update

DESCRIPTION

@@ -9,7 +9,7 @@ Description: Tool-set to support Bayesian evidence synthesis.  This
     <doi:10.1177/1740774509356002> and Schmidli et al. (2014)
     <doi:10.1111/biom.12242> explain details on the methodology.
 Version: 1.7-4
-Date: 2024-11-19
+Date: 2024-11-20
 Authors@R: c(person("Novartis", "Pharma AG", role = "cph")
             ,person("Sebastian", "Weber", email="[email protected]", role=c("aut", "cre"))
             ,person("Beat", "Neuenschwander", email="[email protected]", role="ctb")
@@ -25,7 +25,7 @@ Imports:
     methods,
     Rcpp (>= 0.12.0),
     RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
+    rstan (>= 2.32.0),
     rstantools (>= 2.4.0),
     assertthat,
     mvtnorm,
@@ -44,8 +44,8 @@ LinkingTo:
     Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),
     RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    StanHeaders (>= 2.26.0)
+    rstan (>= 2.32.0),
+    StanHeaders (>= 2.32.0)
 License: GPL (>=3)
 LazyData: true
 Biarch: true

Makefile

@@ -156,6 +156,11 @@ r-source-check : r-source
 	cd build; tar xvzf $(RPKG)-source.tar.gz
 	cd build; NOT_CRAN=true $(RCMD) CMD check $(RPKG)
 
+PHONY += r-source-release-check
+r-source-release-check : r-source-release
+	cd build; tar xvzf $(RPKG)_$(PKG_VERSION).tar.gz
+	cd build; NOT_CRAN=true $(RCMD) CMD check $(RPKG)
+
 build/installed/$(RPKG)/DESCRIPTION : build/r-source-fast
 	rm -rf build/installed
 	install -d build/installed

NEWS.md

@@ -13,6 +13,8 @@
 * Avoid over and underflow of beta-binomial distribution.
 * Replace calls to deprecated `ggplot2::qplot` with respective calls
   to `ggplot2::ggplot`.
+* Use new `array` notation for `mixstanvar` generated Stan code to
+  make generated Stan programs compatible with Stan >= 2.33
 
 # RBesT 1.7-3 - January 2nd, 2024
 

R/mixstanvar.R

@@ -136,7 +136,7 @@ mixstanvar <- function(..., verbose=FALSE) {
 
     if(includes_density("mvnormMix")) {
         sv <- sv + brms::stanvar(name="mixmvnorm_lpdf", scode="
-real mixmvnorm_lpdf(vector y, vector w, vector[] m, matrix[] L) {
+real mixmvnorm_lpdf(vector y, vector w, array[] vector m, array[] matrix L) {
   int Nc = rows(w);
   vector[Nc] lp_mix;
   for(i in 1:Nc) {
@@ -218,10 +218,10 @@ mix2brms.mvnormMix <- function(mix, name, verbose=FALSE) {
     mvprior <-  brms::stanvar(Nc, glue::glue("{prefix}Nc")) +
         brms::stanvar(p, glue::glue("{prefix}p")) +
         brms::stanvar(array(mix[1,,drop=TRUE], dim=Nc), glue::glue("{prefix}w"), scode=glue::glue("vector[{prefix}Nc] {prefix}w;")) +
-        brms::stanvar(t(mix[2:(p+1),,drop=FALSE]), glue::glue("{prefix}m"), scode=glue::glue("vector[{prefix}p] {prefix}m[{prefix}Nc];")) +
-        brms::stanvar(Sigma, glue::glue("{prefix}sigma"), scode=glue::glue("matrix[{prefix}p, {prefix}p] {prefix}sigma[{prefix}Nc];")) +
+        brms::stanvar(t(mix[2:(p+1),,drop=FALSE]), glue::glue("{prefix}m"), scode=glue::glue("array[{prefix}Nc] vector[{prefix}p] {prefix}m;")) +
+        brms::stanvar(Sigma, glue::glue("{prefix}sigma"), scode=glue::glue("array[{prefix}Nc] matrix[{prefix}p, {prefix}p] {prefix}sigma;")) +
         brms::stanvar(scode=glue::glue("
-matrix[{{prefix}}p, {{prefix}}p] {{prefix}}sigma_L[{{prefix}}Nc];
+array[{{prefix}}Nc] matrix[{{prefix}}p, {{prefix}}p] {{prefix}}sigma_L;
 for (i in 1:{{prefix}}Nc) {
     {{prefix}}sigma_L[i] = cholesky_decompose({{prefix}}sigma[i]);
 }", .open="{{", .close="}}"), block="tdata")

tests/testthat/helper-utils.R

@@ -0,0 +1,10 @@
+
+source_example <- function(example, env=parent.frame(), disable_plots=TRUE) {
+    ex_source <- readLines(system.file("examples", example, package="RBesT", mustWork=TRUE))
+    if(disable_plots) {
+        ex_source <- grep("plot\\(", ex_source, value=TRUE, invert=TRUE)
+    }
+    suppressMessages(ex <- source(textConnection(ex_source),
+                                  local=env, echo=FALSE, verbose=FALSE))
+    invisible(ex)
+}

tools/make-ds.R

@@ -43,7 +43,7 @@ make_internal_ds <- function() {
     calibration_meta["MD5"]  <- vals["MD5"]
 
     pkg_create_date  <- Sys.time()
-    pkg_sha <- "87eef77"
+    pkg_sha <- "1f6edf8"
 
     if (gsub("\\$", "", pkg_sha) == "Format:%h") {
         pkg_sha <- system("git rev-parse --short HEAD", intern=TRUE)