dependency fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CausalQueries
 Type: Package
 Title: Make, Update, and Query Binary Causal Models
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: c(person("Clara", "Bicalho", email = "clarabmcorreia@gmail.com", role = c("ctb")),
              person("Jasper", "Cooper", email = "jjc2247@columbia.edu", role = c("ctb")),
              person("Macartan", "Humphreys", email = "macartan@gmail.com", role = c("aut"),
@@ -50,6 +50,8 @@ Suggests:
     rmarkdown,
     DeclareDesign,
     fabricatr,
+    texreg,
+    estimatr,
     bayesplot,
     covr
 SystemRequirements: GNU make

R/CausalQueries-package.R

@@ -4,7 +4,7 @@
 #' update over models given data, and calculate arbitrary causal queries.
 #' Model definition makes use of dagitty type syntax.
 #' Updating is implemented in 'stan'.
-#' @docType _PACKAGE
+#' @docType package
 #'
 #' @name CausalQueries
 #' @importFrom utils globalVariables
@@ -15,5 +15,5 @@ globalVariables(names = c("posterior", "prob", "restrict", "n", "model", "data",
                           "%>%", "node", "nodal_type","param_set", "event",
                           "count", "strategy",  "distinct", "e", "v", "w",
                           "gen","children","given","param_value","priors",
-                          "g"
+                          "g", "label", "query"
     ))

R/stanmodels.R

@@ -21,5 +21,5 @@ stanmodels <- sapply(stanmodels, function(model_name) {
                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)))
+               mk_cppmodule = function(x) get(paste0("model_", model_name)))
 })

src/Makevars.win

@@ -2,9 +2,8 @@
 
 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 $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
+PKG_CPPFLAGS = -I"../inst/include" -I"$(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 = CXX17
+CXX_STD = CXX14

src/stanExports_simplexes.cc

@@ -7,7 +7,7 @@ using namespace Rcpp ;
 RCPP_MODULE(stan_fit4simplexes_mod) {
 
 
-    class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >("rstantools_model_simplexes")
+    class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >("model_simplexes")
 
     .constructor<SEXP,SEXP,SEXP>()
 

src/stanExports_simplexes.h

@@ -17,10 +17,10 @@
 #ifndef MODELS_HPP
 #define MODELS_HPP
 #define STAN__SERVICES__COMMAND_HPP
+#include <rstan/rstaninc.hpp>
 #ifndef USE_STANC3
 #define USE_STANC3
 #endif
-#include <rstan/rstaninc.hpp>
 // Code generated by stanc v2.32.2
 #include <stan/model/model_header.hpp>
 namespace model_simplexes_namespace {
@@ -29,104 +29,104 @@ using namespace stan::math;
 stan::math::profile_map profiles__;
 static constexpr std::array<const char*, 99> locations_array__ =
   {" (found before start of program)",
-  " (in 'string', line 33, column 0 to column 47)",
-  " (in 'string', line 36, column 0 to column 43)",
-  " (in 'string', line 37, column 0 to column 41)",
-  " (in 'string', line 38, column 0 to column 33)",
-  " (in 'string', line 39, column 0 to column 33)",
-  " (in 'string', line 40, column 0 to column 38)",
-  " (in 'string', line 41, column 0 to column 35)",
-  " (in 'string', line 42, column 0 to column 42)",
-  " (in 'string', line 92, column 0 to column 22)",
-  " (in 'string', line 51, column 4 to line 52, column 58)",
-  " (in 'string', line 53, column 4 to line 55, column 20)",
-  " (in 'string', line 50, column 36 to line 56, column 5)",
-  " (in 'string', line 50, column 7 to line 56, column 5)",
-  " (in 'string', line 47, column 4 to column 22)",
-  " (in 'string', line 48, column 4 to column 29)",
-  " (in 'string', line 46, column 32 to line 49, column 5)",
-  " (in 'string', line 46, column 2 to line 56, column 5)",
-  " (in 'string', line 45, column 26 to line 57, column 3)",
-  " (in 'string', line 45, column 0 to line 57, column 3)",
-  " (in 'string', line 60, column 0 to column 49)",
-  " (in 'string', line 63, column 1 to column 66)",
-  " (in 'string', line 62, column 21 to line 64, column 2)",
-  " (in 'string', line 62, column 0 to line 64, column 2)",
-  " (in 'string', line 67, column 2 to column 29)",
-  " (in 'string', line 66, column 21 to line 68, column 2)",
-  " (in 'string', line 66, column 0 to line 68, column 2)",
-  " (in 'string', line 70, column 1 to column 14)",
-  " (in 'string', line 72, column 1 to column 16)",
-  " (in 'string', line 95, column 3 to column 48)",
-  " (in 'string', line 94, column 21 to line 96, column 1)",
-  " (in 'string', line 94, column 0 to line 96, column 1)",
-  " (in 'string', line 93, column 32 to line 96, column 2)",
-  " (in 'string', line 93, column 0 to line 96, column 2)",
-  " (in 'string', line 98, column 4 to column 35)",
-  " (in 'string', line 97, column 33 to line 99, column 2)",
-  " (in 'string', line 97, column 1 to line 99, column 2)",
-  " (in 'string', line 77, column 2 to line 78, column 43)",
-  " (in 'string', line 79, column 2 to column 50)",
-  " (in 'string', line 76, column 26 to line 80, column 2)",
-  " (in 'string', line 76, column 0 to line 80, column 2)",
-  " (in 'string', line 84, column 2 to line 87, column 55)",
-  " (in 'string', line 83, column 26 to line 88, column 2)",
-  " (in 'string', line 83, column 0 to line 88, column 2)",
-  " (in 'string', line 9, column 0 to column 22)",
-  " (in 'string', line 10, column 0 to column 21)",
-  " (in 'string', line 11, column 0 to column 21)",
-  " (in 'string', line 12, column 0 to column 26)",
-  " (in 'string', line 13, column 0 to column 21)",
-  " (in 'string', line 14, column 6 to column 18)",
-  " (in 'string', line 14, column 0 to column 46)",
-  " (in 'string', line 15, column 0 to column 20)",
-  " (in 'string', line 16, column 0 to column 22)",
-  " (in 'string', line 17, column 0 to column 26)",
-  " (in 'string', line 18, column 0 to column 45)",
-  " (in 'string', line 19, column 16 to column 24)",
-  " (in 'string', line 19, column 0 to column 40)",
-  " (in 'string', line 20, column 6 to column 18)",
-  " (in 'string', line 20, column 0 to column 42)",
-  " (in 'string', line 21, column 6 to column 18)",
-  " (in 'string', line 21, column 0 to column 40)",
-  " (in 'string', line 22, column 6 to column 13)",
-  " (in 'string', line 22, column 0 to column 40)",
-  " (in 'string', line 23, column 6 to column 13)",
-  " (in 'string', line 23, column 0 to column 38)",
-  " (in 'string', line 24, column 6 to column 18)",
-  " (in 'string', line 24, column 0 to column 49)",
-  " (in 'string', line 25, column 6 to column 18)",
-  " (in 'string', line 25, column 0 to column 47)",
-  " (in 'string', line 26, column 7 to column 15)",
-  " (in 'string', line 26, column 17 to column 24)",
-  " (in 'string', line 26, column 0 to column 28)",
-  " (in 'string', line 27, column 7 to column 15)",
-  " (in 'string', line 27, column 17 to column 24)",
-  " (in 'string', line 27, column 0 to column 33)",
-  " (in 'string', line 28, column 7 to column 14)",
-  " (in 'string', line 28, column 16 to column 22)",
-  " (in 'string', line 28, column 0 to column 28)",
-  " (in 'string', line 29, column 24 to column 32)",
-  " (in 'string', line 29, column 33 to column 39)",
-  " (in 'string', line 29, column 0 to column 43)",
-  " (in 'string', line 30, column 6 to column 14)",
-  " (in 'string', line 30, column 0 to column 31)",
-  " (in 'string', line 33, column 16 to column 39)",
-  " (in 'string', line 36, column 25 to column 33)",
-  " (in 'string', line 37, column 16 to column 28)",
-  " (in 'string', line 38, column 7 to column 15)",
-  " (in 'string', line 38, column 17 to column 24)",
-  " (in 'string', line 39, column 7 to column 14)",
-  " (in 'string', line 39, column 16 to column 23)",
-  " (in 'string', line 40, column 25 to column 32)",
-  " (in 'string', line 41, column 25 to column 31)",
-  " (in 'string', line 42, column 25 to column 33)",
-  " (in 'string', line 92, column 7 to column 14)",
-  " (in 'string', line 3, column 15 to column 22)",
-  " (in 'string', line 3, column 4 to column 27)",
-  " (in 'string', line 4, column 4 to column 40)",
-  " (in 'string', line 5, column 4 to column 14)",
-  " (in 'string', line 2, column 32 to line 6, column 3)"};
+  " (in 'simplexes', line 33, column 0 to column 47)",
+  " (in 'simplexes', line 36, column 0 to column 43)",
+  " (in 'simplexes', line 37, column 0 to column 41)",
+  " (in 'simplexes', line 38, column 0 to column 33)",
+  " (in 'simplexes', line 39, column 0 to column 33)",
+  " (in 'simplexes', line 40, column 0 to column 38)",
+  " (in 'simplexes', line 41, column 0 to column 35)",
+  " (in 'simplexes', line 42, column 0 to column 42)",
+  " (in 'simplexes', line 92, column 0 to column 22)",
+  " (in 'simplexes', line 51, column 4 to line 52, column 58)",
+  " (in 'simplexes', line 53, column 4 to line 55, column 20)",
+  " (in 'simplexes', line 50, column 36 to line 56, column 5)",
+  " (in 'simplexes', line 50, column 7 to line 56, column 5)",
+  " (in 'simplexes', line 47, column 4 to column 22)",
+  " (in 'simplexes', line 48, column 4 to column 29)",
+  " (in 'simplexes', line 46, column 32 to line 49, column 5)",
+  " (in 'simplexes', line 46, column 2 to line 56, column 5)",
+  " (in 'simplexes', line 45, column 26 to line 57, column 3)",
+  " (in 'simplexes', line 45, column 0 to line 57, column 3)",
+  " (in 'simplexes', line 60, column 0 to column 49)",
+  " (in 'simplexes', line 63, column 1 to column 66)",
+  " (in 'simplexes', line 62, column 21 to line 64, column 2)",
+  " (in 'simplexes', line 62, column 0 to line 64, column 2)",
+  " (in 'simplexes', line 67, column 2 to column 29)",
+  " (in 'simplexes', line 66, column 21 to line 68, column 2)",
+  " (in 'simplexes', line 66, column 0 to line 68, column 2)",
+  " (in 'simplexes', line 70, column 1 to column 14)",
+  " (in 'simplexes', line 72, column 1 to column 16)",
+  " (in 'simplexes', line 95, column 3 to column 48)",
+  " (in 'simplexes', line 94, column 21 to line 96, column 1)",
+  " (in 'simplexes', line 94, column 0 to line 96, column 1)",
+  " (in 'simplexes', line 93, column 32 to line 96, column 2)",
+  " (in 'simplexes', line 93, column 0 to line 96, column 2)",
+  " (in 'simplexes', line 98, column 4 to column 35)",
+  " (in 'simplexes', line 97, column 33 to line 99, column 2)",
+  " (in 'simplexes', line 97, column 1 to line 99, column 2)",
+  " (in 'simplexes', line 77, column 2 to line 78, column 43)",
+  " (in 'simplexes', line 79, column 2 to column 50)",
+  " (in 'simplexes', line 76, column 26 to line 80, column 2)",
+  " (in 'simplexes', line 76, column 0 to line 80, column 2)",
+  " (in 'simplexes', line 84, column 2 to line 87, column 55)",
+  " (in 'simplexes', line 83, column 26 to line 88, column 2)",
+  " (in 'simplexes', line 83, column 0 to line 88, column 2)",
+  " (in 'simplexes', line 9, column 0 to column 22)",
+  " (in 'simplexes', line 10, column 0 to column 21)",
+  " (in 'simplexes', line 11, column 0 to column 21)",
+  " (in 'simplexes', line 12, column 0 to column 26)",
+  " (in 'simplexes', line 13, column 0 to column 21)",
+  " (in 'simplexes', line 14, column 6 to column 18)",
+  " (in 'simplexes', line 14, column 0 to column 46)",
+  " (in 'simplexes', line 15, column 0 to column 20)",
+  " (in 'simplexes', line 16, column 0 to column 22)",
+  " (in 'simplexes', line 17, column 0 to column 26)",
+  " (in 'simplexes', line 18, column 0 to column 45)",
+  " (in 'simplexes', line 19, column 16 to column 24)",
+  " (in 'simplexes', line 19, column 0 to column 40)",
+  " (in 'simplexes', line 20, column 6 to column 18)",
+  " (in 'simplexes', line 20, column 0 to column 42)",
+  " (in 'simplexes', line 21, column 6 to column 18)",
+  " (in 'simplexes', line 21, column 0 to column 40)",
+  " (in 'simplexes', line 22, column 6 to column 13)",
+  " (in 'simplexes', line 22, column 0 to column 40)",
+  " (in 'simplexes', line 23, column 6 to column 13)",
+  " (in 'simplexes', line 23, column 0 to column 38)",
+  " (in 'simplexes', line 24, column 6 to column 18)",
+  " (in 'simplexes', line 24, column 0 to column 49)",
+  " (in 'simplexes', line 25, column 6 to column 18)",
+  " (in 'simplexes', line 25, column 0 to column 47)",
+  " (in 'simplexes', line 26, column 7 to column 15)",
+  " (in 'simplexes', line 26, column 17 to column 24)",
+  " (in 'simplexes', line 26, column 0 to column 28)",
+  " (in 'simplexes', line 27, column 7 to column 15)",
+  " (in 'simplexes', line 27, column 17 to column 24)",
+  " (in 'simplexes', line 27, column 0 to column 33)",
+  " (in 'simplexes', line 28, column 7 to column 14)",
+  " (in 'simplexes', line 28, column 16 to column 22)",
+  " (in 'simplexes', line 28, column 0 to column 28)",
+  " (in 'simplexes', line 29, column 24 to column 32)",
+  " (in 'simplexes', line 29, column 33 to column 39)",
+  " (in 'simplexes', line 29, column 0 to column 43)",
+  " (in 'simplexes', line 30, column 6 to column 14)",
+  " (in 'simplexes', line 30, column 0 to column 31)",
+  " (in 'simplexes', line 33, column 16 to column 39)",
+  " (in 'simplexes', line 36, column 25 to column 33)",
+  " (in 'simplexes', line 37, column 16 to column 28)",
+  " (in 'simplexes', line 38, column 7 to column 15)",
+  " (in 'simplexes', line 38, column 17 to column 24)",
+  " (in 'simplexes', line 39, column 7 to column 14)",
+  " (in 'simplexes', line 39, column 16 to column 23)",
+  " (in 'simplexes', line 40, column 25 to column 32)",
+  " (in 'simplexes', line 41, column 25 to column 31)",
+  " (in 'simplexes', line 42, column 25 to column 33)",
+  " (in 'simplexes', line 92, column 7 to column 14)",
+  " (in 'simplexes', line 3, column 15 to column 22)",
+  " (in 'simplexes', line 3, column 4 to column 27)",
+  " (in 'simplexes', line 4, column 4 to column 40)",
+  " (in 'simplexes', line 5, column 4 to column 14)",
+  " (in 'simplexes', line 2, column 32 to line 6, column 3)"};
 template <typename T0__,
           stan::require_all_t<stan::is_eigen_matrix_dynamic<T0__>,
                               stan::is_vt_not_complex<T0__>>* = nullptr>

vignettes/c-canonical-models.Rmd

@@ -19,8 +19,22 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup, warning = FALSE, message = FALSE}
+if(!requireNamespace("estimatr", quietly = TRUE)) {
+  install.packages("estimatr")
+}
+
+if(!requireNamespace("texreg", quietly = TRUE)) {
+  install.packages("texreg")
+}
+
+
 library(CausalQueries)
-options(mc.cores = parallel::detectCores())
+library(dplyr)
+library(knitr)
+library(estimatr)
+library(texreg)
+
+options(mc.cores = 2)
 set.seed(1)
 ```
 

vignettes/d-front-door.Rmd

@@ -19,7 +19,6 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup, warning = FALSE, message = FALSE}
-
 library(CausalQueries)
 library(dplyr)
 library(knitr)