, property, drop = TRUE],
       error = function(e) stop(e$message, call. = FALSE)
     )
 

R/add_custom_antimicrobials.R

@@ -31,9 +31,13 @@
 #' 
 #' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
 #' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
-#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, for example:
+#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, although this requires to load the `AMR` package at every start-up:
 #' 
 #' ```r
+#' # Open .Rprofile file
+#' utils::file.edit("~/.Rprofile")
+#'
+#' # Add custom antibiotic codes:
 #' library(AMR)
 #' add_custom_antimicrobials(
 #'   data.frame(ab = "TEST",
@@ -46,12 +50,12 @@
 #' @rdname add_custom_antimicrobials
 #' @export
 #' @examples 
-#' \donttest{
+#' # returns NA and throws a warning (which is now suppressed):
-#' 
+#' suppressWarnings(
-#' # returns NA and throws a warning:
 #'   as.ab("test")
+#' )
 #' 
-#' # now a manual entry - it will be considered by as.ab() and
+#' # now add a manual entry - it will be considered by as.ab() and
 #' # all ab_*() functions
 #' add_custom_antimicrobials(
 #'   data.frame(ab = "TEST",
@@ -63,7 +67,8 @@
 #' as.ab("test")
 #' ab_name("test")
 #' ab_group("test")
-#' }
+#' 
+#' ab_info("test")
 add_custom_antimicrobials <- function(x) {
   meet_criteria(x, allow_class = "data.frame")
   stop_ifnot(all(c("ab", "name") %in% colnames(x)),

man/add_custom_antimicrobials.Rd

@@ -16,9 +16,13 @@ clear_custom_antimicrobials()
 With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
 }
 \details{
-Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, for example:
+Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up:
 
-\if{html}{\out{<div class="sourceCode r">}}\preformatted{library(AMR)
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
+utils::file.edit("~/.Rprofile")
+
+# Add custom antibiotic codes:
+library(AMR)
 add_custom_antimicrobials(
   data.frame(ab = "TEST",
              name = "Test Antibiotic",
@@ -29,12 +33,12 @@ add_custom_antimicrobials(
 Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
 }
 \examples{
-\donttest{
+# returns NA and throws a warning (which is now suppressed):
+suppressWarnings(
+  as.ab("test")
+)
 
-# returns NA and throws a warning:
+# now add a manual entry - it will be considered by as.ab() and
-as.ab("test")
-
-# now a manual entry - it will be considered by as.ab() and
 # all ab_*() functions
 add_custom_antimicrobials(
   data.frame(ab = "TEST",
@@ -46,5 +50,6 @@ add_custom_antimicrobials(
 as.ab("test")
 ab_name("test")
 ab_group("test")
-}
+
+ab_info("test")
 }