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set_mo_source

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dr. M.S. (Matthijs) Berends
2019-01-21 15:53:01 +01:00
parent c6c3088e9f
commit 46dcc7e2e8
36 changed files with 1134 additions and 261 deletions
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man/as.mo.Rd
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@ -7,7 +7,7 @@
\title{Transform to microorganism ID}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = NULL)
reference_df = get_mo_source())
is.mo(x)
}
@ -24,7 +24,7 @@ is.mo(x)
\item{allow_uncertain}{a logical to indicate whether the input should be checked for less possible results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid \code{mo} as found in the \code{\link{microorganisms}} data set.}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
}
\value{
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.