801 cleanup pseudo dual simulations (#819)

* update code and test

* update doc

* [skip style] [skip vbump] Restyle files

* update var

* fix methods

* fix par names

* trigger checks

* trigger checks

* trigger checks

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

NAMESPACE

@@ -387,6 +387,7 @@ export(OneParExpPrior)
 export(OneParLogNormalPrior)
 export(ProbitLogNormal)
 export(ProbitLogNormalRel)
+export(PseudoDualSimulations)
 export(PseudoSimulations)
 export(Quantiles2LogisticNormal)
 export(RuleDesign)

R/Design-methods.R

@@ -2878,17 +2878,17 @@ setMethod("simulate",
  final_td_target_end_of_trial_at_dose_grid = TDtargetEndOfTrialDoseGridList,
  final_cis = CIList,
  final_ratios = ratioList,
- FinalGstarEstimates = GstarList,
- FinalGstarAtDoseGrid = GstarAtDoseGridList,
- FinalGstarCIs = CIGstarList,
- FinalGstarRatios = ratioGstarList,
+ final_gstar_estimates = GstarList,
+ final_gstar_at_dose_grid = GstarAtDoseGridList,
+ final_gstar_cis = CIGstarList,
+ final_gstar_ratios = ratioGstarList,
  final_tdeot_cis = CITDEOTList,
  final_tdeot_ratios = ratioTDEOTList,
- FinalOptimalDose = OptimalDoseList,
- FinalOptimalDoseAtDoseGrid = OptimalDoseAtDoseGridList,
+ final_optimal_dose = OptimalDoseList,
+ final_optimal_dose_at_dose_grid = OptimalDoseAtDoseGridList,
  fit = fitDLEList,
- fitEff = fitEffList,
- sigma2est = sigma2Estimates,
+ fit_eff = fitEffList,
+ sigma2_est = sigma2Estimates,
  stop_reasons = stopReasons,
  stop_report = stop_report,
  seed = RNGstate
@@ -3431,17 +3431,17 @@ setMethod("simulate",
  final_td_target_end_of_trial_at_dose_grid = TDtargetEndOfTrialDoseGridList,
  final_cis = CIList,
  final_ratios = ratioList,
- FinalGstarEstimates = GstarList,
- FinalGstarAtDoseGrid = GstarAtDoseGridList,
- FinalGstarCIs = CIGstarList,
- FinalGstarRatios = ratioGstarList,
+ final_gstar_estimates = GstarList,
+ final_gstar_at_dose_grid = GstarAtDoseGridList,
+ final_gstar_cis = CIGstarList,
+ final_gstar_ratios = ratioGstarList,
  final_tdeot_cis = CITDEOTList,
  final_tdeot_ratios = ratioTDEOTList,
- FinalOptimalDose = OptimalDoseList,
- FinalOptimalDoseAtDoseGrid = OptimalDoseAtDoseGridList,
+ final_optimal_dose = OptimalDoseList,
+ final_optimal_dose_at_dose_grid = OptimalDoseAtDoseGridList,
  fit = fitDLEList,
- fitEff = fitEffList,
- sigma2est = sigma2Estimates,
+ fit_eff = fitEffList,
+ sigma2_est = sigma2Estimates,
  sigma2betaWest = sigma2betaWEstimates,
  stop_reasons = stopReasons,
  stop_report = stop_report,
@@ -3904,17 +3904,17 @@ setMethod("simulate",
  final_td_target_end_of_trial_at_dose_grid = TDtargetEndOfTrialDoseGridList,
  final_cis = CIList,
  final_ratios = ratioList,
- FinalGstarEstimates = GstarList,
- FinalGstarAtDoseGrid = GstarAtDoseGridList,
- FinalGstarCIs = CIGstarList,
- FinalGstarRatios = ratioGstarList,
+ final_gstar_estimates = GstarList,
+ final_gstar_at_dose_grid = GstarAtDoseGridList,
+ final_gstar_cis = CIGstarList,
+ final_gstar_ratios = ratioGstarList,
  final_tdeot_cis = CITDEOTList,
  final_tdeot_ratios = ratioTDEOTList,
- FinalOptimalDose = OptimalDoseList,
- FinalOptimalDoseAtDoseGrid = OptimalDoseAtDoseGridList,
+ final_optimal_dose = OptimalDoseList,
+ final_optimal_dose_at_dose_grid = OptimalDoseAtDoseGridList,
  fit = fitDLEList,
- fitEff = fitEffList,
- sigma2est = sigma2Estimates,
+ fit_eff = fitEffList,
+ sigma2_est = sigma2Estimates,
  stop_reasons = stopReasons,
  stop_report = stop_report,
  seed = RNGstate

R/Simulations-class.R

@@ -8,10 +8,7 @@ NULL
 
 ## class ----
 
-#' `GeneralSimulations`
-#'
-#' @description `r lifecycle::badge("stable")`
-#'
+#' `GeneralSimulations` @description `r lifecycle::badge("stable")`
 #' This class captures trial simulations.
 #' Here also the random generator state before starting the simulation is
 #' saved, in order to be able to reproduce the outcome. For this just use
@@ -612,112 +609,100 @@ PseudoSimulations <- function(fit,
  stop("Class PseudoSimulations cannot be instantiated directly. Please use one of its subclasses instead.")
 }
 
-# nolint start
-## ===============================================================================
-## -------------------------------------------------------------------------------
-## Class for Pseudo simulation using DLE and efficacy responses (Pseudo models except 'EffFlexi' model)
-## -----------------------------------------------------------------------------------
+# PseudoDualSimulations ----
 
-##' Class `PseudoDualSimulations`
-##'
-##' This is a class which captures the trial simulations design using both the
-##' DLE and efficacy responses. The design of model from \code{\linkS4class{ModelTox}}
-##' class and the efficacy model from \code{\linkS4class{ModelEff}} class
-##' (except \code{\linkS4class{EffFlexi}} class). It contains all slots from
-##' \code{\linkS4class{GeneralSimulations}} and \code{\linkS4class{PseudoSimulations}} object.
-##' In comparison to the parent class \code{\linkS4class{PseudoSimulations}},
-##' it contains additional slots to
-##' capture the dose-efficacy curve and the sigma2 estimates.
-##'
-##' @slot fitEff list of the final values. If DLE and efficacy samples are generated, it contains the
-##' final fitted values. If no DLE and efficacy samples are used, it contains the modal estimates of the
-##' parameters in the two models and the posterior estimates of the probabilities of the occurrence of a
-##' DLE and the expected efficacy responses.
-##' @slot FinalGstarEstimates a vector of the final estimates of Gstar at the end of each simulations.
-##' @slot FinalGstarAtDoseGrid is a vector of the final estimates of Gstar at dose Grid at the end of each simulations
-##' @slot FinalGstarCIs is the list of all 95% credibility interval of the final estimates of Gstar
-##' @slot FinalGstarRatios is the vector of the ratios of the CI, the ratio of the upper to the lower 95% credibility interval
-##' of the final estimates of Gstar
-##' @slot FinalOptimalDose is the vector of the final optimal dose, the minimum of the final TDtargetEndOfTrial estimates and Gstar
-##' estimates
-##' @slot FinalOptimalDoseAtDoseGrid is the vector of the final optimal dose, the minimum of the final TDtargetEndOfTrial estimates
-##' and Gstar estimates at dose Grid
-##' @slot sigma2est the vector of the final posterior mean sigma2 estimates
-##'
-##' @export
+## class ----
+
+#' `PseudoDualSimulations`
+#'
+#' @description `r lifecycle::badge("stable")`
+#' This class conducts trial simulations for designs using both the
+#' DLE and efficacy responses. It defines final values for
+#' efficacy fit and DLE, estimates of Gstar, optimal dose and sigma2.
+#'
+#' @slot fit_eff (`list`)\cr final values of efficacy fit.
+#' @slot final_gstar_estimates (`numeric`)\cr final Gstar estimates.
+#' @slot final_gstar_at_dose_grid (`numeric`)\cr final Gstar estimates at dose grid.
+#' @slot final_gstar_cis (`list`)\cr list of 95% confidence interval for Gstar estimates.
+#' @slot final_gstar_ratios (`numeric`)\cr ratios of confidence intervals for Gstar estimates.
+#' @slot final_optimal_dose (`numeric`)\cr final optimal dose.
+#' @slot final_optimal_dose_at_dose_grid (`numeric`)\cr final optimal dose at dose grid.
+#' @slot sigma2_est (`numeric`)\cr final sigma2 estimates.
+#'
+#' @aliases PseudoDualSimulations
+#' @export
 .PseudoDualSimulations <-
  setClass(
  Class = "PseudoDualSimulations",
- representation(
- fitEff = "list",
- FinalGstarEstimates = "numeric",
- FinalGstarAtDoseGrid = "numeric",
- FinalGstarCIs = "list",
- FinalGstarRatios = "numeric",
- FinalOptimalDose = "numeric",
- FinalOptimalDoseAtDoseGrid = "numeric",
- sigma2est = "numeric"
+ slots = c(
+ fit_eff = "list",
+ final_gstar_estimates = "numeric",
+ final_gstar_at_dose_grid = "numeric",
+ final_gstar_cis = "list",
+ final_gstar_ratios = "numeric",
+ final_optimal_dose = "numeric",
+ final_optimal_dose_at_dose_grid = "numeric",
+ sigma2_est = "numeric"
  ),
- prototype(
- FinalGstarEstimates = c(0.1, 0.1),
- FinalGstarAtDoseGrid = c(0.1, 0.1),
- FinalGstarCIs = list(
- c(0.1, 0.2),
- c(0.1, 0.2)
- ),
- FinalGstarRatios = c(0.01, 0.01),
- FinalOptimalDose = c(0.01, 0.01),
- FinalOptimalDoseAtDoseGrid = c(0.01, 0.01),
- sigma2est = c(0.001, 0.002)
+ prototype = prototype(
+ final_gstar_estimates = c(0.1, 0.1),
+ final_gstar_at_dose_grid = c(0.1, 0.1),
+ final_gstar_cis = list(c(0.1, 0.2), c(0.1, 0.2)),
+ final_gstar_ratios = c(0.01, 0.01),
+ final_optimal_dose = c(0.01, 0.01),
+ final_optimal_dose_at_dose_grid = c(0.01, 0.01),
+ sigma2_est = c(0.001, 0.002)
  ),
  contains = "PseudoSimulations",
  validity = v_pseudo_dual_simulations
  )
 
-validObject(.PseudoDualSimulations())
-
-##' Initialization function for 'DualPseudoSimulations' class
-##' @param fitEff please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalGstarEstimates please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalGstarAtDoseGrid please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalGstarCIs please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalGstarRatios please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalOptimalDose please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param FinalOptimalDoseAtDoseGrid please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param sigma2est please refer to \code{\linkS4class{PseudoDualSimulations}} class object
-##' @param \dots additional parameters from \code{\linkS4class{PseudoSimulations}}
-##' @return the \code{\linkS4class{PseudoDualSimulations}} object
-PseudoDualSimulations <- function(fitEff,
- FinalGstarEstimates,
- FinalGstarAtDoseGrid,
- FinalGstarCIs,
- FinalGstarRatios,
- FinalOptimalDose,
- FinalOptimalDoseAtDoseGrid,
- sigma2est,
+## constructor ----
+
+#' @rdname PseudoDualSimulations-class
+#'
+#' @param fit_eff (`list`)\cr see slot definition.
+#' @param final_gstar_estimates (`numeric`)\cr see slot definition.
+#' @param final_gstar_at_dose_grid (`numeric`)\cr see slot definition.
+#' @param final_gstar_cis (`list`)\cr see slot definition.
+#' @param final_gstar_ratios (`numeric`)\cr see slot definition.
+#' @param final_optimal_dose (`numeric`)\cr see slot definition.
+#' @param final_optimal_dose_at_dose_grid (`numeric`)\cr see slot definition.
+#' @param sigma2_est (`numeric`)\cr see slot definition.
+#' @param \dots additional parameters from [`PseudoSimulations`]
+#' @export
+PseudoDualSimulations <- function(fit_eff,
+ final_gstar_estimates,
+ final_gstar_at_dose_grid,
+ final_gstar_cis,
+ final_gstar_ratios,
+ final_optimal_dose,
+ final_optimal_dose_at_dose_grid,
+ sigma2_est,
  ...) {
  start <- PseudoSimulations(...)
  .PseudoDualSimulations(start,
- fitEff = fitEff,
- FinalGstarEstimates = FinalGstarEstimates,
- FinalGstarAtDoseGrid = FinalGstarAtDoseGrid,
- FinalGstarCIs = FinalGstarCIs,
- FinalGstarRatios = FinalGstarRatios,
- FinalOptimalDose = FinalOptimalDose,
- FinalOptimalDoseAtDoseGrid = FinalOptimalDoseAtDoseGrid,
- sigma2est = sigma2est
+ fit_eff = fit_eff,
+ final_gstar_estimates = final_gstar_estimates,
+ final_gstar_at_dose_grid = final_gstar_at_dose_grid,
+ final_gstar_cis = final_gstar_cis,
+ final_gstar_ratios = final_gstar_ratios,
+ final_optimal_dose = final_optimal_dose,
+ final_optimal_dose_at_dose_grid = final_optimal_dose_at_dose_grid,
+ sigma2_est = sigma2_est
  )
 }
 
 ## default constructor ----
 
 #' @rdname PseudoDualSimulations-class
-#' @note Typically, end users will not use the `.DefaultPseudoDualSimulations()` function.
+#' @note Do not use the `.DefaultPseudoDualSimulations()` function.
 #' @export
 .DefaultPseudoDualSimulations <- function() {
- stop(paste0("Class PseudoDualSimulations cannot be instantiated directly.  Please use one of its subclasses instead."))
+ stop("Class PseudoDualSimulations cannot be instantiated directly. Please use a subclass.")
 }
 
+# nolint start
 # PseudoDualFlexiSimulations ----
 
 ## class ----

R/Simulations-methods.R

@@ -2304,7 +2304,7 @@ setMethod("plot",
  ## save the plot
  plotList[[plotIndex <- plotIndex + 1L]] <-
  qplot(factor(0),
- y = y, data = data.frame(y = x@sigma2est), geom = "boxplot",
+ y = y, data = data.frame(y = x@sigma2_est), geom = "boxplot",
  xlab = "", ylab = "Efficacy variance estimates"
  ) +
  coord_flip() + scale_x_discrete(breaks = NULL)
@@ -2504,26 +2504,26 @@ setMethod("summary",
  }
 
  ## A summary for all final Gstar obtained
- GstarSummary <- summary(object@FinalGstarEstimates)
- ratioGstarSummary <- summary(object@FinalGstarRatios)
+ GstarSummary <- summary(object@final_gstar_estimates)
+ ratioGstarSummary <- summary(object@final_gstar_ratios)
 
- FinalDoseRecSummary <- summary(object@FinalOptimalDose)
+ FinalDoseRecSummary <- summary(object@final_optimal_dose)
  FinalRatioSummary <- summary(object@final_ratios)
 
 
 
  ## find names in the fit efficacy list (check it is with or without samples)
- FitNames <- sapply(object@fitEff, names)
+ FitNames <- sapply(object@fit_eff, names)
  if ("ExpEff" %in% FitNames) {
  ## fitted efficacy level at dose most often selected
  EffFitAtDoseMostSelected <- sapply(
- object@fitEff,
+ object@fit_eff,
  function(f) {
  f$ExpEff[xMostSelected]
  }
  )
  meanEffFitMatrix <- sapply(
- object@fitEff,
+ object@fit_eff,
  "[[",
  "ExpEff"
  )
@@ -2536,7 +2536,7 @@ setMethod("summary",
  } else { ## fitted efficacy level at dose most often selected
  EffFitAtDoseMostSelected <-
  sapply(
- object@fitEff,
+ object@fit_eff,
  function(f) {
  f$middle[xMostSelected]
  }
@@ -2546,7 +2546,7 @@ setMethod("summary",
  ## at each dose level
  ## (this is required for plotting)
  meanEffFitMatrix <- sapply(
- object@fitEff,
+ object@fit_eff,
  "[[",
  "middle"
  )

R/Simulations-validity.R

@@ -123,16 +123,16 @@ v_pseudo_simulations <- function(object) {
 }
 
 #' @describeIn v_pseudo_simulations validates that the [`PseudoDualSimulations`] object
-#' contains valid `fitEff`, `FinalGstarEstimates` , `FinalGstarAtDoseGrid`,
-#' `FinalGstarCIs` , `FinalGstarRatios`, `FinalOptimalDose`, `FinalOptimalDoseAtDoseGrid`
-#' object and valid `sigma2est` simulations.
+#' contains valid `fit_eff`, `final_gstar_estimates` , `final_gstar_at_dose_grid`,
+#' `final_gstar_cis` , `final_gstar_ratios`, `final_optimal_dose`, `final_optimal_dose_at_dose_grid`
+#' object and valid `sigma2_est` simulations.
 
 v_pseudo_dual_simulations <- function(object) {
  v <- Validate()
  nSims <- length(object@data)
  v$check(
- identical(length(object@sigma2est), nSims),
- "sigma2est has to have same length as data"
+ identical(length(object@sigma2_est), nSims),
+ "sigma2_est has to have same length as data"
  )
  v$result()
 }