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mirror of https://github.com/msberends/AMR.git synced 2025-07-09 02:03:04 +02:00

(v2.1.1.9191) unit tests

This commit is contained in:
2025-03-10 12:16:45 +01:00
parent a2c2be23c1
commit 32024e597a
10 changed files with 37 additions and 22 deletions

View File

@ -870,7 +870,9 @@ antibiogram.default <- function(x,
if (formatting_type == 20) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,", n_susceptible, "/", n_tested, ")"))
if (formatting_type == 21) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), ",N=", n_susceptible, "/", n_tested, ")"))
if (formatting_type == 22) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,N=", n_susceptible, "/", n_tested, ")"))
out$out_value[out$out_value %like% "^NA"] <- NA_character_
if (formatting_type >= 4) {
out$out_value[out$out_value %like% "^NA"] <- NA_character_
}
# transform names of antimicrobials
ab_naming_function <- function(x, t, l, s) {
@ -1260,6 +1262,15 @@ autoplot.antibiogram <- function(object, ...) {
if (!"mo" %in% colnames(df)) {
df$mo <- ""
}
groups <- colnames(df)[seq_len(which(colnames(df) %in% c("mo", "ab"))[1] - 1)]
group_name <- paste(groups, collapse = "/")
if (length(groups) > 1) {
df$syndromic_group <- apply(df[groups], 1, function(x) {
paste(stats::na.omit(x), collapse = "/")
})
} else if ("syndromic_group" %in% colnames(df)) {
group_name <- colnames(object)[1]
}
out <- ggplot2::ggplot(df,
mapping = ggplot2::aes(
x = ab,
@ -1272,7 +1283,6 @@ autoplot.antibiogram <- function(object, ...) {
)
) +
ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) +
ggplot2::facet_wrap("mo") +
ggplot2::geom_errorbar(
mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
position = ggplot2::position_dodge2(preserve = "single", width = 1)
@ -1281,11 +1291,15 @@ autoplot.antibiogram <- function(object, ...) {
y = ifelse(isTRUE(attributes(object)$combine_SI), "%SI", "%S"),
x = NULL,
fill = if ("syndromic_group" %in% colnames(df)) {
colnames(object)[1]
group_name
} else {
NULL
}
)
if (!all(df$mo == "", na.rm = TRUE)) {
out <- out +
ggplot2::facet_wrap("mo")
}
out
}