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