deploy: 6867b6d

R/laplace.R

@@ -96,7 +96,7 @@ stan_laplace <- function(fn, par_inits, additional_args = list(),
   write_inits(mode_vals, mode_file)
   method_args <- list(
     mode = mode_file,
-    jacobian = jacobian,
+    jacobian = format_bool(jacobian),
     draws = draws
   )
 

R/optimize.R

@@ -76,7 +76,6 @@ stan_optimize <- function(fn, par_inits, additional_args = list(), algorithm = "
                           history_size = NULL) {
   inputs <- prepare_inputs(fn, par_inits, additional_args, grad_fun, lower, upper,
                             output_dir, output_basename)
-
   method_args <- list(
     algorithm = algorithm,
     algorithm_args = list(
@@ -88,9 +87,9 @@ stan_optimize <- function(fn, par_inits, additional_args = list(), algorithm = "
       tol_param = tol_param,
       history_size = history_size
     ),
-    jacobian = jacobian,
+    jacobian = format_bool(jacobian),
     iter = iter,
-    save_iterations = save_iterations
+    save_iterations = format_bool(save_iterations)
   )
 
   output <- list(

R/pathfinder.R

@@ -85,7 +85,7 @@ stan_pathfinder <- function(fn, par_inits, additional_args = list(), grad_fun =
     history_size = history_size,
     num_psis_draws = num_psis_draws,
     num_paths = num_paths,
-    save_single_paths = save_single_paths,
+    save_single_paths = format_bool(save_single_paths),
     max_lbfgs_iters = max_lbfgs_iters,
     num_draws = num_draws,
     num_elbo_draws = num_elbo_draws

R/sample.R

@@ -127,7 +127,7 @@ stan_sample <- function(fn, par_inits, additional_args = list(),
       stepsize_jitter = stepsize_jitter
     ),
     adapt = list(
-      engaged = adapt_engaged,
+      engaged = format_bool(adapt_engaged),
       gamma = adapt_gamma,
       delta = adapt_delta,
       kappa = adapt_kappa,
@@ -138,7 +138,7 @@ stan_sample <- function(fn, par_inits, additional_args = list(),
     ),
     num_samples = num_samples,
     num_warmup = num_warmup,
-    save_warmup = save_warmup,
+    save_warmup = format_bool(save_warmup),
     thin = thin,
     num_chains = 1
   )

R/util.R

@@ -321,3 +321,10 @@ call_stan <- function(args_list, ll_fun, grad_fun, quiet) {
     }
   }
 }
+
+format_bool <- function(input) {
+  if (!is.null(input)) {
+    input <- as.integer(input)
+  }
+  input
+}

R/variational.R

@@ -82,10 +82,10 @@ stan_variational <- function(fn, par_inits, additional_args = list(), algorithm
     grad_samples = grad_samples,
     elbo_samples = elbo_samples,
     eta = eta,
-    adapt = list( engaged = adapt_engaged, iter = adapt_iter),
-    tol_rel_obj = NULL,
-    eval_elbo = NULL,
-    output_samples = NULL
+    adapt = list( engaged = format_bool(adapt_engaged), iter = adapt_iter),
+    tol_rel_obj = tol_rel_obj,
+    eval_elbo = eval_elbo,
+    output_samples = output_samples
     )
 
   output <- list(

bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES

@@ -4,4 +4,4 @@ Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
 LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: 74a91242ddaa543226a88d8099bc4a1f
+MD5sum: 9880efe9041e649441773a6864543f7b

bin/macosx/contrib/4.2/PACKAGES

@@ -4,4 +4,4 @@ Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
 LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: 1b5a7ddea9f6b87d1e7bf03542c32bb6
+MD5sum: 0dc4e29754749246ba29600f8e7145f5

src/Makevars

@@ -1,4 +1,4 @@
-PKG_CPPFLAGS = -I"../inst/include" -I"../inst/include/sundials" -D_REENTRANT -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1
+PKG_CPPFLAGS = -I"../inst/include" -I"../inst/include/sundials" -D_REENTRANT
 PKG_CPPFLAGS += -DSTRICT_R_HEADERS -D_HAS_AUTO_PTR_ETC=0 -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
 PKG_CPPFLAGS += $(shell "${R_HOME}/bin/Rscript" -e "RcppParallel::CxxFlags()" | tail -n 1)
 PKG_LIBS = $(shell "${R_HOME}/bin/Rscript" -e "RcppParallel::RcppParallelLibs()" | tail -n 1)

src/contrib/PACKAGES

@@ -4,5 +4,5 @@ Imports: Rcpp, RcppParallel, posterior, methods, stats, callr
 LinkingTo: Rcpp, RcppEigen, BH, RcppParallel, rapidjsonr
 Suggests: testthat (>= 3.0.0)
 License: MIT + file LICENSE
-MD5sum: 5a66f495c292f8971f3ac7d38e06d24d
+MD5sum: 53affb165a139deab308d67bfbdd40a7
 NeedsCompilation: yes