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(v0.8.0.9037) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 23:00:37 +01:00
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man/first_isolate.Rd
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@@ -94,7 +94,7 @@ 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 [\link{1}](https://www.ncbi.nlm.nih.gov/pubmed/17304462). 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}.
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}{(ref)}. 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.