d

earge branch 'main' of https://github.com/google/bsynth into main

merge ok

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,10 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll
+*.cc
+*.h
+*.Rproj

DESCRIPTION

@@ -16,21 +16,28 @@ Depends:
     R (>= 3.4.0)
 Imports:
     R6,
-    Rcpp,
-    RcppParallel,
+    Rcpp (>= 0.12.0),
+    RcppParallel (>= 5.0.1),
     cubelyr,
     dplyr,
     ggplot2,
     glue,
     magrittr,
     methods,
     purrr,
-    rstan,
-    rstantools,
+    rstan (>= 2.18.1),
+    rstantools (>= 2.1.1),
     scales,
     tibble,
     tidyr,
-    vizdraws
+    vizdraws (>= 1.1)
+LinkingTo: 
+    BH (>= 1.66.0),
+    Rcpp (>= 0.12.0),
+    RcppEigen (>= 0.3.3.3.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    StanHeaders (>= 2.18.0)
 Suggests:
     knitr,
     rmarkdown,

Docker/build_test/.gitignore

@@ -0,0 +1 @@
+*.tar.gz

Docker/build_test/Dockerfile

@@ -0,0 +1,45 @@
+FROM rocker/r-base:latest
+LABEL maintainer="Ignacio Martinez <[email protected]>"
+
+RUN apt-get update -qq \
+ && apt-get install -y \
+        libxml2-dev \
+        libssl-dev \
+        libcurl4-openssl-dev \
+        libv8-dev \
+        texlive-latex-extra \
+	libharfbuzz-dev \
+	libfribidi-dev \
+	libpng-dev \
+	libtiff5-dev \
+	libjpeg-dev \
+	libpq5 \
+	pandoc \
+ && install.r \
+  magrittr \
+  R6 \
+  Rcpp \
+  cubelyr \
+  dplyr \
+  ggplot2 \
+  glue \
+  magrittr \
+  methods \
+  purrr \
+  rstan \
+  rstantools \
+  scales \
+  tibble \
+  tidyr \
+  vizdraws \
+  devtools \
+  BH \
+  RcppEigen \
+  methods \
+  rmarkdown \
+  vizdraws \
+  knitr \
+  rmarkdown \
+  roxygen2 \
+  gsynth
+

Docker/build_test/build.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+docker build --tag bsynth .
+
+docker run --rm \
+  -v $(pwd):/tmp/working_dir \
+  -v $(pwd)/../..:/tmp/bsynth \
+  -w /tmp/working_dir \
+  bsynth \
+  R -e "devtools::test(pkg = '/tmp/bsynth'); devtools::build(pkg = '/tmp/bsynth', path = '/tmp/working_dir, binary = TRUE')"
+
+

NAMESPACE

@@ -7,3 +7,4 @@ import(Rcpp)
 import(methods)
 importFrom(magrittr,"%>%")
 importFrom(rstan,sampling)
+useDynLib(bsynth, .registration = TRUE)

R/bfactor.R

@@ -153,9 +153,9 @@ bayesianFactor <- R6::R6Class(
         #  dplyr::select(-{{id}}) %>%
         #  any(is.na()))
 
-        private$stan_model <- bsynth.models::factor_model_with_covariates
+        private$stan_model <- stanmodels$factor_model_with_covariates
       } else {
-        private$stan_model <- bsynth.models::factor_model_without_covariates
+        private$stan_model <- stanmodels$factor_model_without_covariates
       }
 
       private$data <- data %>%

R/factory.R

@@ -248,35 +248,35 @@ bayesianSynth <- R6::R6Class(
       if (length(private$treated_ids) == 1) {
         if (is.null(covariates)) {
           if (gp) {
-            private$stan_model <- bsynth.models::model2 # stanmodels$model2
+            private$stan_model <- stanmodels$model2
           } else {
             if (predictor_match) {
-              private$stan_model <- bsynth.models::model1_gammaOmega # gamma BCS
+              private$stan_model <- stanmodels$model1_gammaOmega
             } else {
-              private$stan_model <- bsynth.models::model1 # stanmodels$model1
+              private$stan_model <- stanmodels$model1
             }
           }
         } else {
           if (gp) {
-            private$stan_model <- bsynth.models::model4 # stanmodels$model4
+            private$stan_model <- stanmodels$model4
           } else {
-            private$stan_model <- bsynth.models::model3 # stanmodels$model3
+            private$stan_model <- stanmodels$model3
           }
           private$covariates <- covariates %>%
             dplyr::arrange(!!private$time)
         }
       } else {
         if (is.null(covariates)) {
           if (gp) {
-            private$stan_model <- bsynth.models::model8 # stanmodels$model8
+            private$stan_model <- stanmodels$model8
           } else {
-            private$stan_model <- bsynth.models::model5 # stanmodels$model5
+            private$stan_model <- stanmodels$model5
           }
         } else {
           if (gp) {
-            private$stan_model <- bsynth.models::model7 # stanmodels$model7
+            private$stan_model <- stanmodels$model7
           } else {
-            private$stan_model <- bsynth.models::model6 # stanmodels$model6
+            private$stan_model <- stanmodels$model6
           }
           private$covariates <- covariates %>%
             dplyr::arrange(!!private$time)

R/stanmodels.R

@@ -0,0 +1,36 @@
+# Generated by rstantools.  Do not edit by hand.
+
+# names of stan models
+stanmodels <- c("factor_functions", "factor_model_with_covariates", "factor_model_without_covariates", "model1_gammaOmega", "model1", "model2", "model3", "model4", "model5", "model6", "model7", "model8")
+
+# load each stan module
+Rcpp::loadModule("stan_fit4factor_functions_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4factor_model_with_covariates_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4factor_model_without_covariates_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model1_gammaOmega_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model1_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model2_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model3_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model4_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model5_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model6_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model7_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4model8_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("model_", model_name)))
+})

inst/include/stan_meta_header.hpp

@@ -0,0 +1 @@
+// Insert all #include<foo.hpp> statements here

src/Makevars

@@ -0,0 +1,9 @@
+# Generated by rstantools.  Do not edit by hand.
+
+STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
+
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error
+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 = CXX14

src/Makevars.win

@@ -0,0 +1,9 @@
+# Generated by rstantools.  Do not edit by hand.
+
+STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
+
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1
+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 = CXX14

src/RcppExports.cpp

@@ -0,0 +1,47 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <RcppEigen.h>
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+
+RcppExport SEXP _rcpp_module_boot_stan_fit4factor_functions_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4factor_model_with_covariates_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4factor_model_without_covariates_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model1_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model1_gammaOmega_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model2_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model3_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model4_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model5_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model6_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model7_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4model8_mod();
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_rcpp_module_boot_stan_fit4factor_functions_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4factor_functions_mod, 0},
+    {"_rcpp_module_boot_stan_fit4factor_model_with_covariates_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4factor_model_with_covariates_mod, 0},
+    {"_rcpp_module_boot_stan_fit4factor_model_without_covariates_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4factor_model_without_covariates_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model1_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model1_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model1_gammaOmega_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model1_gammaOmega_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model2_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model2_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model3_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model3_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model4_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model4_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model5_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model5_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model6_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model6_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model7_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model7_mod, 0},
+    {"_rcpp_module_boot_stan_fit4model8_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4model8_mod, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_bsynth(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

src/stanExports_factor_functions.cc

@@ -0,0 +1,32 @@
+// Generated by rstantools.  Do not edit by hand.
+
+#include <Rcpp.h>
+using namespace Rcpp ;
+#include "stanExports_factor_functions.h"
+
+RCPP_MODULE(stan_fit4factor_functions_mod) {
+
+
+    class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >("model_factor_functions")
+
+    .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)
+    ;
+}