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improvement for forecasting resistance

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dr. M.S. (Matthijs) Berends
2018-07-26 16:30:42 +02:00
parent d9e204031d
commit 498e88b5cf
13 changed files with 438 additions and 145 deletions
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9
R/first_isolate.R
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@ -72,13 +72,13 @@
#' resistance = resistance(gent))
#'
#' B <- my_patients %>%
#' filter(first_isolate == TRUE) %>%
#' filter(first_isolate == TRUE) %>% # the 1st isolate filter
#' group_by(hospital_id) %>%
#' summarise(count = n_rsi(gent), # gentamicin
#' summarise(count = n_rsi(gent),
#' resistance = resistance(gent))
#'
#' # Have a look at A and B. B is more reliable because every isolate is
#' # counted once. Gentamicin resitance in hospital D seems to be 5%
#' # counted once. Gentamicin resitance in hospital D appears to be 5%
#' # higher than originally thought.
#'
#' ## OTHER EXAMPLES:
@ -171,8 +171,9 @@ first_isolate <- function(tbl,
if (!is.na(col_bactid)) {
if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
# warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
}
# join to microorganisms data set
tbl <- tbl %>% left_join_microorganisms(by = col_bactid)
col_genus <- "genus"
col_species <- "species"