diff --git a/NAMESPACE b/NAMESPACE index 1eae13401..b6e7c10b3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -353,7 +353,7 @@ export(prob) export(probFunction) export(probit) export(saveSample) -export(setSeed) +export(set_seed) export(size) export(stopTrial) export(test_length) @@ -539,10 +539,8 @@ importFrom(kableExtra,kbl) importFrom(lifecycle,badge) importFrom(magrittr,"%>%") importFrom(mvtnorm,rmvnorm) -importFrom(parallel,clusterApply) importFrom(parallel,detectCores) importFrom(parallel,makeCluster) -importFrom(parallel,stopCluster) importFrom(parallelly,availableCores) importFrom(rjags,jags.model) importFrom(rjags,jags.samples) diff --git a/R/Design-methods.R b/R/Design-methods.R index c4deb8fc1..2ea7e588a 100644 --- a/R/Design-methods.R +++ b/R/Design-methods.R @@ -1,165 +1,154 @@ -# nolint start -##################################################################################### -## Author: Daniel Sabanes Bove [sabanesd *a*t* roche *.* com] -## Wai Yin Yeung [w*.* yeung1 *a*t* lancaster *.* ac *.* uk] -## Project: Object-oriented implementation of CRM designs -## -## Time-stamp: <[Design-methods.R] by DSB Son 03/05/2015 20:35> -## -## Description: -## Simulate outcomes from a CRM trial, assuming a true dose-toxicity -## relationship. -## -## History: -## 12/02/2014 file creation -## 07/04/2014 start with parallelization on cores -## 02/01/2015 rename: simulate.R --> Design-methods.R -## 10/07/2015 added simulate methods -##################################################################################### - -##' @include Data-methods.R -##' @include Design-class.R -##' @include McmcOptions-class.R -##' @include Rules-methods.R -##' @include Simulations-class.R -##' @include helpers.R -##' @include mcmc.R -{} - -##' Helper function to set and save the RNG seed -##' -##' This is basically copied from simulate.lm -##' -##' @param seed an object specifying if and how the random number generator -##' should be initialized (\dQuote{seeded}). Either \code{NULL} (default) or an -##' integer that will be used in a call to \code{\link{set.seed}} before -##' simulating the response vectors. If set, the value is saved as the -##' \code{seed} slot of the returned object. The default, \code{NULL} will -##' not change the random generator state. -##' @return The RNGstate will be returned, in order to call this function -##' with this input to reproduce the obtained simulation results -##' -##' @export -##' @keywords programming -##' @author Daniel Sabanes Bove \email{sabanesd@@roche.com} -setSeed <- function(seed = NULL) { +#' @include Data-methods.R +#' @include Design-class.R +#' @include McmcOptions-class.R +#' @include Rules-methods.R +#' @include Simulations-class.R +#' @include helpers.R +#' @include mcmc.R +NULL + +# helper functions ---- + +## set_seed ---- + +#' Helper function to set and save the RNG seed +#' +#' @description `r lifecycle::badge("stable")` +#' +#' This code is basically copied from `stats:::simulate.lm`. +#' +#' @param seed an object specifying if and how the random number generator +#' should be initialized ("seeded"). Either `NULL` (default) or an +#' integer that will be used in a call to [set.seed()] before +#' simulating the response vectors. If set, the value is saved as the +#' `seed` slot of the returned object. The default, `NULL` will +#' not change the random generator state. +#' @return The integer vector containing the random number generate state will +#' be returned, in order to call this function with this input to reproduce +#' the obtained simulation results. +#' +#' @export +#' @keywords programming +set_seed <- function(seed = NULL) { + assert_number(seed, null.ok = TRUE) + if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) { runif(1) } if (is.null(seed)) { - RNGstate <- get(".Random.seed", envir = .GlobalEnv) + get(".Random.seed", envir = .GlobalEnv) } else { - R.seed <- get(".Random.seed", envir = .GlobalEnv) - ## make sure R.seed exists in parent frame: - assign("R.seed", R.seed, envir = parent.frame()) + seed <- as.integer(seed) + r_seed <- get(".Random.seed", envir = .GlobalEnv) + # Make sure r_seed exists in parent frame. + assign(".r_seed", r_seed, envir = parent.frame()) set.seed(seed) - RNGstate <- structure(seed, kind = as.list(RNGkind())) - do.call("on.exit", - list(quote(assign(".Random.seed", R.seed, envir = .GlobalEnv))), + # Here we need the r_seed in the parent.frame! + do.call( + "on.exit", + list(quote(assign(".Random.seed", .r_seed, envir = .GlobalEnv))), envir = parent.frame() ) - ## here we need the R.seed in the parent.frame! + structure(seed, kind = as.list(RNGkind())) } - - return(RNGstate) } +## get_result_list ---- -##' Helper function to obtain simulation results list -##' -##' The function \code{fun} can use variables that are visible to itself. -##' The names of these variables have to given in the vector \code{vars}. -##' -##' @param fun the simulation function for a single iteration, which takes as -##' single parameter the iteration index -##' @param nsim number of simulations to be conducted -##' @param vars names of the variables -##' @param parallel shall the iterations be parallelized across the cores? -##' if NULL, then no parallelization will be done. If scalar positive number, -##' then so many cores will be used. -##' @return the list with all simulation results (one iteration corresponds -##' to one list element) -##' -##' @importFrom parallel detectCores makeCluster clusterApply stopCluster -##' @importFrom parallelly availableCores -##' @keywords internal programming -##' @author Daniel Sabanes Bove \email{sabanesd@@roche.com} -getResultList <- function(fun, - nsim, - vars, - parallel = NULL) { - ret <- - if (is.null(parallel)) { - lapply( - X = seq_len(nsim), - FUN = fun - ) - } else { - ## check that parallel parameter makes sense - stopifnot(is.scalar(parallel), parallel > 0) - - ## now process all simulations - cores <- min( - safeInteger(parallel), - parallelly::availableCores() - ) - - ## start the cluster - cl <- parallel::makeCluster(cores) - - ## load the required R package - parallel::clusterEvalQ(cl, { - library(crmPack) - NULL - }) +#' Helper function to obtain simulation results list +#' +#' @description `r lifecycle::badge("stable")` +#' +#' The function `fun` can use variables that are visible to itself. +#' The names of these variables have to be given in the vector `vars`. +#' +#' @param fun (`function`)\cr the simulation function for a single iteration, which takes as +#' single parameter the iteration index. +#' @param nsim number of simulations to be conducted. +#' @param vars names of the variables. +#' @param parallel should the simulation runs be parallelized across the +#' clusters of the computer? +#' @param n_cores how many cores should be used for parallel computing? +#' @return The list with all simulation results (one iteration corresponds +#' to one list element). +#' +#' @importFrom parallel makeCluster +#' @importFrom parallelly availableCores +#' @keywords internal programming +get_result_list <- function( + fun, + nsim, + vars, + parallel, + n_cores) { + assert_flag(parallel) + assert_integerish(n_cores, lower = 1) + + if (!parallel) { + lapply( + X = seq_len(nsim), + FUN = fun + ) + } else { + # Process all simulations. + cores <- min( + safeInteger(n_cores), + parallelly::availableCores() + ) - ## export local variables - parallel::clusterExport( - cl = cl, - varlist = vars, - envir = parent.frame() - ) - ## parent.frame() gives back the caller environment - ## (different from parent.env() which returns - ## the environment where this function has been - ## defined!) - - ## export all global variables - parallel::clusterExport( - cl = cl, - varlist = ls(.GlobalEnv) - ) + # Start the cluster. + cl <- parallel::makeCluster(cores) + + # Load the required R package. + parallel::clusterEvalQ(cl, { + library(crmPack) + NULL + }) + + # Export local variables from the caller environment. + # Note: parent.frame() is different from parent.env() which returns + # the environment where this function has been defined! + parallel::clusterExport( + cl = cl, + varlist = vars, + envir = parent.frame() + ) - # load user extensions from global options - crmpack_extensions <- getOption("crmpack_extensions") - if (is.null(crmpack_extensions) != TRUE) { - tryCatch( - { - parallel::clusterCall(cl, crmpack_extensions) - }, - error = function(e) { - stop("Failed to export crmpack_extensions: ", e$message) - } - ) - } + # Export all global variables. + parallel::clusterExport( + cl = cl, + varlist = ls(.GlobalEnv) + ) - ## now do the computations - res <- parallel::parLapply( - cl = cl, - X = seq_len(nsim), - fun = fun + # Load user extensions from global options. + crmpack_extensions <- getOption("crmpack_extensions") + if (is.null(crmpack_extensions) != TRUE) { + tryCatch( + { + parallel::clusterCall(cl, crmpack_extensions) + }, + error = function(e) { + stop("Failed to export crmpack_extensions: ", e$message) + } ) + } - ## stop the cluster - parallel::stopCluster(cl) + # Do the computations in parallel. + res <- parallel::parLapply( + cl = cl, + X = seq_len(nsim), + fun = fun + ) - res - } + # Stop the cluster. + parallel::stopCluster(cl) - return(ret) + res + } } +# nolint start ## ============================================================ @@ -168,7 +157,7 @@ getResultList <- function(fun, ##' @param object the \code{\linkS4class{Design}} object we want to simulate ##' data from ##' @param nsim the number of simulations (default: 1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param truth a function which takes as input a dose (vector) and returns the ##' true probability (vector) for toxicity. Additional arguments can be supplied ##' in \code{args}. @@ -228,7 +217,7 @@ setMethod("simulate", nArgs <- max(nrow(args), 1L) ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -436,7 +425,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -449,7 +438,8 @@ setMethod("simulate", "object", "mcmcOptions" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: @@ -492,7 +482,7 @@ setMethod("simulate", ##' @param object the \code{\linkS4class{RuleDesign}} object we want to simulate ##' data from ##' @param nsim the number of simulations (default: 1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param truth a function which takes as input a dose (vector) and returns the ##' true probability (vector) for toxicity. Additional arguments can be supplied ##' in \code{args}. @@ -539,7 +529,7 @@ setMethod("simulate", nArgs <- max(nrow(args), 1L) ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -624,7 +614,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -635,7 +625,8 @@ setMethod("simulate", "truth", "object" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the GeneralSimulations format: @@ -663,7 +654,7 @@ setMethod("simulate", ##' @param object the \code{\linkS4class{DualDesign}} object we want to simulate ##' data from ##' @param nsim the number of simulations (default: 1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param trueTox a function which takes as input a dose (vector) and returns the ##' true probability (vector) for toxicity. Additional arguments can be supplied ##' in \code{args}. @@ -739,7 +730,7 @@ setMethod("simulate", ) ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -1031,7 +1022,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -1046,7 +1037,8 @@ setMethod("simulate", "object", "mcmcOptions" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: @@ -1863,7 +1855,7 @@ setMethod("examine", ##' ##' @param object the \code{\linkS4class{TDsamplesDesign}} object we want to simulate the data from ##' @param nsim the number of simulations (default :1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param truth a function which takes as input a dose (vector) and returns the true probability ##' (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}. ##' @param args data frame with arguments for the \code{truth} function. The @@ -1921,7 +1913,7 @@ setMethod("simulate", ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -2147,7 +2139,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -2160,7 +2152,8 @@ setMethod("simulate", "object", "mcmcOptions" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: @@ -2232,7 +2225,7 @@ setMethod("simulate", ##' ##' @param object the \code{\linkS4class{TDDesign}} object we want to simulate the data from ##' @param nsim the number of simulations (default :1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param truth a function which takes as input a dose (vector) and returns the true probability ##' (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}. ##' @param args data frame with arguments for the \code{truth} function. The @@ -2285,7 +2278,7 @@ setMethod("simulate", nArgs <- max(nrow(args), 1L) ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -2494,7 +2487,7 @@ setMethod("simulate", } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -2506,7 +2499,8 @@ setMethod("simulate", "truth", "object" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: @@ -2581,7 +2575,7 @@ setMethod("simulate", ##' ##' @param object the \code{\linkS4class{DualResponsesDesign}} object we want to simulate the data from ##' @param nsim the number of simulations (default :1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param trueDLE a function which takes as input a dose (vector) and returns the true probability ##' (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}. ##' @param trueEff a function which takes as input a dose (vector) and returns the expected efficacy @@ -2644,7 +2638,7 @@ setMethod("simulate", ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -2984,7 +2978,7 @@ setMethod("simulate", } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -2998,7 +2992,8 @@ setMethod("simulate", "trueNu", "object" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) @@ -3111,7 +3106,7 @@ setMethod("simulate", ##' @param object the \code{\linkS4class{DualResponsesSamplesDesign}} object we want to ##' simulate the data from ##' @param nsim the number of simulations (default :1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param trueDLE a function which takes as input a dose (vector) and returns the true probability ##' (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}. ##' @param trueEff a function which takes as input a dose (vector) and returns the expected @@ -3192,7 +3187,7 @@ setMethod("simulate", trueDLEArgnames <- names(formals(trueDLE))[-1] ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -3530,7 +3525,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -3546,7 +3541,8 @@ setMethod("simulate", "object", "mcmcOptions" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: @@ -3657,7 +3653,7 @@ setMethod("simulate", ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -4000,7 +3996,7 @@ setMethod("simulate", } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, nsim = nsim, vars = @@ -4014,7 +4010,8 @@ setMethod("simulate", "trueNu", "object" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) @@ -4113,7 +4110,7 @@ setMethod("simulate", ##' @param object the \code{\linkS4class{DADesign}} object we want to simulate ##' data from ##' @param nsim the number of simulations (default: 1) -##' @param seed see \code{\link{setSeed}} +##' @param seed see \code{\link{set_seed}} ##' @param truthTox a function which takes as input a dose (vector) and returns the ##' true probability (vector) for toxicity and the time DLT occurs. Additional ##' arguments can be supplied in \code{args}. @@ -4181,7 +4178,7 @@ setMethod("simulate", nArgs <- max(nrow(args), 1L) ## seed handling - RNGstate <- setSeed(seed) + RNGstate <- set_seed(seed) ## from this, ## generate the individual seeds for the simulation runs @@ -4655,7 +4652,7 @@ setMethod("simulate", return(thisResult) } - resultList <- getResultList( + resultList <- get_result_list( fun = runSim, ## remove nsim = nsim, vars = @@ -4671,7 +4668,8 @@ setMethod("simulate", "nextOpen", "ready_to_open" ), - parallel = if (parallel) nCores else NULL + parallel = parallel, + n_cores = nCores ) ## put everything in the Simulations format: diff --git a/_pkgdown.yaml b/_pkgdown.yaml index 13dc8284e..33dc7e0f6 100644 --- a/_pkgdown.yaml +++ b/_pkgdown.yaml @@ -440,7 +440,7 @@ reference: - plotDualResponses - plotGain - probit - - setSeed + - set_seed - show,DualSimulationsSummary-method - show,GeneralSimulationsSummary-method - show,PseudoDualSimulationsSummary-method diff --git a/man/getResultList.Rd b/man/getResultList.Rd deleted file mode 100644 index ab543ad78..000000000 --- a/man/getResultList.Rd +++ /dev/null @@ -1,33 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/Design-methods.R -\name{getResultList} -\alias{getResultList} -\title{Helper function to obtain simulation results list} -\usage{ -getResultList(fun, nsim, vars, parallel = NULL) -} -\arguments{ -\item{fun}{the simulation function for a single iteration, which takes as -single parameter the iteration index} - -\item{nsim}{number of simulations to be conducted} - -\item{vars}{names of the variables} - -\item{parallel}{shall the iterations be parallelized across the cores? -if NULL, then no parallelization will be done. If scalar positive number, -then so many cores will be used.} -} -\value{ -the list with all simulation results (one iteration corresponds -to one list element) -} -\description{ -The function \code{fun} can use variables that are visible to itself. -The names of these variables have to given in the vector \code{vars}. -} -\author{ -Daniel Sabanes Bove \email{sabanesd@roche.com} -} -\keyword{internal} -\keyword{programming} diff --git a/man/get_result_list.Rd b/man/get_result_list.Rd new file mode 100644 index 000000000..da89b4edc --- /dev/null +++ b/man/get_result_list.Rd @@ -0,0 +1,33 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Design-methods.R +\name{get_result_list} +\alias{get_result_list} +\title{Helper function to obtain simulation results list} +\usage{ +get_result_list(fun, nsim, vars, parallel, n_cores) +} +\arguments{ +\item{fun}{(\code{function})\cr the simulation function for a single iteration, which takes as +single parameter the iteration index.} + +\item{nsim}{number of simulations to be conducted.} + +\item{vars}{names of the variables.} + +\item{parallel}{should the simulation runs be parallelized across the +clusters of the computer?} + +\item{n_cores}{how many cores should be used for parallel computing?} +} +\value{ +The list with all simulation results (one iteration corresponds +to one list element). +} +\description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} + +The function \code{fun} can use variables that are visible to itself. +The names of these variables have to be given in the vector \code{vars}. +} +\keyword{internal} +\keyword{programming} diff --git a/man/setSeed.Rd b/man/setSeed.Rd deleted file mode 100644 index a2edb14ae..000000000 --- a/man/setSeed.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/Design-methods.R -\name{setSeed} -\alias{setSeed} -\title{Helper function to set and save the RNG seed} -\usage{ -setSeed(seed = NULL) -} -\arguments{ -\item{seed}{an object specifying if and how the random number generator -should be initialized (\dQuote{seeded}). Either \code{NULL} (default) or an -integer that will be used in a call to \code{\link{set.seed}} before -simulating the response vectors. If set, the value is saved as the -\code{seed} slot of the returned object. The default, \code{NULL} will -not change the random generator state.} -} -\value{ -The RNGstate will be returned, in order to call this function -with this input to reproduce the obtained simulation results -} -\description{ -This is basically copied from simulate.lm -} -\author{ -Daniel Sabanes Bove \email{sabanesd@roche.com} -} -\keyword{programming} diff --git a/man/set_seed.Rd b/man/set_seed.Rd new file mode 100644 index 000000000..f63be09de --- /dev/null +++ b/man/set_seed.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Design-methods.R +\name{set_seed} +\alias{set_seed} +\title{Helper function to set and save the RNG seed} +\usage{ +set_seed(seed = NULL) +} +\arguments{ +\item{seed}{an object specifying if and how the random number generator +should be initialized ("seeded"). Either \code{NULL} (default) or an +integer that will be used in a call to \code{\link[=set.seed]{set.seed()}} before +simulating the response vectors. If set, the value is saved as the +\code{seed} slot of the returned object. The default, \code{NULL} will +not change the random generator state.} +} +\value{ +The integer vector containing the random number generate state will +be returned, in order to call this function with this input to reproduce +the obtained simulation results. +} +\description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} + +This code is basically copied from \code{stats:::simulate.lm}. +} +\keyword{programming} diff --git a/man/simulate-DADesign-method.Rd b/man/simulate-DADesign-method.Rd index 0df807d00..00a934b28 100644 --- a/man/simulate-DADesign-method.Rd +++ b/man/simulate-DADesign-method.Rd @@ -27,7 +27,7 @@ data from} \item{nsim}{the number of simulations (default: 1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{truthTox}{a function which takes as input a dose (vector) and returns the true probability (vector) for toxicity and the time DLT occurs. Additional diff --git a/man/simulate-Design-method.Rd b/man/simulate-Design-method.Rd index 0ad3b7fb7..adc12a723 100644 --- a/man/simulate-Design-method.Rd +++ b/man/simulate-Design-method.Rd @@ -23,7 +23,7 @@ data from} \item{nsim}{the number of simulations (default: 1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{truth}{a function which takes as input a dose (vector) and returns the true probability (vector) for toxicity. Additional arguments can be supplied diff --git a/man/simulate-DualDesign-method.Rd b/man/simulate-DualDesign-method.Rd index 12fd29095..8e6d3b813 100644 --- a/man/simulate-DualDesign-method.Rd +++ b/man/simulate-DualDesign-method.Rd @@ -26,7 +26,7 @@ data from} \item{nsim}{the number of simulations (default: 1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{trueTox}{a function which takes as input a dose (vector) and returns the true probability (vector) for toxicity. Additional arguments can be supplied diff --git a/man/simulate-DualResponsesDesign-method.Rd b/man/simulate-DualResponsesDesign-method.Rd index c17e2e58a..6f142be48 100644 --- a/man/simulate-DualResponsesDesign-method.Rd +++ b/man/simulate-DualResponsesDesign-method.Rd @@ -27,7 +27,7 @@ process} \item{nsim}{the number of simulations (default :1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{trueDLE}{a function which takes as input a dose (vector) and returns the true probability (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}.} diff --git a/man/simulate-DualResponsesSamplesDesign-method.Rd b/man/simulate-DualResponsesSamplesDesign-method.Rd index 9a842792f..ba46d32af 100644 --- a/man/simulate-DualResponsesSamplesDesign-method.Rd +++ b/man/simulate-DualResponsesSamplesDesign-method.Rd @@ -34,7 +34,7 @@ simulate the data from} \item{nsim}{the number of simulations (default :1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{trueDLE}{a function which takes as input a dose (vector) and returns the true probability (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}.} diff --git a/man/simulate-RuleDesign-method.Rd b/man/simulate-RuleDesign-method.Rd index 2aa8f6b08..336c475d1 100644 --- a/man/simulate-RuleDesign-method.Rd +++ b/man/simulate-RuleDesign-method.Rd @@ -21,7 +21,7 @@ data from} \item{nsim}{the number of simulations (default: 1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{truth}{a function which takes as input a dose (vector) and returns the true probability (vector) for toxicity. Additional arguments can be supplied diff --git a/man/simulate-TDDesign-method.Rd b/man/simulate-TDDesign-method.Rd index cc5d90f28..e77b2de48 100644 --- a/man/simulate-TDDesign-method.Rd +++ b/man/simulate-TDDesign-method.Rd @@ -23,7 +23,7 @@ This is a method based on the \code{\linkS4class{TDDesign}} where model used are \item{nsim}{the number of simulations (default :1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{truth}{a function which takes as input a dose (vector) and returns the true probability (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}.} diff --git a/man/simulate-TDsamplesDesign-method.Rd b/man/simulate-TDsamplesDesign-method.Rd index 9577f36c0..2b3e0d109 100644 --- a/man/simulate-TDsamplesDesign-method.Rd +++ b/man/simulate-TDsamplesDesign-method.Rd @@ -24,7 +24,7 @@ This is a method based on the \code{\linkS4class{TDsamplesDesign}} where model u \item{nsim}{the number of simulations (default :1)} -\item{seed}{see \code{\link{setSeed}}} +\item{seed}{see \code{\link{set_seed}}} \item{truth}{a function which takes as input a dose (vector) and returns the true probability (vector) of the occurrence of a DLE. Additional arguments can be supplied in \code{args}.} diff --git a/tests/testthat/test-Design-methods.R b/tests/testthat/test-Design-methods.R index f5a7c01eb..1f2521829 100644 --- a/tests/testthat/test-Design-methods.R +++ b/tests/testthat/test-Design-methods.R @@ -1,3 +1,51 @@ +# helper functions ---- + +## set_seed ---- + +test_that("set_seed returns correct value if seed is a value", { + seed <- 1.909 + seed_int <- 1 + + RNGkind("default") + rng_state <- set_seed(seed) + attr(seed_int, "kind") <- list("Mersenne-Twister", "Inversion", "Rejection") + expect_equal(rng_state, seed_int) + + RNGkind("Super-Duper") + rng_state <- set_seed(seed) + attr(seed_int, "kind") <- list("Super-Duper", "Inversion", "Rejection") + expect_equal(rng_state, seed_int) + + RNGkind("default") +}) + +test_that("set_seed returns correct value if seed is NULL", { + seed <- NULL + + RNGkind("default") + rng_state <- set_seed(seed) + expect_equal(rng_state, .Random.seed) + + RNGkind("Super-Duper") + rng_state <- set_seed(seed) + expect_equal(rng_state, .Random.seed) + + RNGkind("default") +}) + +## get_result_list ---- + +test_that("get_result_list returns correct value", { + res <- get_result_list(mean, 2, NULL, FALSE, 5) + expect_equal(res, list(1, 2)) + + res <- get_result_list(length, 2, NULL, FALSE, 5) + expect_equal(res, list(1, 1)) + + expect_error(get_result_list(length, 2, NULL, 5, 5)) + expect_error(get_result_list(length, 2, NULL, FALSE, 0)) +}) + # simulate ---- ## NextBestInfTheory ----