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…salQueries
integrated-inferences · Nov 4, 2024 · 99595fa · 99595fa
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,40 @@
+# CausalQueries 1.2.0
+
+This is a minor release introducing changes meant to focus S3 methods and 
+utility functions around two core classes: `causal_model` and `model_query`. 
+Our aim is to improve the user experience of `CausalQueries` by focusing 
+user facing functionality more clearly around the workflow of making, updating,
+querying and inspecting causal models. 
+With respect to `causal_model` objects this release introduces more expressive 
+and concise S3 summary and print methods for the `causal_model` class and its 
+internal objects. Updates to the `grab()` and `inspect()` functions streamline
+access to objects contained within a `causal_model`, facilitating more advanced
+use-cases or deeper review.
+This release introduces the `model_query` class along with S3 summary, print and 
+plot methods for a more seamless querying workflow. 
+Finally, this release removes dependency on `dagitty`, restoring compatibility of
+`CausalQueries` with systems on which `V8` `JavaScript` `WASM` is not supported. 
+
+### New Functionality
+
+#### 1. Improved causal_model summaries
+The `summary()` method for objects of class `causal_model` now supports an
+`include` argument allowing users to specify additional objects internal 
+to the `causal_model` object for which they would like to have summaries 
+appended to the main output of `summary()`. Summaries have additionally been 
+made more informative and readable. Please see `?summary.causal_model` for 
+extensive documentation on the new functionality.
+
+#### 2. Streamlined causal_model object access
+Internal objects of a `causal_model` instance can now be returned quietly 
+via `grab()` eliminating the need to interact with a `causal_model` instance
+directly. 
+
+#### 3. New querying utility functionality
+The newly introduced `model_query` class comes with a print, summary and plot
+method. `plot()` generates a coefficient plot with credible intervals for 
+evaluated queries. 
+
 # CausalQueries 1.1.1
 
 This is a patch release fixing a bug in the `print.model_query()` S3 method that 

diff --git a/R/stanmodels.R b/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)))
 })
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,25 +1,20 @@
-This is a patch release fixing a bug in the `print.model_query()` S3 method that 
-occurred when querying models using `paramters`.
+This is a minor release introducing changes focusing S3 methods and 
+utility functions around two core classes: `causal_model` and `model_query`.
 
 ## Test environments
 
-* local Ubuntu 22.04.3 LTS install, R 4.3.2
-* win-builder, R version 4.4.0 beta
-* win-builder, R version 4.2.3
+* local Ubuntu 22.04.3 LTS install, R 4.4.1
+* win-builder, R version 4.4.1 
 * win-builder, R version 4.3.3
+* win-builder, R r-devel
 * macOS, R version 4.3.3
 * R-hub Windows Server (r-devel)
 * R-hub Fedora Linux, clang, gfortran (r-devel)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 0 notes
 
-```
-❯ checking for GNU extensions in Makefiles ... NOTE
-  GNU make is a SystemRequirements.
-```
-Explanation: GNU make is required for packages built using rstantools. The requirement is specified in the DESCRIPTION file.
 
 
 
diff --git a/src/Makevars.win b/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
diff --git a/src/stanExports_simplexes.cc b/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>()
 

diff --git a/src/stanExports_simplexes.h b/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>