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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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commit 9feef53bde
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R/first_isolate.R
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@ -41,7 +41,7 @@
#' @param include_unknown logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
#' @param ... parameters passed on to the [first_isolate()] function
#' @details **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 [[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 *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(ref)](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 *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
#'
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
#'