Sync with the development branch of Stan

.gitmodules

@@ -2,4 +2,4 @@
 	path = StanHeaders/inst/include/upstream
 	url = https://github.com/stan-dev/stan.git
 	ignore = dirty
-	branch = StanHeaders_2.26
+	branch = develop

StanHeaders/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: StanHeaders
 Title: C++ Header Files for Stan
-Version: 2.26.23
+Version: 2.33.1.9000
 Authors@R: c(person("Ben",family="Goodrich", email="[email protected]", role=c('cre','aut')),
              person("Joshua", "Pritikin", role = "ctb"),
              person("Andrew", "Gelman", role = "aut"),
@@ -24,7 +24,7 @@ Authors@R: c(person("Ben",family="Goodrich", email="[email protected]
              person("Dustin", "Tran", role = "aut"),
              person("Michael", "Malecki", role = "aut"),
              person("Yuanjun", "Gao", role = "aut"),
-             person("Hamada S.", "Badr", role = c("ctb"),
+             person("Hamada S.", "Badr", role = c("aut"),
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0002-9808-2344")),
              person("Trustees of", "Columbia University", role = "cph"),
@@ -35,7 +35,7 @@ URL: https://mc-stan.org/
 Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
 Imports: RcppParallel (>= 5.1.4)
 Suggests: Rcpp, BH (>= 1.75.0-0), knitr (>= 1.36), rmarkdown, Matrix, methods, rstan, withr
-LinkingTo: RcppEigen, RcppParallel (>= 5.1.4)
+LinkingTo: RcppEigen (>= 0.3.3.9.3), RcppParallel (>= 5.1.4)
 VignetteBuilder: knitr
 SystemRequirements: GNU make, pandoc
 Depends: R (>= 3.4.0)

StanHeaders/inst/include/libsundials

@@ -1 +1 @@
-upstream/lib/stan_math/lib/sundials_5.6.1/
+upstream/lib/stan_math/lib/sundials_6.1.1/

rstan/rstan/DESCRIPTION

@@ -1,18 +1,18 @@
 Package: rstan
 Type: Package
 Title: R Interface to Stan
-Version: 2.26.24
+Version: 2.33.1.9000
 Authors@R: c(person("Jiqiang", "Guo", email = "[email protected]", role = "aut"),
              person("Jonah", "Gabry", email = "[email protected]", role = "aut"),
              person("Ben", "Goodrich", email = "[email protected]", role = c("cre", "aut")),
              person("Andrew", "Johnson", email = "[email protected]", role = "aut"),
              person("Sebastian", "Weber", email = "[email protected]", role = "aut"),
+             person("Hamada S.", "Badr", role = c("aut"),
+                    email = "[email protected]",
+                    comment = c(ORCID = "0000-0002-9808-2344")),
              person("Daniel", "Lee", role = "ctb"),
              person("Krzysztof", "Sakrejda", role = "ctb"),
              person("Modrak", "Martin", role = "ctb"),
-             person("Hamada S.", "Badr", role = c("ctb"),
-                    email = "[email protected]",
-                    comment = c(ORCID = "0000-0002-9808-2344")),
              person("Trustees of", "Columbia University", role = "cph"),
              person("Oleg", "Sklyar", role = "cph", comment = "R/cxxfunplus.R"),
              person("The R", "Core Team", role = "cph", comment = "R/pairs.R, R/dynGet.R"),
@@ -46,12 +46,12 @@ Imports:
     ggplot2 (>= 3.3.5)
 Depends:
     R (>= 3.4.0),
-    StanHeaders (>= 2.26.22)
+    StanHeaders (>= 2.33.1)
 LinkingTo:
     Rcpp (>= 1.0.7),
-    RcppEigen (>= 0.3.3.9.1),
+    RcppEigen (>= 0.3.3.9.3),
     BH (>= 1.75.0-0),
-    StanHeaders (>= 2.26.22),
+    StanHeaders (>= 2.33.1),
     RcppParallel (>= 5.1.4)
 Suggests:
     testthat (>= 3.0.4),
@@ -64,7 +64,6 @@ Suggests:
     rstudioapi,
     Matrix,
     knitr,
-    rstanarm,
     coda,
     V8
 URL: https://mc-stan.org/rstan/, https://discourse.mc-stan.org

rstan/rstan/R/misc.R

@@ -863,7 +863,7 @@ remove_empty_pars <- function(pars, model_dims) {
   # following stan model code:
   #
   # transformed data { int n; n <- 0; }
-  # parameters { real y[n]; }
+  # parameters { array[n] real y; }
   #
   # Args:
   #   pars: a character vector of parameters names

rstan/rstan/inst/NEWS

@@ -1,3 +1,31 @@
+Sat Sep 15, 2023
+
+1. Updated Stan to C++ compiler v2.33.1.
+
+Sun Sep 10, 2023
+
+1. Fixed the deprecated array syntax.
+
+Sat Sep 9, 2023
+
+1. Updated Stan to C++ compiler v2.33.0.
+
+Wed May 17, 2023
+
+1. Updated Stan to C++ compiler v2.32.2 (development).
+
+Tue May 2, 2023
+
+1. Updated Stan to C++ compiler v2.32.1 (development).
+
+Sat April 22, 2023
+
+1. Updated Stan to C++ compiler v2.32.0 (development).
+
+Sun April 16, 2023
+
+1. Updated Stan to C++ compiler v2.32.0-rc1 (development).
+
 Thu March 16, 2023
 
 1. Fixed `rstan::expose_stan_functions()` C++ compilation error (#1050).

rstan/rstan/inst/include/rstan/stan_args.hpp

@@ -9,7 +9,6 @@
 #include <algorithm>
 #include <rstan/io/r_ostream.hpp>
 #include <stan/version.hpp>
-#include <boost/lexical_cast.hpp>
 
 namespace rstan {
 
@@ -46,7 +45,7 @@ namespace rstan {
 
     inline unsigned int sexp2seed(SEXP seed) {
       if (TYPEOF(seed) == STRSXP)
-        return boost::lexical_cast<unsigned int>(Rcpp::as<std::string>(seed));
+        return std::stoull(Rcpp::as<std::string>(seed));
       return Rcpp::as<unsigned int>(seed);
     }
 

rstan/rstan/man/rstan.Rd

@@ -93,7 +93,7 @@
 stanmodelcode <- "
 data {
   int<lower=0> N;
-  real y[N];
+  array[N] real y;
 }
 
 parameters {

rstan/rstan/man/sflist2stanfit.Rd

@@ -72,8 +72,8 @@ data {
   int<lower=1> N;
 } 
 parameters {
-  real y1[N]; 
-  real y2[N]; 
+  array[N] real y1;
+  array[N] real y2; 
 } 
 model {
   y1 ~ normal(0, 1);

rstan/rstan/man/stan.Rd

@@ -386,7 +386,7 @@ stan(file, model_name = "anon_model", model_code = "", fit = NA,
   }
 
   Stan treats a vector of length 1 in R as a scalar.  So technically
-  if, for example, \code{"real y[1];"} is defined in the data block, an array
+  if, for example, \code{"array[1] real y;"} is defined in the data block, an array
   such as \code{"y = array(1.0, dim = 1)"} in R should be used. This
   is also the case for specifying initial values since the same
   underlying approach for reading data from R in Stan is used, in which
@@ -425,7 +425,7 @@ stan(file, model_name = "anon_model", model_code = "", fit = NA,
 library(rstan)
 scode <- "
 parameters {
-  real y[2];
+  array[2] real y;
 }
 model {
   y[1] ~ normal(0, 1);
@@ -447,7 +447,7 @@ e2 <- extract(fit2, permuted = FALSE)
 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] = 0.5796;  y[2] = 0.2276;   y[3]  = -0.2959;
     y[4] = -0.3742; y[5] = 0.3885;   y[6]  = -2.1585;
     y[7] = 0.7111;  y[8] = 1.4424;   y[9]  = 2.5430;

rstan/rstan/man/stanc.Rd

@@ -121,7 +121,7 @@ Translate Stan model specification to C++ code
 stanmodelcode <- "
 data {
   int<lower=0> N;
-  real y[N];
+  array[N] real y;
 }
 
 parameters {

rstan/rstan/man/stanfit-class.Rd

@@ -200,7 +200,7 @@ summarizing results and various access methods also allow the underlying data
 showClass("stanfit")
 ecode <- '
   parameters {
-    real<lower=0> y[2];
+    array[2] real<lower=0> y;
   } 
   model {
     y ~ exponential(1);
@@ -241,7 +241,7 @@ print(y1star) # y1start should equal to y1
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit-method-extract.Rd

@@ -57,8 +57,8 @@
 \examples{\dontrun{
 ex_model_code <- '
   parameters {
-    real alpha[2,3];
-    real beta[2]; 
+    array[2, 3] real alpha;
+    array[2] real beta; 
   } 
   model {
     for (i in 1:2) for (j in 1:3) 
@@ -110,7 +110,7 @@ dimnames(fit_ss2)
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit-method-summary.Rd

@@ -48,7 +48,7 @@ array of MCMC draws as its input rather than a \code{stanfit} object.
 \examples{\dontrun{
 ecode <- '
   parameters {
-    real<lower=0> y[2];
+    array[2] real<lower=0> y;
   } 
   model {
     y ~ exponential(1);

rstan/rstan/man/stanfit-method-traceplot.Rd

@@ -55,7 +55,7 @@
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit2array-method.Rd

@@ -71,8 +71,8 @@
 \examples{\dontrun{
 ex_model_code <- '
   parameters {
-    real alpha[2,3];
-    real beta[2]; 
+    array[2, 3] real alpha;
+    array[2] real beta; 
   } 
   model {
     for (i in 1:2) for (j in 1:3) 

rstan/rstan/src/chains.cpp

@@ -21,7 +21,6 @@
 #include <boost/accumulators/accumulators.hpp>
 #include <boost/accumulators/statistics/stats.hpp>
 #include <boost/accumulators/statistics/mean.hpp>
-#include <boost/lexical_cast.hpp>
 #include <boost/random/additive_combine.hpp> // L'Ecuyer RNG
 #include <boost/random/uniform_int_distribution.hpp>
 #include <fstream>
@@ -51,7 +50,7 @@ class perm_args {
 
   inline unsigned int sexp2seed(SEXP seed) {
     if (TYPEOF(seed) == STRSXP)
-      return boost::lexical_cast<unsigned int>(Rcpp::as<std::string>(seed));
+      return std::stoull(Rcpp::as<std::string>(seed));
     return Rcpp::as<unsigned int>(seed);
   }
 

rstan/rstan/tests/testthat/test-partial_inits.R

@@ -4,7 +4,7 @@ test_that("partial_inits works", {
   stan_model_code <- "
     data {
       int<lower=0> N;
-      real y[N];
+      array[N] real y;
     }
 
     parameters {

rstan/rstan/tests/testthat/test-stan_fun.R

@@ -6,7 +6,7 @@ test_that("Running stan() in parallel works",  {
   data {
     int N;
   } parameters {
-    real y[N];
+    array[N] real y;
   }  model {
     y ~ normal(0, 1);
   }
@@ -48,11 +48,11 @@ test_that("stan() arguments works", {
   diag_fname2 <- "diag2.csv"
   model_code <- "
     parameters {
-      real y[2];
+      array[2] real y;
       real alpha;
     }
     transformed parameters {
-      real y2[2, 2];
+      array[2, 2] real y2;
       y2[1, 1] = y[1];
       y2[1, 2] = -y[1];
       y2[2, 1] = -y[2];

rstan/rstan/tests/testthat/test-stanfit.R

@@ -8,11 +8,11 @@ test_that("outputing csv and extracting work", {
       n = 0;
     }
     parameters {
-      real y[2];
-      real zeroleny[n];
+      array[2] real y;
+      array[n] real zeroleny;
     }
     transformed parameters {
-      real y2[2, 2];
+      array[2, 2] real y2;
       y2[1, 1] = y[1];
       y2[1, 2] = -y[1];
       y2[2, 1] = -y[2];
@@ -22,7 +22,7 @@ test_that("outputing csv and extracting work", {
       y ~ normal(0, 1);
     }
     generated quantities {
-      real y3[3, 2, 3];
+      array[3, 2, 3] real y3;
       y3[1,1,1] = 1;   y3[1,1,2] = 2;   y3[1,1,3] = 3;
       y3[1,2,1] = 4;   y3[1,2,2] = 5;   y3[1,2,3] = 6;
       y3[2,1,1] = 7;   y3[2,1,2] = 8;   y3[2,1,3] = 9;
@@ -182,7 +182,7 @@ test_that("grad log is correct", {
 
   code <- "
     data {
-      real y[20];
+      array[20] real y;
     }
     parameters {
       real mu;
@@ -241,7 +241,7 @@ test_that("Specifying arguments and data works", {
   code <- "
     data {
       int N;
-      real y[N];
+      array[N] real y;
     }
     parameters {
       real mu;

sh_b.sh

@@ -3,7 +3,7 @@
 red='\033[0;31m'
 NC='\033[0m' # no color
 
-STAN_REPO_BRANCH=StanHeaders_2.26
+STAN_REPO_BRANCH=develop
 grepstanbranch=`git ls-remote --heads https://github.com/stan-dev/stan.git | grep "/${STAN_REPO_BRANCH}"`
 if [ -z "$grepstanbranch" ]; then
     echo -e "${red}ERROR:${NC} stan repo does not have {STAN_REPO_BRANCH}"