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guess_ab()

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dr. M.S. (Matthijs) Berends
2019-01-06 20:23:49 +01:00
parent 0205b6178d
commit bc15f660d6
11 changed files with 123 additions and 32 deletions
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3
man/AMR-deprecated.Rd
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@ -3,9 +3,12 @@
\name{AMR-deprecated}
\alias{AMR-deprecated}
\alias{ratio}
\alias{guess_mo}
\title{Deprecated functions}
\usage{
ratio(x, ratio)
guess_mo(...)
}
\description{
These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.

15
man/as.mo.Rd
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@ -4,16 +4,12 @@
\alias{as.mo}
\alias{mo}
\alias{is.mo}
\alias{guess_mo}
\title{Transform to microorganism ID}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = NULL)
is.mo(x)
guess_mo(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = TRUE, reference_df = NULL)
}
\arguments{
\item{x}{a character vector or a \code{data.frame} with one or two columns}
@ -77,8 +73,6 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
}
\code{guess_mo} is an alias of \code{as.mo}.
}
\section{Source}{
@ -124,12 +118,11 @@ as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
as.mo("GBS") # Group B Streptococci
# guess_mo is an alias of as.mo and works the same
guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`