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dr. M.S. (Matthijs) Berends 2022-12-28 15:04:59 +01:00
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commit 61c0bdb7af
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2
DESCRIPTION
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@ -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)

2
NEWS.md
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@ -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!)*

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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")
#'

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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) {

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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"}
}
\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")