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new SDD and N for as.sir()

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dr. M.S. (Matthijs) Berends
2024-05-20 15:27:04 +02:00
parent b68f47d985
commit 08a27922a8
28 changed files with 225 additions and 172 deletions
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16
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, 2, 3))
meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1:5))
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)
@ -249,7 +249,13 @@ 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])
data[, i] <- gsub("(I|S)", "SI", 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)
}
}
data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
}
}
}
@ -272,9 +278,9 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
for (i in seq_len(ncol(.data))) {
values <- .data[, i, drop = TRUE]
if (isTRUE(combine_SI)) {
values <- factor(values, levels = c("SI", "R"), ordered = TRUE)
values <- factor(values, levels = c("SI", "R", "N"), ordered = TRUE)
} else {
values <- factor(values, levels = c("S", "I", "R"), ordered = TRUE)
values <- factor(values, levels = c("S", "SDD", "I", "R", "N"), ordered = TRUE)
}
col_results <- as.data.frame(as.matrix(table(values)), stringsAsFactors = FALSE)
col_results$interpretation <- rownames(col_results)
@ -351,7 +357,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
} else {
# don't use as.sir() here, as it would add the class 'sir' and we would like
# the same data structure as output, regardless of input
out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)
out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R", "N"), ordered = TRUE)
}
if (data_has_groups) {