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dr. M.S. (Matthijs) Berends
2020-11-28 22:15:44 +01:00
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R/first_isolate.R
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@ -50,7 +50,7 @@
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
#'
#' ### Why this is so important
#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(ref)](https:/pubmed.ncbi.nlm.nih.gov/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 [(Hindler *et al.* 2007)](https://pubmed.ncbi.nlm.nih.gov/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).
#'
#' ### `filter_*()` shortcuts
#'
@ -60,6 +60,7 @@
#'
#' ```
#' x[first_isolate(x, ...), ]
#'
#' x %>% filter(first_isolate(x, ...))
#' ```
#'