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new portion functions

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dr. M.S. (Matthijs) Berends
2018-08-10 15:01:05 +02:00
parent ae2433a020
commit 53fa198e35
19 changed files with 892 additions and 1140 deletions
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29
R/first_isolate.R
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@ -55,31 +55,32 @@
#' @return A vector to add to table, see Examples.
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @examples
#' # septic_patients is a dataset available in the AMR package
#' # septic_patients is a dataset available in the AMR package. It is true data.
#' ?septic_patients
#' my_patients <- septic_patients
#'
#' library(dplyr)
#' my_patients$first_isolate <- my_patients %>%
#' first_isolate(col_date = "date",
#' col_patient_id = "patient_id",
#' col_bactid = "bactid")
#' my_patients <- septic_patients %>%
#' mutate(first_isolate = first_isolate(.,
#' col_date = "date",
#' col_patient_id = "patient_id",
#' col_bactid = "bactid"))
#'
#' # Now let's see if first isolates matter:
#' A <- my_patients %>%
#' group_by(hospital_id) %>%
#' summarise(count = n_rsi(gent), # gentamicin
#' resistance = resistance(gent))
#' summarise(count = n_rsi(gent), # gentamicin availability
#' resistance = portion_IR(gent)) # gentamicin resistance
#'
#' B <- my_patients %>%
#' filter(first_isolate == TRUE) %>% # the 1st isolate filter
#' filter(first_isolate == TRUE) %>% # the 1st isolate filter
#' group_by(hospital_id) %>%
#' summarise(count = n_rsi(gent),
#' resistance = resistance(gent))
#' summarise(count = n_rsi(gent), # gentamicin availability
#' resistance = portion_IR(gent)) # gentamicin resistance
#'
#' # Have a look at A and B. B is more reliable because every isolate is
#' # counted once. Gentamicin resitance in hospital D appears to be 5%
#' # higher than originally thought.
#' # Have a look at A and B.
#' # B is more reliable because every isolate is only counted once.
#' # Gentamicin resitance in hospital D appears to be 5.4% higher than
#' # when you (erroneously) would have used all isolates!
#'
#' ## OTHER EXAMPLES:
#'