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(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

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dr. M.S. (Matthijs) Berends
2025-07-17 17:05:41 +02:00
parent 8dab0a3730
commit d94bdd2c6a
23 changed files with 237 additions and 164 deletions
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19
R/sir_calc.R
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@ -244,7 +244,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
translate_ab <- get_translate_ab(translate_ab)
data.bak <- data
# select only groups and antimicrobials
# select only groups and antibiotics
if (is_null_or_grouped_tbl(data)) {
data_has_groups <- TRUE
groups <- get_group_names(data)
@ -255,15 +255,14 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
}
data <- as.data.frame(data, stringsAsFactors = FALSE)
if (isTRUE(combine_SI)) {
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] && 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])
for (i in seq_len(ncol(data))) {
data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
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])
}
}
@ -364,7 +363,7 @@ 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
if (out$value[out$interpretation == "SDD"] > 0) {
if (any(out$value[out$interpretation == "SDD"] > 0, na.rm = TRUE)) {
out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R"), ordered = TRUE)
} else {
out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)