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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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6
R/custom_antimicrobials.R
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@@ -112,8 +112,8 @@
#' # even antibiotic selectors work
#' x <- data.frame(
#' random_column = "some value",
#' coflu = as.rsi("S"),
#' ampicillin = as.rsi("R")
#' coflu = as.sir("S"),
#' ampicillin = as.sir("R")
#' )
#' x
#' x[, betalactams()]
@@ -165,7 +165,7 @@ add_custom_antimicrobials <- function(x) {
#' @export
clear_custom_antimicrobials <- function() {
n <- nrow(AMR_env$AB_lookup)
AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
n2 <- nrow(AMR_env$AB_lookup)
AMR_env$custom_ab_codes <- character(0)
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(AMR_env$ab_previously_coerced$ab %in% AMR_env$AB_lookup$ab), , drop = FALSE]