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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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12
R/custom_eucast_rules.R
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@@ -61,9 +61,9 @@
#'
#' ```r
#' df <- data.frame(mo = c("Escherichia coli", "Klebsiella pneumoniae"),
#' TZP = as.rsi("R"),
#' ampi = as.rsi("S"),
#' cipro = as.rsi("S"))
#' TZP = as.sir("R"),
#' ampi = as.sir("S"),
#' cipro = as.sir("S"))
#' df
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R S S
@@ -181,10 +181,10 @@ custom_eucast_rules <- function(...) {
result_value <- as.character(result)[[3]]
result_value[result_value == "NA"] <- NA
stop_ifnot(
result_value %in% c("R", "S", "I", NA),
"the resulting value of rule ", i, " must be either \"R\", \"S\", \"I\" or NA"
result_value %in% c("S", "I", "R", NA),
"the resulting value of rule ", i, " must be either \"S\", \"I\", \"R\" or NA"
)
result_value <- as.rsi(result_value)
result_value <- as.sir(result_value)
out[[i]]$result_group <- result_group
out[[i]]$result_value <- result_value