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dr. M.S. (Matthijs) Berends 2022-12-28 15:04:59 +01:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.2.9072 Version: 1.8.2.9073
Date: 2022-12-28 Date: 2022-12-28
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# 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!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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R/add_custom_microorganisms.R
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@ -29,7 +29,7 @@
#' Add Custom Microorganisms to This Package #' 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" #' @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*. #' @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: #' # E. asburiae/cloacae is now a new microorganism:
#' mo_name("Enterobacter asburiae/cloacae") #' mo_name("Enterobacter asburiae/cloacae")
#'
#' # its code: #' # its code:
#' as.mo("Enterobacter asburiae/cloacae") #' as.mo("Enterobacter asburiae/cloacae")
#'
#' # all internal algorithms will work as well: #' # all internal algorithms will work as well:
#' mo_name("Ent asburia cloacae") #' mo_name("Ent asburia cloacae")
#' #'

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R/mo.R
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@ -371,7 +371,7 @@ as.mo <- function(x,
} }
msg <- c(msg, paste0( msg <- c(msg, paste0(
"Microorganism translation was uncertain for ", examples, "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) { for (m in msg) {

4
man/add_custom_microorganisms.Rd
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@ -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"} \item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
} }
\description{ \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{ \details{
This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}. 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: # E. asburiae/cloacae is now a new microorganism:
mo_name("Enterobacter asburiae/cloacae") mo_name("Enterobacter asburiae/cloacae")
# its code: # its code:
as.mo("Enterobacter asburiae/cloacae") as.mo("Enterobacter asburiae/cloacae")
# all internal algorithms will work as well: # all internal algorithms will work as well:
mo_name("Ent asburia cloacae") mo_name("Ent asburia cloacae")