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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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10
man/first_isolate.Rd
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@ -48,11 +48,11 @@ filter_first_isolate(
\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), defaults to 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, defaults to 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()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\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.}
@ -60,7 +60,7 @@ filter_first_isolate(
\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}.}
\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}
\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. The default is the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}
\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}.}
@ -78,7 +78,7 @@ filter_first_isolate(
\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, defaults to \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.}