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https://github.com/msberends/AMR.git
synced 2025-07-10 03:02:05 +02:00
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
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@ -481,10 +481,10 @@ antibiogram.default <- function(x,
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x$`.mo` <- x[, col_mo, drop = TRUE]
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if (is.null(mo_transform)) {
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# leave as is, no transformation
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} else if (is.na(mo_transform)) {
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x$`.mo` <- NA_character_
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} else if (is.function(mo_transform)) {
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x$`.mo` <- mo_transform(x$`.mo`)
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} else if (is.na(mo_transform)) {
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x$`.mo` <- NA_character_
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} else if (mo_transform == "gramstain") {
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x$`.mo` <- mo_gramstain(x$`.mo`, language = language)
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} else if (mo_transform == "shortname") {
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@ -602,8 +602,8 @@ antibiogram.default <- function(x,
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on.exit(close(progress))
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out$coverage <- NA_real_
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out$lower <- NA_real_
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out$upper <- NA_real_
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out$lower_ci <- NA_real_
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out$upper_ci <- NA_real_
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out$gamma_posterior <- NA_real_
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out$beta_posterior_1 <- NA_real_
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out$beta_posterior_2 <- NA_real_
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@ -657,8 +657,8 @@ antibiogram.default <- function(x,
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coverage_ci <- unname(stats::quantile(coverage_simulations, probs = probs))
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out$coverage[i] <- coverage_mean
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out$lower[i] <- coverage_ci[1]
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out$upper[i] <- coverage_ci[2]
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out$lower_ci[i] <- coverage_ci[1]
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out$upper_ci[i] <- coverage_ci[2]
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}
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# remove progress bar from console
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close(progress)
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@ -705,8 +705,8 @@ antibiogram.default <- function(x,
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if (wisca == TRUE) {
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long_numeric <- out %pm>%
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pm_summarise(coverage = coverage,
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lower_ci = lower,
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upper_ci = upper,
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lower_ci = lower_ci,
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upper_ci = upper_ci,
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n_tested = total,
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n_total = total_rows,
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n_susceptible = numerator,
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@ -758,12 +758,12 @@ antibiogram.default <- function(x,
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if (formatting_type == 10) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (", numerator, "/", total, ")"))
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if (formatting_type == 11) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), " (N=", numerator, "/", total, ")"))
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if (formatting_type == 12) out <- out %pm>% pm_summarise(out_value = paste0(round((numerator / total) * 100, digits = digits), "% (N=", numerator, "/", total, ")"))
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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), ")"))
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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), "%)"))
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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, ")"))
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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, ")"))
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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, ")"))
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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, ")"))
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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), ")"))
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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), "%)"))
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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, ")"))
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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, ")"))
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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, ")"))
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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, ")"))
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# transform names of antibiotics
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ab_naming_function <- function(x, t, l, s) {
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@ -1100,11 +1100,11 @@ plot.antibiogram <- function(x, ...) {
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)
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if (isTRUE(attributes(x)$wisca)) {
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lower <- df_sub$lower * 100
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upper <- df_sub$upper * 100
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lower_ci <- df_sub$lower_ci * 100
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upper_ci <- df_sub$upper_ci * 100
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arrows(
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x0 = bp, y0 = lower, # Start of error bar (lower bound)
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x1 = bp, y1 = upper, # End of error bar (upper bound)
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x0 = bp, y0 = lower_ci, # Start of error bar (lower bound)
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x1 = bp, y1 = upper_ci, # End of error bar (upper bound)
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angle = 90, code = 3, length = 0.05, col = "black"
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)
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}
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@ -1151,7 +1151,7 @@ autoplot.antibiogram <- function(object, ...) {
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)
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if (isTRUE(attributes(object)$wisca)) {
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out <- out +
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ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower * 100, ymax = upper * 100),
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ggplot2::geom_errorbar(mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
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position = ggplot2::position_dodge2(preserve = "single"),
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width = 0.5)
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}
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