CRAN preparations

Author: wojcieko

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bhmbasket
 Title: Bayesian Hierarchical Models for Basket Trials
-Version: 1.0.0
+Version: 1.1.0
 Authors@R:
   c(
     person(given = 'Stephan',

NEWS.md

@@ -1,3 +1,11 @@
+# bhmbasket 1.1.0
+
+### New and Altered Features
+
+* Added mixture priors and models `"exnex_mix"`, `"exnex_adj_mix"`, `"stratified_mix"`.
+
+* Minor changes in code
+
 # bhmbasket 1.0.0
 
 ### New and Altered Features

R/AnalysisFunctions.R

@@ -818,8 +818,8 @@ mapUniqueTrials <- function (
 #'   \item BHM that combines above approaches: `"exnex_adj"`
 #'   \item Pooled beta-binomial approach: `"pooled"`
 #'   \item Stratified beta-binomial approach: `"stratified"`
-#'   \item BHM with mixture prior on the NEX component: `"exnex_mix"`
-#'   \item Adjusted BHM with mixture prior on the NEX component: `"exnex_adj_mix"`
+#'   \item BHM with mixture prior on the Nex component: `"exnex_mix"`
+#'   \item Adjusted BHM with mixture prior on the Nex component: `"exnex_adj_mix"`
 #'   \item Stratified beta-binomial approach with mixture beta prior: `"stratified_mix"`
 #' }
 #' The posterior distributions of the BHMs are approximated with Markov chain Monte Carlo (MCMC)
@@ -847,9 +847,9 @@ mapUniqueTrials <- function (
 #' The JAGS code for the BHM `"exnex"` was taken from Neuenschwander et al. (2016).
 #' The JAGS code for the BHM `"exnex_adj"` is based on the JAGS code for `"exnex"`.
 #' The JAGS code for the BHM `"exnex_mix"` extends the `"exnex"` model by using
-#' a mixture prior for the NEX component.
+#' a mixture prior for the Nex component.
 #' The JAGS code for the BHM `"exnex_adj_mix"` extends the `"exnex_adj"` model by using
-#' a mixture prior for the NEX component.
+#' a mixture prior for the Nex component.
 #' @seealso
 #'  \code{\link[bhmbasket]{simulateScenarios}}
 #'  \code{\link[bhmbasket]{createTrial}}
@@ -1386,6 +1386,7 @@ prepareAnalysis <- function (
       j_data$Nstrata  <- length(prior_parameters$mu_j)
       j_data$nex_mean <- prior_parameters$mu_j
       j_data$nex_prec <- prior_parameters$tau_j^-2
+      
     }
 
     ## ExNex mix / ExNex Adj mix
@@ -1396,6 +1397,7 @@ prepareAnalysis <- function (
       j_data$w_nex    <- prior_parameters$w_nex
       j_data$mean_nex <- prior_parameters$mean_nex
       j_data$prec_nex <- prior_parameters$sd_nex^-2
+      
     }
 
     ## adjusted models
@@ -1423,11 +1425,12 @@ prepareAnalysis <- function (
 
   }
 
-  return(list(
+  return (list(
     j_parameters = j_parameters,
     j_model_file = j_model_file,
     j_data       = j_data
   ))
+  
 }
 
 #' @export

R/OCFunctions.R

@@ -99,7 +99,7 @@ getAverageNSubjects <- function (
 #' Possible additional parameters for the Bayesian hierarchical models are
 #' `c('mu', 'tau')` for `'berry'`, `'exnex'`, `'exnex_mix'`, `'exnex_adj'`,
 #' and `'exnex_adj_mix'`.
-#' The ExNex-based models can also access posterior weights
+#' The ExNex-based models can also access posterior weights.
 #' `paste0("w_", seq_len(n_cohorts))`.
 #' @return A named list of matrices of estimates of response rates and credible intervals.
 #' Estimates of bias and MSE are included for response rate estimates of simulated trials.

R/PriorFunctions.R

@@ -14,7 +14,7 @@
 #' and `"exnex_adj"`, Default: `0.5`
 #' @return A list with prior parameters of class `prior_parameters_list`
 #' @details
-#' Regarding the default prior parameters for `"berry"`, `"exnex"`, and `"exnex_adj"`:
+#' Regarding the default prior parameters for `"berry"`, `"exnex"`, `"exnex_mix"`, `"exnex_adj"` and `"exnex_adj_mix"`:
 #' \itemize{
 #'   \item `"berry"`: The mean of \eqn{\mu} is set to `0`.
 #'   Its variance is calculated as proposed in "Robust exchangeability designs for early
@@ -29,6 +29,7 @@
 #'   phase clinical trials with multiple strata" (Neuenschwander et al. (2016))
 #'   with regard to `n_worth`.
 #'   The scale parameter of \eqn{\tau} is set to `tau_scale`.
+#'   
 #'   For the Nex components:
 #'   The means of \eqn{\mu_j} are set to the respective target rates.
 #'   The variances of \eqn{\tau_j} are calculated as proposed in "Robust exchangeability designs for early
@@ -42,18 +43,19 @@
 #'   phase clinical trials with multiple strata" (Neuenschwander et al. (2016))
 #'   with regard to `n_worth`, see also \code{\link[bhmbasket]{getMuVar}}.
 #'   The scale parameter of \eqn{\tau} is set to `tau_scale`.
+#'   
 #'   For the Nex components:
 #'   The means of \eqn{\mu_j} are set to the `0`.
 #'   The variances of \eqn{\tau_j} are calculated as proposed in "Robust exchangeability designs for early
 #'   phase clinical trials with multiple strata" (Neuenschwander et al. (2016))
 #'   with regard to `n_worth`, see also \code{\link[bhmbasket]{getMuVar}}.
 #'   \item `"exnex_mix"`: Uses the same default Ex prior construction as `"exnex"`.
-#'   The NEX part is specified as a one-component mixture prior with
+#'   The Nex part default parameters are specified as a one-component mixture prior with
 #'   `w_nex = 1`, `mean_nex = matrix(logit(target_rates), nrow = 1)`,
 #'   and `sd_nex = matrix(sqrt(getMuVar(target_rates, 0, n_worth)), nrow = 1)`.
-#'   This keeps the default mixture representation compatible with the mix-model interface.
+#'   This keeps the default mixture representation compatible with the `getPriorParameter()`'s input.
 #'   \item `"exnex_adj_mix"`: Uses the same default Ex prior construction as `"exnex_adj"`.
-#'   The NEX part is specified as a one-component mixture prior with
+#'   The Nex part is specified as a one-component mixture prior with
 #'   `w_nex = 1`, `mean_nex = matrix(logit(target_rates), nrow = 1)`,
 #'   and `sd_nex = matrix(sqrt(getMuVar(target_rates, 0, n_worth)), nrow = 1)`.
 #'   The Ex component is centered as in `"exnex_adj"`.
@@ -64,9 +66,9 @@
 #'   The scale parameters \eqn{\alpha_j} are set to `target_rates * n_worth`.
 #'   The scale parameters \eqn{\beta_j} are set to `(1 - target_rates) * n_worth`.
 #'   \item `"stratified_mix"`:
-#'   A two-component beta mixture prior is created for each cohort.
-#'   The first component uses
-#'   `a_j = target_rates * n_worth` and `b_j = (1 - target_rates) * n_worth`.
+#'   A two-component beta mixture prior is created by default for each cohort.
+#'   The first component uses `a_j = target_rates * n_worth` and
+#'   `b_j = (1 - target_rates) * n_worth`.
 #'   The second component is a vague prior with `a_j = 1` and `b_j = 1`.
 #'   The default mixture weights are `c(0.8, 0.2)`.
 #' }
@@ -565,34 +567,34 @@ getPriorParametersExNex <- function (
 #' @description This function sets prior parameters for the analysis method `"exnex"`
 #' for use in \code{\link[bhmbasket]{performAnalyses}}.
 #'
-#' It supports two specifications for the NEX part:
+#' It supports two specifications for the Nex part:
 #' \itemize{
-#'   \item the standard ExNex specification with cohort-specific NEX priors via `mu_j` and `tau_j`
-#'   \item an extended specification with a mixture prior on the NEX part via `w_nex`, `mean_nex`, and `sd_nex`
+#'   \item the standard ExNex specification with cohort-specific Nex priors via `mu_j` and `tau_j`
+#'   \item an extended specification with a mixture prior on the Nex part via `w_nex`, `mean_nex`, and `sd_nex`
 #' }
 #'
 #' @param mu_mean A numeric for the mean of \eqn{\mu}
 #' @param mu_sd A positive numeric for the standard deviation of \eqn{\mu}
 #' @param tau_scale A positive numeric for the scale parameter of \eqn{\tau}
-#' @param mu_j A vector of numerics for the means \eqn{\mu_j} of the standard NEX priors.
+#' @param mu_j A vector of numerics for the means \eqn{\mu_j} of the standard Nex priors.
 #'   Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
 #' @param tau_j A vector of positive numerics for the standard deviations \eqn{\tau_j}
-#'   of the standard NEX priors. Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
+#'   of the standard Nex priors. Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
 #' @param w_j A numeric in `(0, 1)` for the weight of the Ex component, or a numeric vector
 #'   of mixture weights summing to 1 if multiple Ex components are specified.
 #' @param w_nex An optional numeric vector of mixture weights in \eqn{[0,1]} summing to 1
-#'   for the NEX mixture prior.
-#' @param mean_nex An optional numeric matrix of NEX mixture means with one row per NEX
+#'   for the Nex mixture prior.
+#' @param mean_nex An optional numeric matrix of Nex mixture means with one row per Nex
 #'   mixture component and one column per cohort.
-#' @param sd_nex An optional positive numeric matrix of NEX mixture standard deviations with
-#'   one row per NEX mixture component and one column per cohort.
+#' @param sd_nex An optional positive numeric matrix of Nex mixture standard deviations with
+#'   one row per Nex mixture component and one column per cohort.
 #'
 #' @return A list with prior parameters of class `prior_parameters_list`
 #'
 #' @details
 #' This function sets the prior parameters for the method proposed by Neuenschwander et al. (2016).
 #' If `w_nex`, `mean_nex`, and `sd_nex` are all `NULL`, the standard ExNex formulation is used.
-#' Otherwise, the NEX part is specified as a finite mixture prior.
+#' Otherwise, the Nex part is specified as a finite mixture prior.
 #'
 #' @author Stephan Wojciekowski
 #'
@@ -607,7 +609,7 @@ getPriorParametersExNex <- function (
 #'   w_j       = 0.8
 #' )
 #'
-#' ## ExNex with NEX mixture prior
+#' ## ExNex with Nex mixture prior
 #' prior_parameters_exnex_mix <- setPriorParametersExNex(
 #'   mu_mean   = 0,
 #'   mu_sd     = 1,
@@ -784,7 +786,7 @@ getPriorParametersExNexAdj <- function (
     w_j, lower = 0, upper = 1, len = 1, .var.name = error_w_j
   )
 
-  ## mixed NEX validation only if mixture inputs are supplied
+  ## mixed Nex validation only if mixture inputs are supplied
   if (!(is.null(w_nex) && is.null(mean_nex) && is.null(sd_nex))) {
     checkmate::assertNumeric(
       w_nex, any.missing = FALSE, lower = 0, upper = 1, .var.name = error_w_nex
@@ -842,35 +844,35 @@ getPriorParametersExNexAdj <- function (
 #' @description This function sets prior parameters for the analysis method `"exnex_adj"`
 #' for use in \code{\link[bhmbasket]{performAnalyses}}.
 #'
-#' It supports two specifications for the NEX part:
+#' It supports two specifications for the Nex part:
 #' \itemize{
-#'   \item the standard ExNex Adjusted specification with cohort-specific NEX priors via `mu_j` and `tau_j`
-#'   \item an extended specification with a mixture prior on the NEX part via `w_nex`, `mean_nex`, and `sd_nex`
+#'   \item the standard ExNex Adjusted specification with cohort-specific Nex priors via `mu_j` and `tau_j`
+#'   \item an extended specification with a mixture prior on the Nex part via `w_nex`, `mean_nex`, and `sd_nex`
 #' }
 #'
 #' @param mu_mean [numeric] Mean of \eqn{\mu}
 #' @param mu_sd [numeric] Positive standard deviation of \eqn{\mu}
 #' @param tau_scale [numeric] Positive scale parameter of \eqn{\tau}
-#' @param mu_j [numeric] Vector of means \eqn{\mu_j} for the standard NEX priors.
+#' @param mu_j [numeric] Vector of means \eqn{\mu_j} for the standard Nex priors.
 #'   Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
 #' @param tau_j [numeric] Vector of positive standard deviations \eqn{\tau_j}
-#'   for the standard NEX priors. Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
+#'   for the standard Nex priors. Ignored if `w_nex`, `mean_nex`, and `sd_nex` are provided.
 #' @param w_j [numeric] Weight of the Ex component in `(0, 1)`, or a numeric vector
 #'   of mixture weights summing to 1 if multiple Ex components are specified.
 #' @param w_nex [numeric] Optional vector of mixture weights in \eqn{[0,1]} summing to 1
-#'   for the NEX mixture prior.
-#' @param mean_nex [numeric] Optional matrix of NEX mixture means with one row per NEX
+#'   for the Nex mixture prior.
+#' @param mean_nex [numeric] Optional matrix of Nex mixture means with one row per Nex
 #'   mixture component and one column per cohort.
-#' @param sd_nex [numeric] Optional positive matrix of NEX mixture standard deviations with
-#'   one row per NEX mixture component and one column per cohort.
+#' @param sd_nex [numeric] Optional positive matrix of Nex mixture standard deviations with
+#'   one row per Nex mixture component and one column per cohort.
 #'
 #' @return A list with prior parameters of class `prior_parameters_list`
 #'
 #' @details
 #' This function sets prior parameters for the ExNex Adjusted method, which combines
 #' the approach proposed by Neuenschwander et al. (2016) and the approach proposed by
 #' Berry et al. (2013). If `w_nex`, `mean_nex`, and `sd_nex` are all `NULL`, the standard
-#' ExNex Adjusted formulation is used. Otherwise, the NEX part is specified as a finite
+#' ExNex Adjusted formulation is used. Otherwise, the Nex part is specified as a finite
 #' mixture prior.
 #'
 #' @author Stephan Wojciekowski
@@ -886,7 +888,7 @@ getPriorParametersExNexAdj <- function (
 #'   w_j       = 0.8
 #' )
 #'
-#' ## ExNex Adjusted with NEX mixture prior
+#' ## ExNex Adjusted with Nex mixture prior
 #' prior_parameters_exnex_adj_mix <- setPriorParametersExNexAdj(
 #'   mu_mean   = 0,
 #'   mu_sd     = 1,
@@ -1004,7 +1006,7 @@ setPriorParametersExNexAdj <- function (
 
   } else {
 
-    ## mixed NEX version
+    ## mixed Nex version
     checkmate::assertNumeric(
       w_nex, any.missing = FALSE, lower = 0, upper = 1, .var.name = error_w_nex
     )
@@ -1326,13 +1328,14 @@ getPriorParametersStratifiedMix <- function (
 #' for use in \code{\link[bhmbasket]{performAnalyses}}.
 #' @param w A numeric vector of mixture weights in \eqn{[0,1]} summing to 1.
 #' @param a_j A positive numeric matrix of beta shape parameters \eqn{\alpha_j},
-#' with one row per mixture component and one column per cohort.
+#' with rows per mixture component and columns per cohort.
 #' @param b_j A positive numeric matrix of beta shape parameters \eqn{\beta_j},
-#' with one row per mixture component and one column per cohort.
+#' with rows per mixture component and columns per cohort.
 #' @return A list with prior parameters of class `prior_parameters_list`
 #' @details
 #' The method `"stratified_mix"` is a beta-binomial model that assesses each cohort
 #' individually with a finite mixture beta prior.
+#' See also the R package `RBesT`.
 #' @author Stephan Wojciekowski
 #' @examples
 #' prior_parameters_stratified_mix <- setPriorParametersStratifiedMix(

cran-comments.md

@@ -2,27 +2,21 @@ Maintainer: 'Stephan Wojciekowski <[email protected]
 
 ## Test environments & R CMD check results
 
-- Macbuilder aarch64-aarch64-apple-darwin20, macOS 26.2 (25C56), Apple M1, R 4.6.0 (r-devel-macosx-arm64), SDK 14.4 (clang-1700.6.3.2)  
+- Macbuilder aarch64-aarch64-apple-darwin20, R Under development (unstable) (2026-03-22 r89674)
   - Status: OK
-- Winbuilder Windows Server 2022 x64 (build 20348), x86_64-w64-mingw32, R Under development (unstable) (2026-02-18 r89435 ucrt)
+- Winbuilder Windows Server 2022 x64 (build 20348), x86_64-w64-mingw32, R 4.6.0 beta (2026-04-12 r89874 ucrt)
   - Status: OK
-- GitHub Action Linux: R 4.5.2 (2025-10-31), x86_64-pc-linux-gnu
+- GitHub Action Linux: R version 4.5.3 (2026-03-11), x86_64-pc-linux-gnu
   - Status: OK
-- GitHub Action Mac: R 4.5.2 (2025-10-31), aarch64-apple-darwin20
+- GitHub Action Mac: R version 4.5.3 (2026-03-11), aarch64-apple-darwin20
   - Status: OK
-- GitHub Action Windows: R 4.5.2 (2025-10-31 ucrt), x86_64-w64-mingw32  
+- GitHub Action Windows: R version 4.5.3 (2026-03-11 ucrt), x86_64-w64-mingw32  
   - Status: OK
 
-## From NEWS.md: bhmbasket 1.0.0
+## bhmbasket 1.1.0
 
-* Added structured unit tests for core functionality
+### New and Altered Features
 
-* Integrated code coverage
-
-* Replaced validation logic with checkmate assertions and removed unused helper functions
-
-* Replaced dependency on R2jags to rjags
-
-* Added Github Actions workflows for automated R CMD check and CI validation
+* Added mixture priors and models `"exnex_mix"`, `"exnex_adj_mix"`, `"stratified_mix"`.
 
 * Minor changes in code

devtools_script.R

@@ -49,12 +49,14 @@ devtools::install_deps()
 devtools::run_examples()
 devtools::spell_check()
 devtools::check()
-devtools::check_win_devel()
+devtools::check_win_devel() # https://win-builder.r-project.org/upload.aspx
+devtools::check_mac_release()
 # devtools::check_rhub()
 devtools::document()
 ## Update your NEWS file
 ## Update DESCRIPTION (e.g. version number)
 devtools::spell_check()
+spelling::update_wordlist()
 ## Update cran-comments.md
 devtools::check()