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fix parallel

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dr. M.S. (Matthijs) Berends
2026-04-30 00:41:17 +02:00
parent 20c9447096
commit 49e440d037
14 changed files with 155 additions and 174 deletions
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26
man/amr-tidymodels.Rd
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@@ -31,24 +31,22 @@ step_sir_numeric(recipe, ..., role = NA, trained = FALSE, columns = NULL,
skip = FALSE, id = recipes::rand_id("sir_numeric"))
}
\arguments{
\item{recipe}{A recipe object. The step will be added to the
sequence of operations for this recipe.}
\item{recipe}{A recipe object. The step will be added to the sequence of
operations for this recipe.}
\item{...}{One or more selector functions to choose variables
for this step. See \code{\link[recipes:selections]{selections()}} for more details.}
\item{...}{One or more selector functions to choose variables for this step.
See \code{\link[recipes:selections]{selections()}} for more details.}
\item{role}{Not used by this step since no new variables are
created.}
\item{role}{Not used by this step since no new variables are created.}
\item{trained}{A logical to indicate if the quantities for
preprocessing have been estimated.}
\item{trained}{A logical to indicate if the quantities for preprocessing have
been estimated.}
\item{skip}{A logical. Should the step be skipped when the
recipe is baked by \code{\link[recipes:bake]{bake()}}? While all operations are baked
when \code{\link[recipes:prep]{prep()}} is run, some operations may not be able to be
conducted on new data (e.g. processing the outcome variable(s)).
Care should be taken when using \code{skip = TRUE} as it may affect
the computations for subsequent operations.}
\item{skip}{A logical. Should the step be skipped when the recipe is baked by
\code{\link[recipes:bake]{bake()}}? While all operations are baked when \code{\link[recipes:prep]{prep()}} is run, some
operations may not be able to be conducted on new data (e.g. processing the
outcome variable(s)). Care should be taken when using \code{skip = TRUE} as it
may affect the computations for subsequent operations.}
\item{id}{A character string that is unique to this step to identify it.}
}

2
man/antibiogram.Rd
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@@ -72,7 +72,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): \code{"ab"}, \code{"cid"}, \code{"name"}, \code{"group"}, \code{"atc"}, \code{"atc_group1"}, \code{"atc_group2"}, \code{"abbreviations"}, \code{"synonyms"}, \code{"oral_ddd"}, \code{"oral_units"}, \code{"iv_ddd"}, \code{"iv_units"}, or \code{"loinc"}. Can also be \code{NULL} to not transform the input.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}
\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}

4
man/as.sir.Rd
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@@ -73,7 +73,7 @@ is_sir_eligible(x, threshold = 0.05)
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
parallel = FALSE, max_cores = -1, conserve_capped_values = NULL)
parallel = FALSE, conserve_capped_values = NULL)
sir_interpretation_history(clean = FALSE)
}
@@ -152,8 +152,6 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain
\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. \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. Parallelism distributes columns (and optionally row batches) across workers; it is most beneficial when there are many antibiotic columns and a large number of rows.}
\item{max_cores}{Maximum number of workers to use when \code{parallel = TRUE}. Use a negative value to subtract that number from the available workers, e.g. a value of \code{-2} means at most \code{nbrOfWorkers() - 2} workers will be used. Defaults to \code{-1} (all but one worker). There will never be more workers used than there are antibiotic columns to analyse.}
\item{clean}{A \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results.}
}
\value{

2
man/custom_eucast_rules.Rd
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@@ -19,7 +19,7 @@ Define custom EUCAST rules for your organisation or specific analysis and use th
Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function.
\subsection{Basics}{
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
TZP == "R" ~ aminopenicillins == "R")

2
man/custom_mdro_guideline.Rd
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@@ -26,7 +26,7 @@ Define custom a MDRO guideline for your organisation or specific analysis and us
Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
\subsection{Basics}{
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
ERY == "R" & age > 60 ~ "Elderly Type B")

5
man/g.test.Rd
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@@ -45,8 +45,9 @@ 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}).

2
man/pca.Rd
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@@ -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 tol could be
less than \code{min(dim(x))}.). Other settings for \code{tol} could be
\code{tol = 0} or \code{tol = sqrt(.Machine$double.eps)}, which
would omit essentially constant components.}