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(v1.6.0.9009) key_antibiotics update

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dr. M.S. (Matthijs) Berends
2021-04-23 16:13:26 +02:00
parent 70b803dbb6
commit 5f9e7bd3ee
20 changed files with 100 additions and 98 deletions
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2
man/first_isolate.Rd
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@ -81,7 +81,7 @@ filter_first_weighted_isolate(
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}
\item{include_unknown}{logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}

8
man/key_antibiotics.Rd
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@ -36,7 +36,9 @@ key_antibiotics_equal(
type = c("keyantibiotics", "points"),
ignore_I = TRUE,
points_threshold = 2,
info = FALSE
info = FALSE,
na.rm = TRUE,
...
)
}
\arguments{
@ -62,7 +64,9 @@ key_antibiotics_equal(
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{info}{unused - previously used to indicate whether a progress bar should print}
\item{na.rm}{a \link{logical} to indicate whether comparison with \code{NA} should return \code{FALSE} (defaults to \code{TRUE} for backwards compatibility)}
}
\description{
These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.