From 36b8ae98d30f819635aa0801e5dc7d784ff9cf7c Mon Sep 17 00:00:00 2001 From: Friedrich Pahlke Date: Tue, 7 Feb 2023 17:04:44 +0100 Subject: [PATCH 1/2] Man pages improved --- LICENSE | 165 ------------------ R/class_analysis_results.R | 1 + man/AnalysisResults_as.data.frame.Rd | 25 --- man/AnalysisResults_names.Rd | 22 --- man/AnalysisResults_summary.Rd | 64 ------- man/Dataset_print.Rd | 31 ---- man/Dataset_summary.Rd | 64 ------- man/FieldSet_names.Rd | 22 --- man/FieldSet_print.Rd | 22 --- man/FrameSet_as.matrix.Rd | 32 ---- man/ParameterSet_as.data.frame.Rd | 40 ----- man/ParameterSet_print.Rd | 25 --- man/ParameterSet_summary.Rd | 70 -------- ...AverageSampleNumberResult_as.data.frame.Rd | 46 ----- man/SimulationResults_names.Rd | 22 --- man/SimulationResults_print.Rd | 25 --- man/StageResults_as.data.frame.Rd | 41 ----- man/StageResults_names.Rd | 22 --- ...rialDesignCharacteristics_as.data.frame.Rd | 44 ----- man/TrialDesignPlan_as.data.frame.Rd | 44 ----- man/TrialDesignSet_as.data.frame.Rd | 55 ------ man/TrialDesignSet_length.Rd | 28 --- man/TrialDesignSet_names.Rd | 27 --- man/TrialDesign_as.data.frame.Rd | 44 ----- man/Trial_Design_Set_summary.Rd | 64 ------- man/as.data.frame.AnalysisResults.Rd | 4 + 26 files changed, 5 insertions(+), 1044 deletions(-) delete mode 100644 LICENSE delete mode 100644 man/AnalysisResults_as.data.frame.Rd delete mode 100644 man/AnalysisResults_names.Rd delete mode 100644 man/AnalysisResults_summary.Rd delete mode 100644 man/Dataset_print.Rd delete mode 100644 man/Dataset_summary.Rd delete mode 100644 man/FieldSet_names.Rd delete mode 100644 man/FieldSet_print.Rd delete mode 100644 man/FrameSet_as.matrix.Rd delete mode 100644 man/ParameterSet_as.data.frame.Rd delete mode 100644 man/ParameterSet_print.Rd delete mode 100644 man/ParameterSet_summary.Rd delete mode 100644 man/PowerAndAverageSampleNumberResult_as.data.frame.Rd delete mode 100644 man/SimulationResults_names.Rd delete mode 100644 man/SimulationResults_print.Rd delete mode 100644 man/StageResults_as.data.frame.Rd delete mode 100644 man/StageResults_names.Rd delete mode 100644 man/TrialDesignCharacteristics_as.data.frame.Rd delete mode 100644 man/TrialDesignPlan_as.data.frame.Rd delete mode 100644 man/TrialDesignSet_as.data.frame.Rd delete mode 100644 man/TrialDesignSet_length.Rd delete mode 100644 man/TrialDesignSet_names.Rd delete mode 100644 man/TrialDesign_as.data.frame.Rd delete mode 100644 man/Trial_Design_Set_summary.Rd diff --git a/LICENSE b/LICENSE deleted file mode 100644 index fc8a5de7..00000000 --- a/LICENSE +++ /dev/null @@ -1,165 +0,0 @@ - GNU LESSER GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - - This version of the GNU Lesser General Public License incorporates -the terms and conditions of version 3 of the GNU General Public -License, supplemented by the additional permissions listed below. - - 0. 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If the Library as you -received it does not specify a version number of the GNU Lesser -General Public License, you may choose any version of the GNU Lesser -General Public License ever published by the Free Software Foundation. - - If the Library as you received it specifies that a proxy can decide -whether future versions of the GNU Lesser General Public License shall -apply, that proxy's public statement of acceptance of any version is -permanent authorization for you to choose that version for the -Library. diff --git a/R/class_analysis_results.R b/R/class_analysis_results.R index bc8be0fa..3cd2d32d 100644 --- a/R/class_analysis_results.R +++ b/R/class_analysis_results.R @@ -991,6 +991,7 @@ summary.AnalysisResults <- function(object, ..., type = 1, digits = NA_integer_) #' Returns the \code{\link{AnalysisResults}} object as data frame. #' #' @param x An \code{\link{AnalysisResults}} object created by \code{\link[=getAnalysisResults]{getAnalysisResults()}}. +#' @inheritParams param_niceColumnNamesEnabled #' @inheritParams param_three_dots #' #' @details diff --git a/man/AnalysisResults_as.data.frame.Rd b/man/AnalysisResults_as.data.frame.Rd deleted file mode 100644 index 61d56c4f..00000000 --- a/man/AnalysisResults_as.data.frame.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_results.R -\name{AnalysisResults_as.data.frame} -\alias{AnalysisResults_as.data.frame} -\alias{as.data.frame.AnalysisResults} -\title{Coerce AnalysisResults to a Data Frame} -\usage{ -\method{as.data.frame}{AnalysisResults}(x, row.names = NULL, optional = FALSE, ...) -} -\arguments{ -\item{x}{An \code{\link{AnalysisResults}} object created by \code{\link{getAnalysisResults}}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{\link{AnalysisResults}} object as data frame. -} -\details{ -Coerces the analysis results to a data frame. -} -\keyword{internal} diff --git a/man/AnalysisResults_names.Rd b/man/AnalysisResults_names.Rd deleted file mode 100644 index 26f30044..00000000 --- a/man/AnalysisResults_names.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_results.R -\name{AnalysisResults_names} -\alias{AnalysisResults_names} -\alias{names.AnalysisResults} -\title{Names of a Analysis Results Object} -\usage{ -\method{names}{AnalysisResults}(x) -} -\arguments{ -\item{x}{An \code{\link{AnalysisResults}} object created by \code{\link{getAnalysisResults}}.} -} -\value{ -Returns a \code{\link[base]{character}} vector containing the names of the \code{\link{AnalysisResults}} object. -} -\description{ -Function to get the names of an \code{\link{AnalysisResults}} object. -} -\details{ -Returns the names of an analysis results that can be accessed by the user. -} -\keyword{internal} diff --git a/man/AnalysisResults_summary.Rd b/man/AnalysisResults_summary.Rd deleted file mode 100644 index e46eaf0b..00000000 --- a/man/AnalysisResults_summary.Rd +++ /dev/null @@ -1,64 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_results.R -\name{AnalysisResults_summary} -\alias{AnalysisResults_summary} -\alias{summary.AnalysisResults} -\title{Analysis Results Summary} -\usage{ -\method{summary}{AnalysisResults}(object, ..., type = 1, digits = NA_integer_) -} -\arguments{ -\item{object}{An \code{\link{AnalysisResults}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{digits}{Defines how many digits are to be used for numeric values.} -} -\value{ -Returns a \code{\link{SummaryFactory}} object. -The following generics (R generic functions) are available for this result object: -\itemize{ - \item \code{\link[=names.FieldSet]{names}} to obtain the field names, - \item \code{\link[=print.FieldSet]{print}} to print the object -} -} -\description{ -Displays a summary of \code{\link{AnalysisResults}} object. -} -\details{ -Summarizes the parameters and results of an analysis results object. -} -\section{Summary options}{ - -The following options can be set globally: -\enumerate{ - \item \code{rpact.summary.output.size}: one of \code{c("small", "medium", "large")}; - defines how many details will be included into the summary; - default is \code{"large"}, i.e., all available details are displayed. - \item \code{rpact.summary.justify}: one of \code{c("right", "left", "centre")}; - shall the values be right-justified (the default), left-justified or centered. - \item \code{rpact.summary.width}: defines the maximum number of characters to be used per line (default is \code{83}). - \item \code{rpact.summary.intervalFormat}: defines how intervals will be displayed in the summary, - default is \code{"[\%s; \%s]"}. - \item \code{rpact.summary.digits}: defines how many digits are to be used for numeric values (default is \code{3}). - \item \code{rpact.summary.digits.probs}: defines how many digits are to be used for numeric values - (default is one more than value of \code{rpact.summary.digits}, i.e., \code{4}). - \item \code{rpact.summary.trim.zeroes}: if \code{TRUE} (default) zeroes will always displayed as "0", - e.g. "0.000" will become "0". -} -Example: \code{options("rpact.summary.intervalFormat" = "\%s - \%s")} -} - -\section{How to get help for generic functions}{ - -Click on the link of a generic in the list above to go directly to the help documentation of -the \code{rpact} specific implementation of the generic. -Note that you can use the R function \code{\link[utils]{methods}} to get all the methods of a generic and -to identify the object specific name of it, e.g., -use \code{methods("plot")} to get all the methods for the \code{plot} generic. -There you can find, e.g., \code{plot.AnalysisResults} and -obtain the specific help documentation linked above by typing \code{?plot.AnalysisResults}. -} - -\keyword{internal} diff --git a/man/Dataset_print.Rd b/man/Dataset_print.Rd deleted file mode 100644 index eac4898a..00000000 --- a/man/Dataset_print.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_dataset.R -\name{Dataset_print} -\alias{Dataset_print} -\alias{print.Dataset} -\title{Print Dataset Values} -\usage{ -\method{print}{Dataset}( - x, - ..., - markdown = FALSE, - output = c("list", "long", "wide", "r", "rComplete") -) -} -\arguments{ -\item{x}{A \code{\link{Dataset}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{markdown}{If \code{TRUE}, the output will be created in Markdown.} - -\item{output}{A character defining the output type, default is "list".} -} -\description{ -\code{print} prints its \code{\link{Dataset}} argument and returns it invisibly (via \code{invisible(x)}). -} -\details{ -Prints the dataset. -} -\keyword{internal} diff --git a/man/Dataset_summary.Rd b/man/Dataset_summary.Rd deleted file mode 100644 index a964e452..00000000 --- a/man/Dataset_summary.Rd +++ /dev/null @@ -1,64 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_dataset.R -\name{Dataset_summary} -\alias{Dataset_summary} -\alias{summary.Dataset} -\title{Dataset Summary} -\usage{ -\method{summary}{Dataset}(object, ..., type = 1, digits = NA_integer_) -} -\arguments{ -\item{object}{A \code{\link{Dataset}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{digits}{Defines how many digits are to be used for numeric values.} -} -\value{ -Returns a \code{\link{SummaryFactory}} object. -The following generics (R generic functions) are available for this result object: -\itemize{ - \item \code{\link[=names.FieldSet]{names}} to obtain the field names, - \item \code{\link[=print.FieldSet]{print}} to print the object -} -} -\description{ -Displays a summary of \code{\link{Dataset}} object. -} -\details{ -Summarizes the parameters and results of a dataset. -} -\section{Summary options}{ - -The following options can be set globally: -\enumerate{ - \item \code{rpact.summary.output.size}: one of \code{c("small", "medium", "large")}; - defines how many details will be included into the summary; - default is \code{"large"}, i.e., all available details are displayed. - \item \code{rpact.summary.justify}: one of \code{c("right", "left", "centre")}; - shall the values be right-justified (the default), left-justified or centered. - \item \code{rpact.summary.width}: defines the maximum number of characters to be used per line (default is \code{83}). - \item \code{rpact.summary.intervalFormat}: defines how intervals will be displayed in the summary, - default is \code{"[\%s; \%s]"}. - \item \code{rpact.summary.digits}: defines how many digits are to be used for numeric values (default is \code{3}). - \item \code{rpact.summary.digits.probs}: defines how many digits are to be used for numeric values - (default is one more than value of \code{rpact.summary.digits}, i.e., \code{4}). - \item \code{rpact.summary.trim.zeroes}: if \code{TRUE} (default) zeroes will always displayed as "0", - e.g. "0.000" will become "0". -} -Example: \code{options("rpact.summary.intervalFormat" = "\%s - \%s")} -} - -\section{How to get help for generic functions}{ - -Click on the link of a generic in the list above to go directly to the help documentation of -the \code{rpact} specific implementation of the generic. -Note that you can use the R function \code{\link[utils]{methods}} to get all the methods of a generic and -to identify the object specific name of it, e.g., -use \code{methods("plot")} to get all the methods for the \code{plot} generic. -There you can find, e.g., \code{plot.AnalysisResults} and -obtain the specific help documentation linked above by typing \code{?plot.AnalysisResults}. -} - -\keyword{internal} diff --git a/man/FieldSet_names.Rd b/man/FieldSet_names.Rd deleted file mode 100644 index 74652671..00000000 --- a/man/FieldSet_names.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{FieldSet_names} -\alias{FieldSet_names} -\alias{names.FieldSet} -\title{Names of a Field Set Object} -\usage{ -\method{names}{FieldSet}(x) -} -\arguments{ -\item{x}{A \code{\link{FieldSet}} object.} -} -\value{ -Returns a \code{\link[base]{character}} vector containing the names of the \code{\link{AnalysisResults}} object. -} -\description{ -Function to get the names of a \code{\link{FieldSet}} object. -} -\details{ -Returns the names of a field set that can be accessed by the user. -} -\keyword{internal} diff --git a/man/FieldSet_print.Rd b/man/FieldSet_print.Rd deleted file mode 100644 index 95105b1b..00000000 --- a/man/FieldSet_print.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{FieldSet_print} -\alias{FieldSet_print} -\alias{print.FieldSet} -\title{Print Field Set Values} -\usage{ -\method{print}{FieldSet}(x, ...) -} -\arguments{ -\item{x}{A \code{\link{FieldSet}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\description{ -\code{print} prints its \code{\link{FieldSet}} argument and returns it invisibly (via \code{invisible(x)}). -} -\details{ -Prints the field set. -} -\keyword{internal} diff --git a/man/FrameSet_as.matrix.Rd b/man/FrameSet_as.matrix.Rd deleted file mode 100644 index 12dc70ce..00000000 --- a/man/FrameSet_as.matrix.Rd +++ /dev/null @@ -1,32 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{FrameSet_as.matrix} -\alias{FrameSet_as.matrix} -\alias{as.matrix.FieldSet} -\title{Coerce Frame Set to a Matrix} -\usage{ -\method{as.matrix}{FieldSet}(x, ..., enforceRowNames = TRUE, niceColumnNamesEnabled = TRUE) -} -\arguments{ -\item{x}{A \code{\link{FieldSet}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{enforceRowNames}{If \code{TRUE}, row names will be created -depending on the object type, default is \code{TRUE}.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} -} -\value{ -Returns a \code{\link[base]{matrix}}. -} -\description{ -Returns the \code{FrameSet} as matrix. -} -\details{ -Coerces the frame set to a matrix. -} -\keyword{internal} diff --git a/man/ParameterSet_as.data.frame.Rd b/man/ParameterSet_as.data.frame.Rd deleted file mode 100644 index 66465d3c..00000000 --- a/man/ParameterSet_as.data.frame.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{ParameterSet_as.data.frame} -\alias{ParameterSet_as.data.frame} -\alias{as.data.frame.ParameterSet} -\title{Coerce Parameter Set to a Data Frame} -\usage{ -\method{as.data.frame}{ParameterSet}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - ... -) -} -\arguments{ -\item{x}{A \code{\link{FieldSet}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{ParameterSet} as data frame. -} -\details{ -Coerces the parameter set to a data frame. -} -\keyword{internal} diff --git a/man/ParameterSet_print.Rd b/man/ParameterSet_print.Rd deleted file mode 100644 index 1e77d6cb..00000000 --- a/man/ParameterSet_print.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{ParameterSet_print} -\alias{ParameterSet_print} -\alias{print.ParameterSet} -\title{Print Parameter Set Values} -\usage{ -\method{print}{ParameterSet}(x, ..., markdown = FALSE) -} -\arguments{ -\item{x}{The \code{\link{ParameterSet}} object to print.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{markdown}{If \code{TRUE}, the object \code{x} will be printed using markdown syntax; -normal representation will be used otherwise (default is \code{FALSE})} -} -\description{ -\code{print} prints its \code{ParameterSet} argument and returns it invisibly (via \code{invisible(x)}). -} -\details{ -Prints the parameters and results of a parameter set. -} -\keyword{internal} diff --git a/man/ParameterSet_summary.Rd b/man/ParameterSet_summary.Rd deleted file mode 100644 index b13e0f2c..00000000 --- a/man/ParameterSet_summary.Rd +++ /dev/null @@ -1,70 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_core_parameter_set.R -\name{ParameterSet_summary} -\alias{ParameterSet_summary} -\alias{summary.ParameterSet} -\title{Parameter Set Summary} -\usage{ -\method{summary}{ParameterSet}( - object, - ..., - type = 1, - digits = NA_integer_, - output = c("all", "title", "overview", "body") -) -} -\arguments{ -\item{object}{A \code{\link{ParameterSet}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{digits}{Defines how many digits are to be used for numeric values.} -} -\value{ -Returns a \code{\link{SummaryFactory}} object. -The following generics (R generic functions) are available for this result object: -\itemize{ - \item \code{\link[=names.FieldSet]{names}} to obtain the field names, - \item \code{\link[=print.FieldSet]{print}} to print the object -} -} -\description{ -Displays a summary of \code{\link{ParameterSet}} object. -} -\details{ -Summarizes the parameters and results of a parameter set. -} -\section{Summary options}{ - -The following options can be set globally: -\enumerate{ - \item \code{rpact.summary.output.size}: one of \code{c("small", "medium", "large")}; - defines how many details will be included into the summary; - default is \code{"large"}, i.e., all available details are displayed. - \item \code{rpact.summary.justify}: one of \code{c("right", "left", "centre")}; - shall the values be right-justified (the default), left-justified or centered. - \item \code{rpact.summary.width}: defines the maximum number of characters to be used per line (default is \code{83}). - \item \code{rpact.summary.intervalFormat}: defines how intervals will be displayed in the summary, - default is \code{"[\%s; \%s]"}. - \item \code{rpact.summary.digits}: defines how many digits are to be used for numeric values (default is \code{3}). - \item \code{rpact.summary.digits.probs}: defines how many digits are to be used for numeric values - (default is one more than value of \code{rpact.summary.digits}, i.e., \code{4}). - \item \code{rpact.summary.trim.zeroes}: if \code{TRUE} (default) zeroes will always displayed as "0", - e.g. "0.000" will become "0". -} -Example: \code{options("rpact.summary.intervalFormat" = "\%s - \%s")} -} - -\section{How to get help for generic functions}{ - -Click on the link of a generic in the list above to go directly to the help documentation of -the \code{rpact} specific implementation of the generic. -Note that you can use the R function \code{\link[utils]{methods}} to get all the methods of a generic and -to identify the object specific name of it, e.g., -use \code{methods("plot")} to get all the methods for the \code{plot} generic. -There you can find, e.g., \code{plot.AnalysisResults} and -obtain the specific help documentation linked above by typing \code{?plot.AnalysisResults}. -} - -\keyword{internal} diff --git a/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd b/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd deleted file mode 100644 index 09f3c76f..00000000 --- a/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_power_and_asn.R -\name{PowerAndAverageSampleNumberResult_as.data.frame} -\alias{PowerAndAverageSampleNumberResult_as.data.frame} -\alias{as.data.frame.PowerAndAverageSampleNumberResult} -\title{Coerce Power And Average Sample Number Result to a Data Frame} -\usage{ -\method{as.data.frame}{PowerAndAverageSampleNumberResult}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - ... -) -} -\arguments{ -\item{x}{A \code{\link{PowerAndAverageSampleNumberResult}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{\link{PowerAndAverageSampleNumberResult}} as data frame. -} -\details{ -Coerces the \code{\link{PowerAndAverageSampleNumberResult}} object to a data frame. -} -\examples{ -data <- as.data.frame(getPowerAndAverageSampleNumber(getDesignGroupSequential())) -head(data) -dim(data) - -} -\keyword{internal} diff --git a/man/SimulationResults_names.Rd b/man/SimulationResults_names.Rd deleted file mode 100644 index 11096a87..00000000 --- a/man/SimulationResults_names.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_simulation_results.R -\name{SimulationResults_names} -\alias{SimulationResults_names} -\alias{names.SimulationResults} -\title{Names of a Simulation Results Object} -\usage{ -\method{names}{SimulationResults}(x) -} -\arguments{ -\item{x}{A \code{\link{SimulationResults}} object created by \code{getSimulationResults[MultiArm/Enrichment][Means/Rates/Survival]}.} -} -\value{ -Returns a \code{\link[base]{character}} vector containing the names of the \code{\link{AnalysisResults}} object. -} -\description{ -Function to get the names of a \code{\link{SimulationResults}} object. -} -\details{ -Returns the names of a simulation results that can be accessed by the user. -} -\keyword{internal} diff --git a/man/SimulationResults_print.Rd b/man/SimulationResults_print.Rd deleted file mode 100644 index 49ddbf19..00000000 --- a/man/SimulationResults_print.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_simulation_results.R -\name{SimulationResults_print} -\alias{SimulationResults_print} -\alias{print.SimulationResults} -\title{Print Simulation Results} -\usage{ -\method{print}{SimulationResults}(x, ..., showStatistics = FALSE, markdown = FALSE) -} -\arguments{ -\item{x}{The \code{\link{SimulationResults}} object to print.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{markdown}{If \code{TRUE}, the object \code{x} will be printed using markdown syntax; -normal representation will be used otherwise (default is \code{FALSE})} -} -\description{ -\code{print} prints its \code{SimulationResults} argument and returns it invisibly (via \code{invisible(x)}). -} -\details{ -Prints the parameters and results of an \code{SimulationResults} object. -} -\keyword{internal} diff --git a/man/StageResults_as.data.frame.Rd b/man/StageResults_as.data.frame.Rd deleted file mode 100644 index 70d38343..00000000 --- a/man/StageResults_as.data.frame.Rd +++ /dev/null @@ -1,41 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_stage_results.R -\name{StageResults_as.data.frame} -\alias{StageResults_as.data.frame} -\alias{as.data.frame.StageResults} -\title{Coerce Stage Results to a Data Frame} -\usage{ -\method{as.data.frame}{StageResults}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - type = 1, - ... -) -} -\arguments{ -\item{x}{A \code{\link{StageResults}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{StageResults} as data frame. -} -\details{ -Coerces the stage results to a data frame. -} -\keyword{internal} diff --git a/man/StageResults_names.Rd b/man/StageResults_names.Rd deleted file mode 100644 index 9eb52c23..00000000 --- a/man/StageResults_names.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_analysis_stage_results.R -\name{StageResults_names} -\alias{StageResults_names} -\alias{names.StageResults} -\title{Names of a Stage Results Object} -\usage{ -\method{names}{StageResults}(x) -} -\arguments{ -\item{x}{A \code{\link{StageResults}} object.} -} -\value{ -Returns a \code{\link[base]{character}} vector containing the names of the \code{\link{AnalysisResults}} object. -} -\description{ -Function to get the names of a \code{\link{StageResults}} object. -} -\details{ -Returns the names of stage results that can be accessed by the user. -} -\keyword{internal} diff --git a/man/TrialDesignCharacteristics_as.data.frame.Rd b/man/TrialDesignCharacteristics_as.data.frame.Rd deleted file mode 100644 index 8cf4383b..00000000 --- a/man/TrialDesignCharacteristics_as.data.frame.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design.R -\name{TrialDesignCharacteristics_as.data.frame} -\alias{TrialDesignCharacteristics_as.data.frame} -\alias{as.data.frame.TrialDesignCharacteristics} -\title{Coerce TrialDesignCharacteristics to a Data Frame} -\usage{ -\method{as.data.frame}{TrialDesignCharacteristics}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - ... -) -} -\arguments{ -\item{x}{A \code{\link{TrialDesignCharacteristics}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{TrialDesignCharacteristics} as data frame. -} -\details{ -Each element of the \code{\link{TrialDesignCharacteristics}} is converted to a column in the data frame. -} -\examples{ -as.data.frame(getDesignCharacteristics(getDesignGroupSequential())) - -} -\keyword{internal} diff --git a/man/TrialDesignPlan_as.data.frame.Rd b/man/TrialDesignPlan_as.data.frame.Rd deleted file mode 100644 index 35c2220d..00000000 --- a/man/TrialDesignPlan_as.data.frame.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_plan.R -\name{TrialDesignPlan_as.data.frame} -\alias{TrialDesignPlan_as.data.frame} -\alias{as.data.frame.TrialDesignPlan} -\title{Coerce Trial Design Plan to a Data Frame} -\usage{ -\method{as.data.frame}{TrialDesignPlan}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - ... -) -} -\arguments{ -\item{x}{A \code{\link{TrialDesignPlan}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{\link{TrialDesignPlan}} as data frame. -} -\details{ -Coerces the design plan to a data frame. -} -\examples{ -as.data.frame(getSampleSizeMeans()) - -} -\keyword{internal} diff --git a/man/TrialDesignSet_as.data.frame.Rd b/man/TrialDesignSet_as.data.frame.Rd deleted file mode 100644 index bed2fc88..00000000 --- a/man/TrialDesignSet_as.data.frame.Rd +++ /dev/null @@ -1,55 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_set.R -\name{TrialDesignSet_as.data.frame} -\alias{TrialDesignSet_as.data.frame} -\alias{as.data.frame.TrialDesignSet} -\title{Coerce Trial Design Set to a Data Frame} -\usage{ -\method{as.data.frame}{TrialDesignSet}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - addPowerAndAverageSampleNumber = FALSE, - theta = seq(-1, 1, 0.02), - nMax = NA_integer_, - ... -) -} -\arguments{ -\item{x}{A \code{\link{TrialDesignSet}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{addPowerAndAverageSampleNumber}{If \code{TRUE}, power and average sample size will -be added to data frame, default is \code{FALSE}.} - -\item{theta}{A vector of standardized effect sizes (theta values), default is a sequence from -1 to 1.} - -\item{nMax}{The maximum sample size.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{TrialDesignSet} as data frame. -} -\details{ -Coerces the design set to a data frame. -} -\examples{ -designSet <- getDesignSet(design = getDesignGroupSequential(), alpha = c(0.01, 0.05)) -as.data.frame(designSet) - -} -\keyword{internal} diff --git a/man/TrialDesignSet_length.Rd b/man/TrialDesignSet_length.Rd deleted file mode 100644 index 8b9e876d..00000000 --- a/man/TrialDesignSet_length.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_set.R -\name{TrialDesignSet_length} -\alias{TrialDesignSet_length} -\alias{length.TrialDesignSet} -\title{Length of Trial Design Set} -\usage{ -\method{length}{TrialDesignSet}(x) -} -\arguments{ -\item{x}{A \code{\link{TrialDesignSet}} object.} -} -\value{ -Returns a non-negative \code{\link[base]{integer}} of length 1 -representing the number of design in the \code{TrialDesignSet}. -} -\description{ -Returns the number of designs in a \code{TrialDesignSet}. -} -\details{ -Is helpful for iteration over all designs in a design set with "[index]"-syntax. -} -\examples{ -designSet <- getDesignSet(design = getDesignGroupSequential(), alpha = c(0.01, 0.05)) -length(designSet) - -} -\keyword{internal} diff --git a/man/TrialDesignSet_names.Rd b/man/TrialDesignSet_names.Rd deleted file mode 100644 index 0f142ebe..00000000 --- a/man/TrialDesignSet_names.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_set.R -\name{TrialDesignSet_names} -\alias{TrialDesignSet_names} -\alias{names.TrialDesignSet} -\title{Names of a Trial Design Set Object} -\usage{ -\method{names}{TrialDesignSet}(x) -} -\arguments{ -\item{x}{A \code{\link{TrialDesignSet}} object.} -} -\value{ -Returns a \code{\link[base]{character}} vector containing the names of the \code{\link{AnalysisResults}} object. -} -\description{ -Function to get the names of a \code{\link{TrialDesignSet}} object. -} -\details{ -Returns the names of a design set that can be accessed by the user. -} -\examples{ -designSet <- getDesignSet(design = getDesignGroupSequential(), alpha = c(0.01, 0.05)) -names(designSet) - -} -\keyword{internal} diff --git a/man/TrialDesign_as.data.frame.Rd b/man/TrialDesign_as.data.frame.Rd deleted file mode 100644 index b0f4a763..00000000 --- a/man/TrialDesign_as.data.frame.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design.R -\name{TrialDesign_as.data.frame} -\alias{TrialDesign_as.data.frame} -\alias{as.data.frame.TrialDesign} -\title{Coerce TrialDesign to a Data Frame} -\usage{ -\method{as.data.frame}{TrialDesign}( - x, - row.names = NULL, - optional = FALSE, - niceColumnNamesEnabled = FALSE, - includeAllParameters = FALSE, - ... -) -} -\arguments{ -\item{x}{A \code{\link{TrialDesign}} object.} - -\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column -names will be used; syntactic names (variable names) otherwise -(see \code{\link[base]{make.names}}).} - -\item{includeAllParameters}{Logical. If \code{TRUE}, all available -parameters will be included in the data frame; -a meaningful parameter selection otherwise, default is \code{FALSE}.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} -} -\value{ -Returns a \code{\link[base]{data.frame}}. -} -\description{ -Returns the \code{TrialDesign} as data frame. -} -\details{ -Each element of the \code{\link{TrialDesign}} is converted to a column in the data frame. -} -\examples{ -as.data.frame(getDesignGroupSequential()) - -} -\keyword{internal} diff --git a/man/Trial_Design_Set_summary.Rd b/man/Trial_Design_Set_summary.Rd deleted file mode 100644 index 64e431f7..00000000 --- a/man/Trial_Design_Set_summary.Rd +++ /dev/null @@ -1,64 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/class_design_set.R -\name{Trial_Design_Set_summary} -\alias{Trial_Design_Set_summary} -\alias{summary.TrialDesignSet} -\title{Trial Design Set Summary} -\usage{ -\method{summary}{TrialDesignSet}(object, ..., type = 1, digits = NA_integer_) -} -\arguments{ -\item{object}{A \code{\link{ParameterSet}} object.} - -\item{...}{Ensures that all arguments (starting from the "...") are to be named and -that a warning will be displayed if unknown arguments are passed.} - -\item{digits}{Defines how many digits are to be used for numeric values.} -} -\value{ -Returns a \code{\link{SummaryFactory}} object. -The following generics (R generic functions) are available for this result object: -\itemize{ - \item \code{\link[=names.FieldSet]{names}} to obtain the field names, - \item \code{\link[=print.FieldSet]{print}} to print the object -} -} -\description{ -Displays a summary of \code{\link{ParameterSet}} object. -} -\details{ -Summarizes the trial designs. -} -\section{Summary options}{ - -The following options can be set globally: -\enumerate{ - \item \code{rpact.summary.output.size}: one of \code{c("small", "medium", "large")}; - defines how many details will be included into the summary; - default is \code{"large"}, i.e., all available details are displayed. - \item \code{rpact.summary.justify}: one of \code{c("right", "left", "centre")}; - shall the values be right-justified (the default), left-justified or centered. - \item \code{rpact.summary.width}: defines the maximum number of characters to be used per line (default is \code{83}). - \item \code{rpact.summary.intervalFormat}: defines how intervals will be displayed in the summary, - default is \code{"[\%s; \%s]"}. - \item \code{rpact.summary.digits}: defines how many digits are to be used for numeric values (default is \code{3}). - \item \code{rpact.summary.digits.probs}: defines how many digits are to be used for numeric values - (default is one more than value of \code{rpact.summary.digits}, i.e., \code{4}). - \item \code{rpact.summary.trim.zeroes}: if \code{TRUE} (default) zeroes will always displayed as "0", - e.g. "0.000" will become "0". -} -Example: \code{options("rpact.summary.intervalFormat" = "\%s - \%s")} -} - -\section{How to get help for generic functions}{ - -Click on the link of a generic in the list above to go directly to the help documentation of -the \code{rpact} specific implementation of the generic. -Note that you can use the R function \code{\link[utils]{methods}} to get all the methods of a generic and -to identify the object specific name of it, e.g., -use \code{methods("plot")} to get all the methods for the \code{plot} generic. -There you can find, e.g., \code{plot.AnalysisResults} and -obtain the specific help documentation linked above by typing \code{?plot.AnalysisResults}. -} - -\keyword{internal} diff --git a/man/as.data.frame.AnalysisResults.Rd b/man/as.data.frame.AnalysisResults.Rd index b9466f3e..21c6cfe5 100644 --- a/man/as.data.frame.AnalysisResults.Rd +++ b/man/as.data.frame.AnalysisResults.Rd @@ -17,6 +17,10 @@ \item{...}{Ensures that all arguments (starting from the "...") are to be named and that a warning will be displayed if unknown arguments are passed.} + +\item{niceColumnNamesEnabled}{Logical. If \code{TRUE}, nice looking column +names will be used; syntactic names (variable names) otherwise +(see \code{\link[base]{make.names}}).} } \value{ Returns a \code{\link[base]{data.frame}}. From 54f35e192f710ef6fc14105f1e3d723fc1a5780a Mon Sep 17 00:00:00 2001 From: Friedrich Pahlke Date: Wed, 8 Feb 2023 09:41:53 +0100 Subject: [PATCH 2/2] The C++11 specification has been dropped from DESCRIPTION to prevent a note on that. --- DESCRIPTION | 5 ++--- NEWS.md | 1 + R/class_core_plot_settings.R | 31 +++++++++++++++++++++++-------- 3 files changed, 26 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 65a534ce..70ca821d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: rpact Title: Confirmatory Adaptive Clinical Trial Design and Analysis Version: 3.3.3 -Date: 2023-02-07 +Date: 2023-02-08 Authors@R: c( person( given = "Gernot", @@ -23,7 +23,7 @@ URL: https://www.rpact.org, https://www.rpact.com, https://github.com/rpact-com/ BugReports: https://github.com/rpact-com/rpact/issues Language: en-US Depends: - R (>= 3.5.0) + R (>= 3.6.0) Imports: methods, stats, @@ -33,7 +33,6 @@ Imports: rlang, Rcpp (>= 1.0.3) LinkingTo: Rcpp -SystemRequirements: C++11 Suggests: parallel, ggplot2 (>= 2.2.0), diff --git a/NEWS.md b/NEWS.md index 5df9a55d..2cdae734 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,7 @@ * Performance of simulation means improved for 1 and 2 groups * Two-sided O'Brien and Fleming beta-spending function corrected * Issue in plot type 5 for sample size means and rates fixed +* Added dependency on R >= 3.6.0 * Minor improvements # rpact 3.3.2 diff --git a/R/class_core_plot_settings.R b/R/class_core_plot_settings.R index 23654b74..baebd06c 100644 --- a/R/class_core_plot_settings.R +++ b/R/class_core_plot_settings.R @@ -13,8 +13,8 @@ ## | ## | Contact us for information about our services: info@rpact.com ## | -## | File version: $Revision: 6801 $ -## | Last changed: $Date: 2023-02-06 15:29:57 +0100 (Mon, 06 Feb 2023) $ +## | File version: $Revision: 6805 $ +## | Last changed: $Date: 2023-02-08 09:30:19 +0100 (Mi, 08 Feb 2023) $ ## | Last changed by: $Author: pahlke $ ## | @@ -514,10 +514,17 @@ PlotSettings <- setRefClass("PlotSettings", }, setLegendBorder = function(p) { "Sets the legend border" - p <- p + ggplot2::theme( - legend.background = - ggplot2::element_rect(fill = "white", colour = "black", linewidth = scaleSize(0.4)) - ) + if (packageVersion("ggplot2") >= "3.4.0") { + p <- p + ggplot2::theme( + legend.background = + ggplot2::element_rect(fill = "white", colour = "black", linewidth = scaleSize(0.4)) + ) + } else { + p <- p + ggplot2::theme( + legend.background = + ggplot2::element_rect(fill = "white", colour = "black", size = scaleSize(0.4)) + ) + } return(p) }, adjustPointSize = function(adjustingValue) { @@ -679,7 +686,11 @@ PlotSettings <- setRefClass("PlotSettings", plotValues = function(p, ..., plotLineEnabled = TRUE, plotPointsEnabled = TRUE, pointBorder = 4) { if (plotLineEnabled) { - p <- p + ggplot2::geom_line(size = scaleSize(.self$lineSize)) + if (packageVersion("ggplot2") >= "3.4.0") { + p <- p + ggplot2::geom_line(linewidth = scaleSize(.self$lineSize)) + } else { + p <- p + ggplot2::geom_line(size = scaleSize(.self$lineSize)) + } } if (plotPointsEnabled) { p <- plotPoints(p, pointBorder) @@ -689,7 +700,11 @@ PlotSettings <- setRefClass("PlotSettings", mirrorYValues = function(p, yValues, plotLineEnabled = TRUE, plotPointsEnabled = TRUE, pointBorder = 4) { if (plotLineEnabled) { - p <- p + ggplot2::geom_line(ggplot2::aes(y = -yValues), size = scaleSize(.self$lineSize)) + if (packageVersion("ggplot2") >= "3.4.0") { + p <- p + ggplot2::geom_line(ggplot2::aes(y = -yValues), linewidth = scaleSize(.self$lineSize)) + } else { + p <- p + ggplot2::geom_line(ggplot2::aes(y = -yValues), size = scaleSize(.self$lineSize)) + } } if (plotPointsEnabled) { p <- plotPoints(p, pointBorder, mapping = ggplot2::aes(y = -yValues))