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(v1.5.0.9039) handle first isolates for missing antibiograms

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dr. M.S. (Matthijs) Berends
2021-03-08 02:38:32 +01:00
parent 461793dc34
commit a7c9b4c295
21 changed files with 79 additions and 62 deletions
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9
man/first_isolate.Rd
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@ -29,6 +29,7 @@ first_isolate(
points_threshold = 2,
info = interactive(),
include_unknown = FALSE,
include_untested_rsi = TRUE,
...
)
@ -70,19 +71,21 @@ filter_first_weighted_isolate(
\item{testcodes_exclude}{character vector with test codes that should be excluded (case-insensitive)}
\item{icu_exclude}{logical whether ICU isolates should be excluded (rows with value \code{TRUE} in the column set with \code{col_icu})}
\item{icu_exclude}{logical to indicate whether ICU isolates should be excluded (rows with value \code{TRUE} in the column set with \code{col_icu})}
\item{specimen_group}{value in the column set with \code{col_specimen} to filter on}
\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see \emph{Details}}
\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see \emph{Details}}
\item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see \emph{Details}}
\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}{print progress}
\item{include_unknown}{logical to determine 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.}
\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.}
\item{include_untested_rsi}{logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \verb{<rsi>} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.}
\item{...}{arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, or arguments passed on to \code{\link[=key_antibiotics]{key_antibiotics()}} when using \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}}}
}

2
man/key_antibiotics.Rd
View File

@ -58,7 +58,7 @@ key_antibiotics_equal(
\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see \emph{Details}}
\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see \emph{Details}}
\item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see \emph{Details}}
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}