update with newest rstantools

DESCRIPTION

@@ -49,7 +49,7 @@ LinkingTo:
 SystemRequirements: C++14, GNU make 
 Biarch: true
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 ByteCompile: true
 URL: https://github.com/helske/walker
 BugReports: https://github.com/helske/walker/issues

R/stanmodels.R

@@ -0,0 +1,28 @@
+# Generated by rstantools.  Do not edit by hand.
+
+# names of stan models
+stanmodels <- c("rw1_model", "rw1_model_naive", "walker_glm", "walker_lm")
+
+# load each stan module
+Rcpp::loadModule("stan_fit4rw1_model_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4rw1_model_naive_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4walker_glm_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4walker_lm_mod", what = TRUE)
+
+# instantiate each stanmodel object
+stanmodels <- sapply(stanmodels, function(model_name) {
+  # create C++ code for stan model
+  stan_file <- if(dir.exists("stan")) "stan" else file.path("inst", "stan")
+  stan_file <- file.path(stan_file, paste0(model_name, ".stan"))
+  stanfit <- rstan::stanc_builder(stan_file,
+                                  allow_undefined = TRUE,
+                                  obfuscate_model_name = FALSE)
+  stanfit$model_cpp <- list(model_cppname = stanfit$model_name,
+                            model_cppcode = stanfit$cppcode)
+  # create stanmodel object
+  methods::new(Class = "stanmodel",
+               model_name = stanfit$model_name,
+               model_code = stanfit$model_code,
+               model_cpp = stanfit$model_cpp,
+               mk_cppmodule = function(x) get(paste0("rstantools_model_", model_name)))
+})

src/Makevars.win

@@ -0,0 +1,11 @@
+# Generated by rstantools.  Do not edit by hand.
+
+STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
+
+STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= '2.26', '-DUSE_STANC3',''))")
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
+PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
+
+CXX_STD = CXX17
+PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/RcppExports.cpp

@@ -61,9 +61,18 @@ BEGIN_RCPP
 END_RCPP
 }
 
+RcppExport SEXP _rcpp_module_boot_stan_fit4rw1_model_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4rw1_model_naive_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4walker_glm_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4walker_lm_mod();
+
 static const R_CallMethodDef CallEntries[] = {
     {"_walker_predict_walker", (DL_FUNC) &_walker_predict_walker, 13},
     {"_walker_predict_walker_glm", (DL_FUNC) &_walker_predict_walker_glm, 15},
+    {"_rcpp_module_boot_stan_fit4rw1_model_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4rw1_model_mod, 0},
+    {"_rcpp_module_boot_stan_fit4rw1_model_naive_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4rw1_model_naive_mod, 0},
+    {"_rcpp_module_boot_stan_fit4walker_glm_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4walker_glm_mod, 0},
+    {"_rcpp_module_boot_stan_fit4walker_lm_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4walker_lm_mod, 0},
     {NULL, NULL, 0}
 };
 

src/stanExports_rw1_model.cc

@@ -0,0 +1,32 @@
+// Generated by rstantools.  Do not edit by hand.
+
+#include <Rcpp.h>
+using namespace Rcpp ;
+#include "stanExports_rw1_model.h"
+
+RCPP_MODULE(stan_fit4rw1_model_mod) {
+
+
+    class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >("rstantools_model_rw1_model")
+
+    .constructor<SEXP,SEXP,SEXP>()
+
+
+    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
+    .method("param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_names)
+    .method("param_names_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_names_oi)
+    .method("param_fnames_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_fnames_oi)
+    .method("param_dims", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_dims)
+    .method("param_dims_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_dims_oi)
+    .method("update_param_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::update_param_oi)
+    .method("param_oi_tidx", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_oi_tidx)
+    .method("grad_log_prob", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::grad_log_prob)
+    .method("log_prob", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::log_prob)
+    .method("unconstrain_pars", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::unconstrain_pars)
+    .method("constrain_pars", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::constrain_pars)
+    .method("num_pars_unconstrained", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::num_pars_unconstrained)
+    .method("unconstrained_param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::unconstrained_param_names)
+    .method("constrained_param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::constrained_param_names)
+    .method("standalone_gqs", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::standalone_gqs)
+    ;
+}