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(v2.1.1.9233) chore: make all argument texts full sentences

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dr. M.S. (Matthijs) Berends
2025-03-31 14:53:24 +02:00
parent 63099cd81e
commit 1fdab84103
91 changed files with 720 additions and 701 deletions
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22
man/first_isolate.Rd
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@@ -28,15 +28,15 @@ filter_first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
\arguments{
\item{x}{A \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
\item{col_date}{Column name of the result date (or date that is was received on the lab) - the default is the first column with a date class}
\item{col_date}{Column name of the result date (or date that is was received on the lab) - the default is the first column with a date class.}
\item{col_patient_id}{Column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive)}
\item{col_patient_id}{Column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive).}
\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_testcode}{Column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (such as test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
\item{col_specimen}{Column name of the specimen type or group}
\item{col_specimen}{Column name of the specimen type or group.}
\item{col_icu}{Column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU). This can also be a \link{logical} vector with the same length as rows in \code{x}.}
@@ -44,27 +44,27 @@ filter_first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
\item{episode_days}{Episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see \emph{Source}.}
\item{testcodes_exclude}{A \link{character} vector with test codes that should be excluded (case-insensitive)}
\item{testcodes_exclude}{A \link{character} vector with test codes that should be excluded (case-insensitive).}
\item{icu_exclude}{A \link{logical} to indicate whether ICU isolates should be excluded (rows with value \code{TRUE} in the column set with \code{col_icu})}
\item{icu_exclude}{A \link{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{specimen_group}{Value in the column set with \code{col_specimen} to filter on.}
\item{type}{Type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}}
\item{type}{Type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}.}
\item{method}{The method to apply, either \code{"phenotype-based"}, \code{"episode-based"}, \code{"patient-based"} or \code{"isolate-based"} (can be abbreviated), see \emph{Details}. The default is \code{"phenotype-based"} if antimicrobial test results are present in the data, and \code{"episode-based"} otherwise.}
\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}.}
\item{points_threshold}{Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{points_threshold}{Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}.}
\item{info}{A \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode}
\item{info}{A \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode.}
\item{include_unknown}{A \link{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_sir}{A \link{logical} to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_sir = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \code{sir} and consequently requires transforming columns with antibiotic results using \code{\link[=as.sir]{as.sir()}} first.}
\item{...}{Arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, otherwise arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} (such as \code{universal}, \code{gram_negative}, \code{gram_positive})}
\item{...}{Arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, otherwise arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} (such as \code{universal}, \code{gram_negative}, \code{gram_positive}).}
}
\value{
A \link{logical} vector