diff --git a/DESCRIPTION b/DESCRIPTION index 391816c7..55d22b7d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9072 +Version: 1.8.2.9073 Date: 2022-12-28 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index fb432123..b91ba92f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9072 +# AMR 1.8.2.9073 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* diff --git a/R/add_custom_microorganisms.R b/R/add_custom_microorganisms.R index ecf27866..296011f5 100644 --- a/R/add_custom_microorganisms.R +++ b/R/add_custom_microorganisms.R @@ -29,7 +29,7 @@ #' Add Custom Microorganisms to This Package #' -#' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` package. +#' With [add_custom_microorganisms()] you can add your own custom microorganisms to the `AMR` package, such the non-taxonomic outcome of laboratory analysis. #' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "genus" and "species" #' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*. #' @@ -86,9 +86,10 @@ #' #' # E. asburiae/cloacae is now a new microorganism: #' mo_name("Enterobacter asburiae/cloacae") +#' #' # its code: #' as.mo("Enterobacter asburiae/cloacae") - +#' #' # all internal algorithms will work as well: #' mo_name("Ent asburia cloacae") #' diff --git a/R/mo.R b/R/mo.R index f1f52dca..b9173223 100755 --- a/R/mo.R +++ b/R/mo.R @@ -371,7 +371,7 @@ as.mo <- function(x, } msg <- c(msg, paste0( "Microorganism translation was uncertain for ", examples, - ". Run `mo_uncertainties()` to review ", plural[2], "." + ". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add own entries." )) for (m in msg) { diff --git a/man/add_custom_microorganisms.Rd b/man/add_custom_microorganisms.Rd index 7b764a76..891db595 100644 --- a/man/add_custom_microorganisms.Rd +++ b/man/add_custom_microorganisms.Rd @@ -13,7 +13,7 @@ clear_custom_microorganisms() \item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"} } \description{ -With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package. +With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms to the \code{AMR} package, such the non-taxonomic outcome of laboratory analysis. } \details{ This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}. @@ -67,8 +67,10 @@ add_custom_microorganisms( # E. asburiae/cloacae is now a new microorganism: mo_name("Enterobacter asburiae/cloacae") + # its code: as.mo("Enterobacter asburiae/cloacae") + # all internal algorithms will work as well: mo_name("Ent asburia cloacae")