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2026-04-30 17:52:11 +00:00
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commit 6fbd9e4b9f
89 changed files with 553 additions and 154 deletions
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reference/antibiogram.md
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@@ -19,7 +19,8 @@ antibiogram(x, antimicrobials = where(is.sir), mo_transform = "shortname",
ifelse(wisca, 14, 18)), col_mo = NULL, language = get_AMR_locale(),
minimum = 30, combine_SI = TRUE, sep = " + ", sort_columns = TRUE,
wisca = FALSE, simulations = 1000, conf_interval = 0.95,
interval_side = "two-tailed", info = interactive(), ...)
interval_side = "two-tailed", info = interactive(), parallel = FALSE,
...)
wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
syndromic_group = NULL, only_all_tested = FALSE, digits = 1,
@@ -27,7 +28,7 @@ wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
col_mo = NULL, language = get_AMR_locale(), combine_SI = TRUE,
sep = " + ", sort_columns = TRUE, simulations = 1000,
conf_interval = 0.95, interval_side = "two-tailed",
info = interactive(), ...)
info = interactive(), parallel = FALSE, ...)
retrieve_wisca_parameters(wisca_model, ...)
@@ -183,7 +184,7 @@ knit_print(x, italicise = TRUE,
- formatting_type:
Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the
Numeric value (1-22 for WISCA, 1-12 for non-WISCA) indicating how the
'cells' of the antibiogram table should be formatted. See *Details* \>
*Formatting Type* for a list of options.
@@ -251,6 +252,19 @@ knit_print(x, italicise = TRUE,
A [logical](https://rdrr.io/r/base/logical.html) to indicate info
should be printed - the default is `TRUE` only in interactive mode.
- parallel:
A [logical](https://rdrr.io/r/base/logical.html) to indicate if
parallel computing must be used, defaults to `FALSE`. Requires the
[`future.apply`](https://future.apply.futureverse.org/reference/future_lapply.html)
package. For WISCA, Monte Carlo simulations are distributed across
workers; for grouped antibiograms, each group is processed by a
separate worker. **A non-sequential
[`future::plan()`](https://future.futureverse.org/reference/plan.html)
must already be active before setting `parallel = TRUE`** – for
example, `future::plan(future::multisession)`. An error is thrown if
`parallel = TRUE` is used without a plan set by the user.
- ...:
When used in [R Markdown or