diff --git a/DESCRIPTION b/DESCRIPTION index 0e542fcf..b867668a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9012 +Version: 1.8.2.9013 Date: 2022-10-10 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 71a1d94c..1fa982fa 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9012 +# AMR 1.8.2.9013 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/add_custom_antimicrobials.R b/R/add_custom_antimicrobials.R index 9c320f93..bd7a4051 100644 --- a/R/add_custom_antimicrobials.R +++ b/R/add_custom_antimicrobials.R @@ -27,9 +27,9 @@ # 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, although this requires to load the `AMR` package at every start-up: #' @@ -55,15 +55,17 @@ #' as.ab("test") #' ) #' -#' # now add 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") @@ -99,5 +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.") } diff --git a/man/add_custom_antimicrobials.Rd b/man/add_custom_antimicrobials.Rd index 36b1f450..bcfeed11 100644 --- a/man/add_custom_antimicrobials.Rd +++ b/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) @@ -13,7 +13,7 @@ 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, although this requires to load the \code{AMR} package at every start-up: @@ -38,15 +38,17 @@ suppressWarnings( as.ab("test") ) -# now add 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")