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dr. M.S. (Matthijs) Berends
2022-12-28 15:04:59 +01:00
parent ba3b237bdf
commit 61c0bdb7af
5 changed files with 9 additions and 6 deletions
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5
R/add_custom_microorganisms.R
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@ -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")
#'

2
R/mo.R
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@ -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) {