Merge branch 'release/1.2.11'

.Rbuildignore

@@ -6,3 +6,5 @@ cran-comments.md
 ^doc$
 ^Meta$
 ^CRAN-RELEASE$
+^\.github$
+^CRAN-SUBMISSION$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'

.gitignore

@@ -41,6 +41,5 @@ vignettes/*.pdf
 *.o
 *.so
 *.cc
-*.hpp
 doc
 Meta

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.2.11
+Date: 2023-03-22 19:58:11 UTC
+SHA: ebd5258c187e9b08ce60238e50168d25c2b5e910

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: bayes4psy
-Version: 1.2.10
+Version: 1.2.11
 Title: User Friendly Bayesian Data Analysis for Psychology
 Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
 Authors@R:
@@ -28,10 +28,9 @@ Imports:
     rstan (>= 2.21.2),
     rstantools (>= 2.1.1),
     mcmcse (>= 1.4.1),
-    scales (>= 1.1.1),
     stats (>= 4.0.0),
-    utils (>= 4.0.0)
-Suggests: 
+    RcppParallel
+Suggests:
     testthat (>= 3.0.0),
     rmarkdown (>= 2.5.0),
     knitr (>= 1.30.0)
@@ -40,10 +39,12 @@ LinkingTo:
     rstan (>= 2.21.0),
     BH (>= 1.72.0.3),
     Rcpp (>= 1.0.5),
-    RcppEigen (>= 0.3.3.7.0)
+    RcppEigen (>= 0.3.3.7.0),
+    RcppParallel
 SystemRequirements: GNU make
 VignetteBuilder: knitr
 NeedsCompilation: yes
-RoxygenNote: 7.1.1
+UseLTO: true
+RoxygenNote: 7.2.3
 URL: https://github.com/bstatcomp/bayes4psy
 BugReports: https://github.com/bstatcomp/bayes4psy/issues

NAMESPACE

@@ -32,6 +32,7 @@ import(dplyr)
 import(ggplot2)
 import(methods)
 import(rstan)
-import(rstantools)
+importFrom(RcppParallel,RcppParallelLibs)
 importFrom(rstan,sampling)
+importFrom(rstantools,rstan_config)
 useDynLib(bayes4psy, .registration = TRUE)

NEWS.md

@@ -1,5 +1,9 @@
 # bayes4psy change log
 
+## bayes4psy 1.2.11
+
+Optimized building of RStan models.
+
 ## bayes4psy 1.2.10
 
 Tidied up the README file.

R/b_bootstrap.R

@@ -1,7 +1,7 @@
 #' @title b_bootstrap
 #' @description Performs a Bayesian bootstrap and returns a sample of size n1 representing the posterior distribution of the statistic. Returns a vector if the statistic is one-dimensional (like for mean(...)) or a data.frame if the statistic is multi-dimensional (like for the coefficients of lm).
 #' @author Rasmus Baath
-#' @references \url{http://www.sumsar.net/blog/2015/07/easy-bayesian-bootstrap-in-r/}
+#' @references \url{https://www.sumsar.net/blog/2015/07/easy-bayesian-bootstrap-in-r/}
 #' @references Rubin, D. B. (1981). The Bayesian Bootstrap. The annals of statistics, 9(1), 130-134.
 #' @export
 #' @param data The data as either a vector, matrix or data.frame.
@@ -24,35 +24,35 @@
 #' data <- adaptation_level_small
 #'
 #' # bootstrap
-#' data_bootstrap <- b_bootstrap(data, lm_statistic, n1=1000, n2=1000)
+#' data_bootstrap <- b_bootstrap(data, lm_statistic, n1 = 1000, n2 = 1000)
 #'
-b_bootstrap <- function(data, statistic, n1=1000, n2=1000, use_weights=FALSE, weight_arg=NULL, ...) {
+b_bootstrap <- function(data, statistic, n1 = 1000, n2 = 1000, use_weights = FALSE, weight_arg = NULL, ...) {
   # Draw from a uniform Dirichlet dist. with alpha set to rep(1, n_dim).
   # Using the facts that you can transform gamma distributed draws into
   # Dirichlet draws and that rgamma(n, 1) <=> rexp(n, 1)
-  dirichlet_weights <- matrix(stats::rexp(NROW(data) * n1, 1) , ncol=NROW(data), byrow=TRUE)
+  dirichlet_weights <- matrix(stats::rexp(NROW(data) * n1, 1), ncol = NROW(data), byrow = TRUE)
   dirichlet_weights <- dirichlet_weights / rowSums(dirichlet_weights)
 
-  if(use_weights) {
+  if (use_weights) {
     stat_call <- quote(statistic(data, w, ...))
     names(stat_call)[3] <- weight_arg
     boot_sample <- apply(dirichlet_weights, 1, function(w) {
       eval(stat_call)
     })
   } else {
-    if(is.null(dim(data)) || length(dim(data)) < 2) { # data is a list type of object
+    if (is.null(dim(data)) || length(dim(data)) < 2) { # data is a list type of object
       boot_sample <- apply(dirichlet_weights, 1, function(w) {
-        data_sample <- sample(data, size=n2, replace=TRUE, prob=w)
+        data_sample <- sample(data, size = n2, replace = TRUE, prob = w)
         statistic(data_sample, ...)
       })
     } else { # data is a table type of object
       boot_sample <- apply(dirichlet_weights, 1, function(w) {
-        index_sample <- sample(nrow(data), size=n2, replace=TRUE, prob=w)
-        statistic(data[index_sample, , drop=FALSE], ...)
+        index_sample <- sample(nrow(data), size = n2, replace = TRUE, prob = w)
+        statistic(data[index_sample, , drop = FALSE], ...)
       })
     }
   }
-  if(is.null(dim(boot_sample)) || length(dim(boot_sample)) < 2) {
+  if (is.null(dim(boot_sample)) || length(dim(boot_sample)) < 2) {
     # If the bootstrap sample is just a simple vector return it.
     boot_sample
   } else {

R/bayes4psy-package.R

@@ -8,7 +8,8 @@
 #' @useDynLib bayes4psy, .registration = TRUE
 #' @import methods
 #' @import Rcpp
-#' @import rstantools
+#' @importFrom rstantools rstan_config
+#' @importFrom RcppParallel RcppParallelLibs
 #' @importFrom rstan sampling
 #'
 #' @references

R/reaction_time_class.R

@@ -485,7 +485,7 @@ setMethod(f="compare_means", signature(object="reaction_time_class"), definition
     # provided a list of fits
     i <- 2
     for (fit in arguments$fits) {
-      if (class(fit) != "reaction_time_class") {
+      if (!("reaction_time_class" %in% class(fit))) {
         stop("One of the fits in the fits list is not a valid reaction_time_class object.")
       }
 
@@ -608,7 +608,7 @@ setMethod(f="plot_means_difference", signature(object="reaction_time_class"), de
   } else if (!is.null(arguments$fits)) {
     i <- 2
     for (fit in arguments$fits) {
-      if (class(fit) != "reaction_time_class") {
+      if (!("reaction_time_class" %in% class(fit))) {
         stop("One of the fits in the fits list is not a valid reaction_time_class object.")
       }
 
@@ -737,7 +737,7 @@ setMethod(f="plot_means", signature(object="reaction_time_class"), definition=fu
     } else if (!is.null(arguments$fits)) {
       i <- 2
       for (fit in arguments$fits) {
-        if (class(fit) != "reaction_time_class") {
+        if (!("reaction_time_class" %in% class(fit))) {
           stop("One of the fits in the fits list is not a valid reaction_time_class object.")
         }
 
@@ -836,7 +836,7 @@ setMethod(f="compare_distributions", signature(object="reaction_time_class"), de
     # provided a list of fits
     i <- 2
     for (fit in arguments$fits) {
-      if (class(fit) != "reaction_time_class") {
+      if (!("reaction_time_class" %in% class(fit))) {
         stop("One of the fits in the fits list is not a valid reaction_time_class object.")
       }
 
@@ -927,7 +927,7 @@ setMethod(f="plot_distributions", signature(object="reaction_time_class"), defin
     } else if (!is.null(arguments$fits)) {
       i <- 2
       for (fit in arguments$fits) {
-        if (class(fit) != "reaction_time_class") {
+        if (!("reaction_time_class" %in% class(fit))) {
           stop("One of the fits in the fits list is not a valid reaction_time_class object.")
         }
 
@@ -1040,7 +1040,7 @@ setMethod(f="plot_distributions_difference", signature(object="reaction_time_cla
   } else if (!is.null(arguments$fits)) {
     i <- 2
     for (fit in arguments$fits) {
-      if (class(fit) != "reaction_time_class") {
+      if (!("reaction_time_class" %in% class(fit))) {
         stop("One of the fits in the fits list is not a valid reaction_time_class object.")
       }