P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 05:21:50 +02:00
Code Releases Activity

new algorithm key abs

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-07-17 13:02:05 +02:00
parent 967ee86757
commit 5cb9c541f8
8 changed files with 315 additions and 230 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
man/first_isolate.Rd
View File

@ -62,13 +62,18 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
\details{
\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}.
\strong{DETERMINING WEIGHTED ISOLATES} \cr
\strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr
To determine weighted isolates, the difference between key antibiotics will be checked. Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. \cr
\strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr
To determine weighted isolates, difference between antimicrobial interpretations will be measured with points. A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate. This method is being used by the Infection Prevention department (Dr M. Lokate) of the University Medical Center Groningen (UMCG).
}
\section{Key antibiotics}{
There are two ways to determine whether isolates can be included as first \emph{weighted} isolates: \cr
\strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. \cr
\strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate.
}
\examples{
# septic_patients is a dataset available in the AMR package
?septic_patients
@ -120,6 +125,9 @@ tbl$first_resp_isolate_weighed <-
col_keyantibiotics = 'keyab')
}
}
\seealso{
\code{\link{keyantibiotics}}
}
\keyword{first}
\keyword{isolate}
\keyword{isolates}