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(v0.7.1.9031) include_unknown for first_isolate()

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dr. M.S. (Matthijs) Berends
2019-08-08 22:39:42 +02:00
parent 22a206ffd8
commit 1ce4b72dd2
17 changed files with 173 additions and 164 deletions
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8
man/first_isolate.Rd
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@ -14,7 +14,7 @@ first_isolate(x, col_date = NULL, col_patient_id = NULL,
col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE,
specimen_group = NULL, type = "keyantibiotics", ignore_I = TRUE,
points_threshold = 2, info = TRUE, ...)
points_threshold = 2, info = TRUE, include_unknown = FALSE, ...)
filter_first_isolate(x, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, ...)
@ -40,7 +40,7 @@ filter_first_weighted_isolate(x, col_date = NULL,
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.}
\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again}
\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 Source.}
\item{testcodes_exclude}{character vector with test codes that should be excluded (case-insensitive)}
@ -56,6 +56,8 @@ filter_first_weighted_isolate(x, col_date = NULL,
\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{...}{parameters passed on to the \code{first_isolate} function}
}
\value{
@ -68,6 +70,8 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
\strong{WHY THIS IS SO IMPORTANT} \cr
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{[1]}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
The functions \code{filter_first_isolate} and \code{filter_first_weighted_isolate} are helper functions to quickly filter on first isolates. The function \code{filter_first_isolate} is essentially equal to:
\preformatted{
x \%>\%