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(v2.1.1.9141) new AMR selectors, eucast overwrite arg

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dr. M.S. (Matthijs) Berends
2025-02-07 18:01:22 +01:00
parent baea4323c7
commit 8ba2e4ed94
42 changed files with 282 additions and 197 deletions
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38
R/antibiogram.R
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@ -481,10 +481,10 @@ antibiogram.default <- function(x,
x$`.mo` <- x[, col_mo, drop = TRUE]
if (is.null(mo_transform)) {
# leave as is, no transformation
} else if (is.na(mo_transform)) {
x$`.mo` <- NA_character_
} else if (is.function(mo_transform)) {
x$`.mo` <- mo_transform(x$`.mo`)
} else if (is.na(mo_transform)) {
x$`.mo` <- NA_character_
} else if (mo_transform == "gramstain") {
x$`.mo` <- mo_gramstain(x$`.mo`, language = language)
} else if (mo_transform == "shortname") {
@ -602,8 +602,8 @@ antibiogram.default <- function(x,
on.exit(close(progress))
out$coverage <- NA_real_
out$lower <- NA_real_
out$upper <- NA_real_
out$lower_ci <- NA_real_
out$upper_ci <- NA_real_
out$gamma_posterior <- NA_real_
out$beta_posterior_1 <- NA_real_
out$beta_posterior_2 <- NA_real_
@ -657,8 +657,8 @@ antibiogram.default <- function(x,
coverage_ci <- unname(stats::quantile(coverage_simulations, probs = probs))
out$coverage[i] <- coverage_mean
out$lower[i] <- coverage_ci[1]
out$upper[i] <- coverage_ci[2]
out$lower_ci[i] <- coverage_ci[1]
out$upper_ci[i] <- coverage_ci[2]
}
# remove progress bar from console
close(progress)
@ -705,8 +705,8 @@ antibiogram.default <- function(x,
if (wisca == TRUE) {
long_numeric <- out %pm>%
pm_summarise(coverage = coverage,
lower_ci = lower,
upper_ci = upper,
lower_ci = lower_ci,
upper_ci = upper_ci,
n_tested = total,
n_total = total_rows,
n_susceptible = numerator,
@ -758,12 +758,12 @@ antibiogram.default <- function(x,
if (formatting_type == 10) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (", numerator, "/", total, ")"))
if (formatting_type == 11) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), " (N=", numerator, "/", total, ")"))
if (formatting_type == 12) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (N=", numerator, "/", total, ")"))
if (formatting_type == 13) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ")"))
if (formatting_type == 14) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%)"))
if (formatting_type == 15) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ",", total, ")"))
if (formatting_type == 16) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%,", total, ")"))
if (formatting_type == 17) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), ",N=", total, ")"))
if (formatting_type == 18) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower * 100, digits = digits), "-", round(upper * 100, digits = digits), "%,N=", total, ")"))
if (formatting_type == 13) 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), ")"))
if (formatting_type == 14) 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), "%)"))
if (formatting_type == 15) 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), ",", total, ")"))
if (formatting_type == 16) 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), "%,", total, ")"))
if (formatting_type == 17) 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=", total, ")"))
if (formatting_type == 18) 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=", total, ")"))
# transform names of antibiotics
ab_naming_function <- function(x, t, l, s) {
@ -1100,11 +1100,11 @@ plot.antibiogram <- function(x, ...) {
)
if (isTRUE(attributes(x)$wisca)) {
lower <- df_sub$lower * 100
upper <- df_sub$upper * 100
lower_ci <- df_sub$lower_ci * 100
upper_ci <- df_sub$upper_ci * 100
arrows(
x0 = bp, y0 = lower, # Start of error bar (lower bound)
x1 = bp, y1 = upper, # End of error bar (upper bound)
x0 = bp, y0 = lower_ci, # Start of error bar (lower bound)
x1 = bp, y1 = upper_ci, # End of error bar (upper bound)
angle = 90, code = 3, length = 0.05, col = "black"
)
}
@ -1151,7 +1151,7 @@ autoplot.antibiogram <- function(object, ...) {
)
if (isTRUE(attributes(object)$wisca)) {
out <- out +
ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower * 100, ymax = upper * 100),
ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
position = ggplot2::position_dodge2(preserve = "single"),
width = 0.5)
}