Update auto-generated Rd files after documentation rebuild

https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF

R/antibiogram.R

@@ -54,7 +54,7 @@
 #' @param add_total_n *(deprecated in favour of `formatting_type`)* A [logical] to indicate whether `n_tested` available numbers per pathogen should be added to the table (default is `TRUE`). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for *E. coli* 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when `wisca = TRUE`; in that case, use [retrieve_wisca_parameters()] to get the parameters used for WISCA.
 #' @param only_all_tested (for combination antibiograms): a [logical] to indicate that isolates must be tested for all antimicrobials, see *Details*.
 #' @param digits Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise.
-#' @param formatting_type 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.
+#' @param formatting_type 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.
 #' @param col_mo Column name of the names or codes of the microorganisms (see [as.mo()]) - the default is the first column of class [`mo`]. Values will be coerced using [as.mo()].
 #' @param language Language to translate text, which defaults to the system language (see [get_AMR_locale()]).
 #' @param minimum The minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
@@ -65,7 +65,7 @@
 #' @param simulations (for WISCA) a numerical value to set the number of Monte Carlo simulations.
 #' @param conf_interval A numerical value to set confidence interval (default is `0.95`).
 #' @param interval_side The side of the confidence interval, either `"two-tailed"` (default), `"left"` or `"right"`.
-#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. Requires the [`future.apply`][future.apply::future_lapply()] 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()] 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.
+#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. Requires the [`future.apply`][future.apply::future_lapply()] 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()] 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.
 #' @param info A [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode.
 #' @param object An [antibiogram()] object.
 #' @param ... When used in [R Markdown or Quarto][knitr::kable()]: arguments passed on to [knitr::kable()] (otherwise, has no use).
@@ -720,7 +720,7 @@ antibiogram.default <- function(x,
 
     unique_groups <- unique(wisca_parameters$group)
 
-    # parallel gate for WISCA — identical pattern to as.sir()
+    # parallel gate for WISCA - identical pattern to as.sir()
     if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
       if (isFALSE(parallel)) {
         message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")
@@ -787,7 +787,7 @@ antibiogram.default <- function(x,
         out_wisca$upper_ci[out_wisca$group == g] <- ci_vals[2]
       }
 
-      if (isTRUE(info)) message_(font_green_bg(" DONE "), as_note = FALSE)
+      if (isTRUE(info)) message_(font_green_bg(" DONE "), as_note = FALSE)
 
     } else {
       progress <- progress_ticker(
@@ -1071,7 +1071,7 @@ antibiogram.grouped_df <- function(x,
   groups <- attributes(x)$groups
   n_groups <- NROW(groups)
 
-  # parallel gate — identical pattern to as.sir()
+  # parallel gate - identical pattern to as.sir()
   if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
     if (isFALSE(parallel)) {
       message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")

man/antibiogram.Rd

@@ -25,7 +25,8 @@ 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,
@@ -33,7 +34,7 @@ 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, ...)
 
@@ -80,7 +81,7 @@ retrieve_wisca_parameters(wisca_model, ...)
 
 \item{digits}{Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise.}
 
-\item{formatting_type}{Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See \emph{Details} > \emph{Formatting Type} for a list of options.}
+\item{formatting_type}{Numeric value (1-22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See \emph{Details} > \emph{Formatting Type} for a list of options.}
 
 \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
@@ -104,6 +105,8 @@ retrieve_wisca_parameters(wisca_model, ...)
 
 \item{info}{A \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode.}
 
+\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. Requires the \code{\link[future.apply:future_lapply]{future.apply}} package. For WISCA, Monte Carlo simulations are distributed across workers; for grouped antibiograms, each group is processed by a separate worker. \strong{A non-sequential \code{\link[future:plan]{future::plan()}} must already be active before setting \code{parallel = TRUE}} -- for example, \code{future::plan(future::multisession)}. An error is thrown if \code{parallel = TRUE} is used without a plan set by the user.}
+
 \item{...}{When used in \link[knitr:kable]{R Markdown or Quarto}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use).}
 
 \item{wisca_model}{The outcome of \code{\link[=wisca]{wisca()}} or \code{\link[=antibiogram]{antibiogram(..., wisca = TRUE)}}.}

man/g.test.Rd

@@ -45,9 +45,8 @@ A list with class \code{"htest"} containing the following
   \item{residuals}{the Pearson residuals,
     \code{(observed - expected) / sqrt(expected)}.}
   \item{stdres}{standardized residuals,
-    \code{(observed - expected) / sqrt(V)}, where \code{V} is the
-    residual cell variance (Agresti, 2007, section 2.4.5
-    for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).}
+    \code{(observed - expected) / sqrt(V)}, where \code{V} is the residual cell variance (Agresti, 2007,
+    section 2.4.5 for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).}
 }
 \description{
 \code{\link[=g.test]{g.test()}} performs chi-squared contingency table tests and goodness-of-fit tests, just like \code{\link[=chisq.test]{chisq.test()}} but is more reliable (1). A \emph{G}-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a \strong{\emph{G}-test of goodness-of-fit}), or to see whether the proportions of one variable are different for different values of the other variable (called a \strong{\emph{G}-test of independence}).

man/pca.Rd

@@ -32,7 +32,7 @@ pca(x, ..., retx = TRUE, center = TRUE, scale. = TRUE, tol = NULL,
     standard deviations are less than or equal to \code{tol} times the
     standard deviation of the first component.)  With the default null
     setting, no components are omitted (unless \code{rank.} is specified
-    less than \code{min(dim(x))}.).  Other settings for \code{tol} could be
+    less than \code{min(dim(x))}.).  Other settings for tol could be
     \code{tol = 0} or \code{tol = sqrt(.Machine$double.eps)}, which
     would omit essentially constant components.}