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(v2.1.1.9143) unit tests
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@ -138,12 +138,15 @@ globalVariables(c(
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"atc_group1",
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"atc_group2",
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"base_ab",
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"beta_posterior_1",
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"beta_posterior_2",
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"ci_max",
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"ci_min",
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"clinical_breakpoints",
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"code",
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"cols",
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"count",
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"coverage",
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"data",
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"disk",
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"dosage",
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@ -152,6 +155,7 @@ globalVariables(c(
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"fullname",
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"fullname_lower",
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"g_species",
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"gamma_posterior",
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"genus",
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"gr",
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"group",
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@ -166,6 +170,7 @@ globalVariables(c(
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"language",
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"lookup",
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"lower",
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"lower_ci",
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"method",
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"mic ",
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"mic",
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@ -197,9 +202,11 @@ globalVariables(c(
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"species",
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"syndromic_group",
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"total",
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"total_rows",
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"txt",
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"type",
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"upper",
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"upper_ci",
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"uti_index",
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"value",
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"varname",
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@ -625,7 +625,7 @@ antibiogram.default <- function(x,
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# simulate pathogen incidence
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# = Dirichlet (Gamma) parameters
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random_incidence <- runif(1, min = 0, max = 1)
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random_incidence <- stats::runif(1, min = 0, max = 1)
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simulated_incidence <- stats::qgamma(
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p = random_incidence,
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shape = priors$gamma_posterior,
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@ -636,7 +636,7 @@ antibiogram.default <- function(x,
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# simulate susceptibility
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# = Beta parameters
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random_susceptibity <- runif(1, min = 0, max = 1)
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random_susceptibity <- stats::runif(1, min = 0, max = 1)
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simulated_susceptibility <- stats::qbeta(
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p = random_susceptibity,
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shape1 = priors$beta_posterior_1,
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@ -1009,7 +1009,7 @@ wisca <- function(x,
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}
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#' @export
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#' @param wisca_model the outcome of [wisca()] or [antibiogram(..., wisca = TRUE)]
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#' @param wisca_model the outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()]
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#' @rdname antibiogram
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retrieve_wisca_parameters <- function(wisca_model, ...) {
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stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use `wisca()` or `antibiogram(..., wisca = TRUE)` to create a WISCA model.")
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