Extend get_dims and get_param_names in model_base

src/stan/model/model_base.hpp

@@ -71,9 +71,14 @@ class model_base : public prob_grad {
    *
    * @param[in,out] names sequence of names parameters, transformed
    * parameters, and generated quantities
+   * @param[in] include_tparams true if transformed parameters should
+   * be included
+   * @param[in] include_gqs true if generated quantities should be
+   * included
    */
-  virtual void get_param_names(std::vector<std::string>& names) const = 0;
-
+  virtual void get_param_names(std::vector<std::string>& names,
+                               bool include_tparams = true,
+                               bool include_gqs = true) const = 0;
   /**
    * Set the dimensionalities of constrained parameters, transformed
    * parameters, and generated quantities.  The input sequence is
@@ -90,9 +95,14 @@ class model_base : public prob_grad {
    * dimensionality `std::vector<size_t>{2, 3, 4}`.
    *
    * @param[in,out] dimss sequence of dimensions specifications to set
+   * @param[in] include_tparams true if transformed parameters should
+   * be included
+   * @param[in] include_gqs true if generated quantities should be
+   * included
    */
-  virtual void get_dims(std::vector<std::vector<size_t> >& dimss) const = 0;
-
+  virtual void get_dims(std::vector<std::vector<size_t> >& dimss,
+                        bool include_tparams = true,
+                        bool include_gqs = true) const = 0;
   /**
    *  Set the specified sequence to the indexed, scalar, constrained
    *  parameter names.  Each variable is output with a

src/stan/services/sample/standalone_gqs.hpp

@@ -9,7 +9,6 @@
 #include <stan/services/error_codes.hpp>
 #include <stan/services/util/create_rng.hpp>
 #include <stan/services/util/gq_writer.hpp>
-#include <boost/algorithm/string.hpp>
 #include <iostream>
 #include <string>
 #include <vector>
@@ -31,27 +30,16 @@ template <class Model>
 void get_model_parameters(const Model &model,
                           std::vector<std::string> &param_names,
                           std::vector<std::vector<size_t>> &param_dimss) {
-  std::vector<std::string> param_cols;
-  model.constrained_param_names(param_cols, false, false);
-  std::string cur_name("");
-  std::vector<std::string> splits;
-  for (size_t i = 0; i < param_cols.size(); ++i) {
-    boost::algorithm::split(splits, param_cols[i], boost::is_any_of("."));
-    if (splits.size() == 1 || splits[0] != cur_name) {
-      cur_name = splits[0];
-      param_names.emplace_back(cur_name);
-    }
-  }
   std::vector<std::string> all_param_names;
-  model.get_param_names(all_param_names);
+  model.get_param_names(all_param_names, false, false);
   std::vector<std::vector<size_t>> dimss;
-  model.get_dims(dimss);
-  for (size_t i = 0; i < param_names.size(); i++) {
-    for (size_t j = i; j < all_param_names.size(); ++j) {
-      if (param_names[i].compare(all_param_names[j]) == 0) {
-        param_dimss.emplace_back(dimss[j]);
-        break;
-      }
+  model.get_dims(dimss, false, false);
+  // remove zero-size
+  for (size_t i = 0; i < all_param_names.size(); i++) {
+    auto &v = dimss[i];
+    if (std::find(v.begin(), v.end(), 0) == v.end()) {
+      param_names.emplace_back(all_param_names[i]);
+      param_dimss.emplace_back(dimss[i]);
     }
   }
 }

src/stan/services/util/initialize.hpp

@@ -77,7 +77,7 @@ std::vector<double> initialize(Model& model, const InitContext& init, RNG& rng,
   bool is_fully_initialized = true;
   bool any_initialized = false;
   std::vector<std::string> param_names;
-  model.get_param_names(param_names);
+  model.get_param_names(param_names, false, false);
   for (size_t n = 0; n < param_names.size(); n++) {
     is_fully_initialized &= init.contains_r(param_names[n]);
     any_initialized |= init.contains_r(param_names[n]);

src/test/unit/model/model_base_crtp_test.cpp

@@ -21,8 +21,10 @@ struct mock_model : public stan::model::model_base_crtp<mock_model> {
     return stanc_info;
   }
 
-  void get_param_names(std::vector<std::string>& names) const override {}
-  void get_dims(std::vector<std::vector<size_t> >& dimss) const override {}
+  void get_param_names(std::vector<std::string>& names, bool include_tparams,
+                       bool include_gqs) const override {}
+  void get_dims(std::vector<std::vector<size_t> >& dimss, bool include_tparams,
+                bool include_gqs) const override {}
 
   void constrained_param_names(std::vector<std::string>& param_names,
                                bool include_tparams,

src/test/unit/model/model_base_test.cpp

@@ -19,8 +19,10 @@ struct mock_model : public stan::model::model_base {
     return stanc_info;
   }
 
-  void get_param_names(std::vector<std::string>& names) const override {}
-  void get_dims(std::vector<std::vector<size_t> >& dimss) const override {}
+  void get_param_names(std::vector<std::string>& names, bool include_tparams,
+                       bool include_gqs) const override {}
+  void get_dims(std::vector<std::vector<size_t> >& dimss, bool include_tparams,
+                bool include_gqs) const override {}
 
   void constrained_param_names(std::vector<std::string>& param_names,
                                bool include_tparams,

src/test/unit/services/util/initialize_test.cpp

@@ -201,7 +201,8 @@ class mock_throwing_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -213,7 +214,9 @@ class mock_throwing_model : public stan::model::prob_grad {
     param_names__.push_back("theta");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 
@@ -336,7 +339,8 @@ class mock_error_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -348,7 +352,9 @@ class mock_error_model : public stan::model::prob_grad {
     param_names__.push_back("theta");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 
@@ -471,7 +477,8 @@ class mock_throwing_model_in_write_array : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -483,7 +490,9 @@ class mock_throwing_model_in_write_array : public stan::model::prob_grad {
     param_names__.push_back("theta");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 

src/test/unit/services/util/mcmc_writer_test.cpp

@@ -57,14 +57,18 @@ class throwing_model : public stan::model::model_base_crtp<throwing_model> {
 
   }  // transform_inits()
 
-  inline void get_param_names(std::vector<std::string>& names__) const {
+  inline void get_param_names(std::vector<std::string>& names__,
+                              bool include_tparams = true,
+                              bool include_gqs = true) const {
     names__.clear();
     names__.emplace_back("y");
     names__.emplace_back("z");
     names__.emplace_back("xgq");
   }  // get_param_names()
 
-  inline void get_dims(std::vector<std::vector<size_t>>& dimss__) const final {
+  inline void get_dims(std::vector<std::vector<size_t>>& dimss__,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const final {
     dimss__.clear();
     dimss__.emplace_back(std::vector<size_t>{static_cast<size_t>(2)});
 

src/test/unit/variational/eta_adapt_mock_models_test.cpp

@@ -43,7 +43,8 @@ class mock_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -59,7 +60,9 @@ class mock_model : public stan::model::prob_grad {
     param_names__.push_back("c");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 
@@ -124,7 +127,8 @@ class mock_throwing_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -140,7 +144,9 @@ class mock_throwing_model : public stan::model::prob_grad {
     param_names__.push_back("c");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 

src/test/unit/variational/stochastic_gradient_ascent_test.cpp

@@ -44,7 +44,8 @@ class mock_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -60,7 +61,9 @@ class mock_model : public stan::model::prob_grad {
     param_names__.push_back("c");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }
 
@@ -125,7 +128,8 @@ class mock_throwing_model : public stan::model::prob_grad {
     }
   }
 
-  void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
+  void get_dims(std::vector<std::vector<size_t> >& dimss__,
+                bool include_tparams = true, bool include_gqs = true) const {
     dimss__.resize(0);
     std::vector<size_t> scalar_dim;
     dimss__.push_back(scalar_dim);
@@ -141,7 +145,9 @@ class mock_throwing_model : public stan::model::prob_grad {
     param_names__.push_back("c");
   }
 
-  void get_param_names(std::vector<std::string>& names) const {
+  void get_param_names(std::vector<std::string>& names,
+                       bool include_tparams = true,
+                       bool include_gqs = true) const {
     constrained_param_names(names);
   }