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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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18
R/sir_calc.R
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@@ -41,7 +41,7 @@ sir_calc <- function(...,
as_percent = FALSE,
only_all_tested = FALSE,
only_count = FALSE) {
meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1:5))
meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = seq_along(VALID_SIR_LEVELS), is_in = VALID_SIR_LEVELS)
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
meet_criteria(as_percent, allow_class = "logical", has_length = 1)
meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@@ -117,6 +117,8 @@ sir_calc <- function(...,
print_warning <- FALSE
ab_result <- as.sir(ab_result)
denominator_vals <- levels(ab_result)
denominator_vals <- denominator_vals[denominator_vals != "NI"]
if (is.data.frame(x)) {
sir_integrity_check <- character(0)
@@ -148,7 +150,7 @@ sir_calc <- function(...,
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)
other_values <- setdiff(c(NA, denominator_vals), 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)
}
@@ -165,7 +167,7 @@ sir_calc <- function(...,
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)
denominator <- sum(x %in% denominator_vals, na.rm = TRUE)
}
if (print_warning == TRUE) {
@@ -259,13 +261,13 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
for (i in seq_len(ncol(data))) {
# transform SIR columns
if (is.sir(data[, i, drop = TRUE])) {
data[, i] <- as.character(data[, i, drop = TRUE])
data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
data[which(data[, i, drop = TRUE] %in% c("S", "SDD", "WT")), i] <- "S"
data[which(data[, i, drop = TRUE] %in% c("R", "NWT", "NS")), i] <- "R"
if (isTRUE(combine_SI)) {
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])
data[which(data[, i, drop = TRUE] %in% c("I", "S")), i] <- "SI"
}
data[which(!data[, i, drop = TRUE] %in% c("S", "SI", "I", "R")), i] <- NA_character_
}
}