doc fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9011
+Version: 1.8.2.9013
 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 1.8.2.9013
 
 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

@@ -27,13 +27,17 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Add Manual Antimicrobials to This Package
+#' Add Custom Antimicrobials to This Package
 #' 
-#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
+#' With [add_custom_antimicrobials()] you can add your own custom 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",
@@ -46,24 +50,27 @@
 #' @rdname add_custom_antimicrobials
 #' @export
 #' @examples 
-#' \donttest{
+#' # returns NA and throws a warning (which is now suppressed):
+#' suppressWarnings(
+#'   as.ab("test")
+#' )
 #' 
-#' # returns NA and throws a warning:
-#' as.ab("test")
-#' 
-#' # now a manual entry - it will be considered by as.ab() and
+#' # now add a custom entry - it will be considered by as.ab() and
 #' # all ab_*() functions
 #' add_custom_antimicrobials(
 #'   data.frame(ab = "TEST",
 #'              name = "Test Antibiotic",
+#'              # you can add any property present in the
+#'              # 'antibiotics' data set, such as 'group':
 #'              group = "Test Group")
 #' )
 #' 
-#' "test" is now a new antibiotic:
+#' # "test" is now a new antibiotic:
 #' 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)),
@@ -94,5 +101,5 @@ clear_custom_antimicrobials <- function() {
   assignInNamespace(x = "AB_lookup",
                     value = create_AB_lookup(),
                     ns = asNamespace("AMR"))
-  message_("Manual antimicrobials cleared.")
+  message_("Custom antimicrobials cleared.")
 }

man/add_custom_antimicrobials.Rd

@@ -3,7 +3,7 @@
 \name{add_custom_antimicrobials}
 \alias{add_custom_antimicrobials}
 \alias{clear_custom_antimicrobials}
-\title{Add Manual Antimicrobials to This Package}
+\title{Add Custom Antimicrobials to This Package}
 \usage{
 add_custom_antimicrobials(x)
 
@@ -13,12 +13,16 @@ clear_custom_antimicrobials()
 \item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
 }
 \description{
-With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
+With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom 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",
@@ -29,22 +33,25 @@ 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:
-as.ab("test")
-
-# now a manual entry - it will be considered by as.ab() and
+# now add a custom entry - it will be considered by as.ab() and
 # all ab_*() functions
 add_custom_antimicrobials(
   data.frame(ab = "TEST",
              name = "Test Antibiotic",
+             # you can add any property present in the
+             # 'antibiotics' data set, such as 'group':
              group = "Test Group")
 )
 
-"test" is now a new antibiotic:
+# "test" is now a new antibiotic:
 as.ab("test")
 ab_name("test")
 ab_group("test")
-}
+
+ab_info("test")
 }