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(v2.1.1.9234) fix CLSI

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dr. M.S. (Matthijs) Berends
2025-04-07 17:36:01 +01:00
parent 1fdab84103
commit a905303296
18 changed files with 117 additions and 235 deletions
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12
R/count.R
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@@ -146,9 +146,6 @@ count_susceptible <- function(..., only_all_tested = FALSE) {
#' @rdname count
#' @export
count_S <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_S", entire_session = TRUE)) {
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" and \"SDD\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = "S",
@@ -162,9 +159,6 @@ count_S <- function(..., only_all_tested = FALSE) {
#' @rdname count
#' @export
count_SI <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_SI", entire_session = TRUE)) {
message_("Note that `count_SI()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("S", "SDD", "I"),
@@ -178,9 +172,6 @@ count_SI <- function(..., only_all_tested = FALSE) {
#' @rdname count
#' @export
count_I <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_I", entire_session = TRUE)) {
message_("Note that `count_I()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD"),
@@ -194,9 +185,6 @@ count_I <- function(..., only_all_tested = FALSE) {
#' @rdname count
#' @export
count_IR <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" and \"SDD\" being resistant. This note will be shown once for this session.", as_note = FALSE)
}
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD", "R"),