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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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15
R/sir_calc.R
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@ -141,11 +141,17 @@ sir_calc <- function(...,
MARGIN = 1,
FUN = min
)
if ("SDD" %in% ab_result && "SDD" %in% y && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(!is.na(y) & y %in% as.double(ab_result), na.rm = TRUE)
denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
} else {
# may contain NAs in any column
other_values <- setdiff(c(NA, levels(ab_result)), ab_result)
if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(all(y %in% other_values) & anyNA(y))))
}
@ -155,6 +161,9 @@ sir_calc <- function(...,
x <- as.sir(x)
print_warning <- TRUE
}
if ("SDD" %in% ab_result && "SDD" %in% x && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(x %in% ab_result, na.rm = TRUE)
denominator <- sum(x %in% levels(ab_result), na.rm = TRUE)
}
@ -250,10 +259,8 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
for (i in seq_len(ncol(data))) {
if (is.sir(data[, i, drop = TRUE])) {
data[, i] <- as.character(data[, i, drop = TRUE])
if ("SDD" %in% data[, i, drop = TRUE]) {
if (message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
}
if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
}
data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
}