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(v2.1.1.9268) WISCA vignette, antibiogram sorting, fix translations

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dr. M.S. (Matthijs) Berends
2025-05-01 14:38:51 +02:00
parent 5e6bbdf3d1
commit 2461631bce
16 changed files with 156 additions and 134 deletions
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13
man/antibiogram.Rd
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@ -23,16 +23,17 @@ antibiogram(x, antimicrobials = where(is.sir), mo_transform = "shortname",
only_all_tested = FALSE, digits = ifelse(wisca, 1, 0),
formatting_type = getOption("AMR_antibiogram_formatting_type",
ifelse(wisca, 14, 18)), col_mo = NULL, language = get_AMR_locale(),
minimum = 30, combine_SI = TRUE, sep = " + ", wisca = FALSE,
simulations = 1000, conf_interval = 0.95, interval_side = "two-tailed",
info = interactive(), ...)
minimum = 30, combine_SI = TRUE, sep = " + ", sort_columns = TRUE,
wisca = FALSE, simulations = 1000, conf_interval = 0.95,
interval_side = "two-tailed", info = interactive(), ...)
wisca(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, language = get_AMR_locale(), combine_SI = TRUE,
sep = " + ", simulations = 1000, conf_interval = 0.95,
interval_side = "two-tailed", info = interactive(), ...)
sep = " + ", sort_columns = TRUE, simulations = 1000,
conf_interval = 0.95, interval_side = "two-tailed",
info = interactive(), ...)
retrieve_wisca_parameters(wisca_model, ...)
@ -90,6 +91,8 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{sep}{A separating character for antimicrobial columns in combination antibiograms.}
\item{sort_columns}{A \link{logical} to indicate whether the antimicrobial columns must be sorted on name.}
\item{wisca}{A \link{logical} to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is \code{FALSE}). This will use a Bayesian decision model to estimate regimen coverage probabilities using \href{https://en.wikipedia.org/wiki/Monte_Carlo_method}{Monte Carlo simulations}. Set \code{simulations}, \code{conf_interval}, and \code{interval_side} to adjust.}
\item{simulations}{(for WISCA) a numerical value to set the number of Monte Carlo simulations.}