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https://github.com/msberends/AMR.git
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adding mo fixes
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@ -3,7 +3,7 @@
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\name{add_custom_antimicrobials}
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\alias{add_custom_antimicrobials}
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\alias{clear_custom_antimicrobials}
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\title{Add Custom Antimicrobials to This Package}
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\title{Add Custom Antimicrobials}
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\usage{
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add_custom_antimicrobials(x)
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@ -13,7 +13,7 @@ clear_custom_antimicrobials()
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\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
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}
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\description{
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug names and codes.
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}
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\details{
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\strong{Important:} Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited.
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@ -52,7 +52,7 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to
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\examples{
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\donttest{
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# returns NA and throws a warning (which is now suppressed):
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# returns NA and throws a warning (which is suppressed here):
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suppressWarnings(
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as.ab("testab")
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)
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@ -101,5 +101,5 @@ x[, betalactams()]
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}
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}
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\seealso{
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\code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} to add custom microorganisms to this package.
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\code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} to add custom microorganisms.
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}
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@ -3,7 +3,7 @@
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\name{add_custom_microorganisms}
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\alias{add_custom_microorganisms}
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\alias{clear_custom_microorganisms}
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\title{Add Custom Microorganisms to This Package}
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\title{Add Custom Microorganisms}
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\usage{
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add_custom_microorganisms(x)
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@ -13,7 +13,7 @@ clear_custom_microorganisms()
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\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing column "genus" (case-insensitive)}
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}
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\description{
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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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With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
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}
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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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@ -83,17 +83,25 @@ mo_info("Enterobacter asburiae/cloacae")
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# the function tries to be forgiving:
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add_custom_microorganisms(
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data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
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SPECIES = "SPECIES"))
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data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
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SPECIES = "SPECIES")
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)
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mo_name("ESCHERICHIA / KLEBSIELLA")
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mo_rank("ESCHERICHIA / KLEBSIELLA")
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# taxonomy still works, although a slashline genus was given as input:
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mo_family("Escherichia/Klebsiella")
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# for groups and complexes, set them as species or subspecies:
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add_custom_microorganisms(
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data.frame(genus = "Citrobacter", species = "freundii complex"))
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mo_name("C. freundii complex")
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mo_gramstain("C. freundii complex")
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data.frame(genus = "Citrobacter",
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species = c("freundii", "braakii complex"),
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subspecies = c("complex", ""))
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)
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mo_name(c("C. freundii complex", "C. braakii complex"))
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mo_species(c("C. freundii complex", "C. braakii complex"))
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mo_gramstain(c("C. freundii complex", "C. braakii complex"))
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}
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}
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\seealso{
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\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials to this package.
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\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials.
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}
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