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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 12:21:53 +02:00

new antibiotics

This commit is contained in:
2019-05-10 16:44:59 +02:00
parent 73f1ee1159
commit 68cc7ef0d0
147 changed files with 6228 additions and 4187 deletions

View File

@ -44,55 +44,55 @@
#' ?septic_patients
#'
#' # Count resistant isolates
#' count_R(septic_patients$amox)
#' count_IR(septic_patients$amox)
#' count_R(septic_patients$AMX)
#' count_IR(septic_patients$AMX)
#'
#' # Or susceptible isolates
#' count_S(septic_patients$amox)
#' count_SI(septic_patients$amox)
#' count_S(septic_patients$AMX)
#' count_SI(septic_patients$AMX)
#'
#' # Count all available isolates
#' count_all(septic_patients$amox)
#' n_rsi(septic_patients$amox)
#' count_all(septic_patients$AMX)
#' n_rsi(septic_patients$AMX)
#'
#' # Since n_rsi counts available isolates, you can
#' # calculate back to count e.g. non-susceptible isolates.
#' # This results in the same:
#' count_IR(septic_patients$amox)
#' portion_IR(septic_patients$amox) * n_rsi(septic_patients$amox)
#' count_IR(septic_patients$AMX)
#' portion_IR(septic_patients$AMX) * n_rsi(septic_patients$AMX)
#'
#' library(dplyr)
#' septic_patients %>%
#' group_by(hospital_id) %>%
#' summarise(R = count_R(cipr),
#' I = count_I(cipr),
#' S = count_S(cipr),
#' n1 = count_all(cipr), # the actual total; sum of all three
#' n2 = n_rsi(cipr), # same - analogous to n_distinct
#' summarise(R = count_R(CIP),
#' I = count_I(CIP),
#' S = count_S(CIP),
#' n1 = count_all(CIP), # the actual total; sum of all three
#' n2 = n_rsi(CIP), # same - analogous to n_distinct
#' total = n()) # NOT the number of tested isolates!
#'
#' # Count co-resistance between amoxicillin/clav acid and gentamicin,
#' # so we can see that combination therapy does a lot more than mono therapy.
#' # Please mind that `portion_S` calculates percentages right away instead.
#' count_S(septic_patients$amcl) # S = 1342 (71.4%)
#' count_all(septic_patients$amcl) # n = 1879
#' count_S(septic_patients$AMC) # S = 1342 (71.4%)
#' count_all(septic_patients$AMC) # n = 1879
#'
#' count_S(septic_patients$gent) # S = 1372 (74.0%)
#' count_all(septic_patients$gent) # n = 1855
#' count_S(septic_patients$GEN) # S = 1372 (74.0%)
#' count_all(septic_patients$GEN) # n = 1855
#'
#' with(septic_patients,
#' count_S(amcl, gent)) # S = 1660 (92.3%)
#' count_S(AMC, GEN)) # S = 1660 (92.3%)
#' with(septic_patients, # n = 1798
#' n_rsi(amcl, gent))
#' n_rsi(AMC, GEN))
#'
#' # Get portions S/I/R immediately of all rsi columns
#' septic_patients %>%
#' select(amox, cipr) %>%
#' select(AMX, CIP) %>%
#' count_df(translate = FALSE)
#'
#' # It also supports grouping variables
#' septic_patients %>%
#' select(hospital_id, amox, cipr) %>%
#' select(hospital_id, AMX, CIP) %>%
#' group_by(hospital_id) %>%
#' count_df(translate = FALSE)
#'
@ -172,7 +172,8 @@ n_rsi <- function(...) {
#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
#' @export
count_df <- function(data,
translate_ab = getOption("get_antibiotic_names", "official"),
translate_ab = "name",
language = get_locale(),
combine_IR = FALSE) {
if (!"data.frame" %in% class(data)) {
@ -183,10 +184,9 @@ count_df <- function(data,
stop("No columns with class 'rsi' found. See ?as.rsi.")
}
if (as.character(translate_ab) == "TRUE") {
translate_ab <- "official"
if (as.character(translate_ab) %in% c("TRUE", "official")) {
translate_ab <- "name"
}
options(get_antibiotic_names = translate_ab)
resS <- summarise_if(.tbl = data,
.predicate = is.rsi,
@ -227,10 +227,7 @@ count_df <- function(data,
}
if (!translate_ab == FALSE) {
if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
stop("Parameter `translate_ab` does not occur in the `antibiotics` data set.", call. = FALSE)
}
res <- res %>% mutate(Antibiotic = abname(Antibiotic, from = "guess", to = translate_ab))
res <- res %>% mutate(Antibiotic = ab_property(Antibiotic, property = translate_ab, language = language))
}
res