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(v2.1.1.9234) fix CLSI

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dr. M.S. (Matthijs) Berends
2025-04-07 17:36:01 +01:00
parent 1fdab84103
commit a905303296
18 changed files with 117 additions and 235 deletions
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21
R/antibiogram.R
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@ -609,7 +609,6 @@ antibiogram.default <- function(x,
pm_select(.mo, antimicrobials)
}
# get numbers of S, I, R (per group)
out <- out %pm>%
bug_drug_combinations(
@ -706,6 +705,7 @@ antibiogram.default <- function(x,
}
out_wisca$p_susceptible <- out_wisca$n_susceptible / out_wisca$n_tested
out_wisca$p_susceptible[is.nan(out_wisca$p_susceptible)] <- 0
if (isTRUE(has_syndromic_group)) {
out$group <- paste(out$syndromic_group, out$ab)
@ -721,10 +721,6 @@ antibiogram.default <- function(x,
out$beta_posterior_2 <- NA_real_
for (i in seq_len(NROW(out))) {
if (out$n_tested[i] == 0) {
next
}
out_current <- out[i, , drop = FALSE]
## calculate priors ----
@ -767,18 +763,19 @@ antibiogram.default <- function(x,
# simulate pathogen incidence
# = Dirichlet (Gamma) parameters
random_incidence <- stats::runif(1, min = 0, max = 1)
random_incidence <- stats::runif(n = 1, min = 0, max = 1)
simulated_incidence <- stats::qgamma(
p = random_incidence,
shape = params_current$gamma_posterior,
scale = 1
)
# normalise
simulated_incidence <- simulated_incidence / sum(simulated_incidence, na.rm = TRUE)
# simulate susceptibility
# = Beta parameters
random_susceptibity <- stats::runif(1, min = 0, max = 1)
random_susceptibity <- stats::runif(n = 1, min = 0, max = 1)
simulated_susceptibility <- stats::qbeta(
p = random_susceptibity,
shape1 = params_current$beta_posterior_1,
@ -804,7 +801,6 @@ antibiogram.default <- function(x,
}
# remove progress bar from console
close(progress)
# prepare for definitive output
out <- out_wisca
wisca_parameters <- wisca_parameters[, colnames(wisca_parameters)[!colnames(wisca_parameters) %in% c(levels(NA_sir_), "lower_ci", "upper_ci", "group")], drop = FALSE]
@ -836,7 +832,6 @@ antibiogram.default <- function(x,
}
}
out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
if (isFALSE(wisca)) {
out$coverage <- out$p_susceptible
}
@ -867,6 +862,7 @@ antibiogram.default <- function(x,
if (wisca == TRUE && !formatting_type %in% c(1, 2, 13, 14) && info == TRUE && message_not_thrown_before("antibiogram", wisca, formatting_type)) {
message_("Using WISCA with a `formatting_type` that includes the denominator is not useful")
}
out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
if (formatting_type == 1) out <- out %pm>% pm_summarise(out_value = round(coverage * 100, digits = digits))
if (formatting_type == 2) out <- out %pm>% pm_summarise(out_value = n_susceptible)
if (formatting_type == 3) out <- out %pm>% pm_summarise(out_value = n_tested)
@ -1148,6 +1144,7 @@ wisca <- function(x,
antimicrobials = where(is.sir),
ab_transform = "name",
syndromic_group = NULL,
only_all_tested = FALSE,
digits = 1,
formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
col_mo = NULL,
@ -1166,7 +1163,7 @@ wisca <- function(x,
mo_transform = NULL,
syndromic_group = syndromic_group,
add_total_n = FALSE,
only_all_tested = FALSE,
only_all_tested = only_all_tested,
digits = digits,
formatting_type = formatting_type,
col_mo = col_mo,
@ -1236,7 +1233,7 @@ plot.antibiogram <- function(x, ...) {
for (i in seq_along(mo_levels)) {
mo <- mo_levels[i]
df_sub <- df[df$mo == mo, , drop = FALSE]
df_sub <- df[as.character(df$mo) == mo, , drop = FALSE]
bp <- barplot(
height = df_sub$coverage * 100,
@ -1311,7 +1308,7 @@ autoplot.antibiogram <- function(object, ...) {
NULL
}
)
if (!all(df$mo == "", na.rm = TRUE)) {
if (!all(as.character(df$mo) == "", na.rm = TRUE)) {
out <- out +
ggplot2::facet_wrap("mo")
}