Merge pull request #36 from rsetienne/develop

Develop
rsetienne · Apr 26, 2024 · 615cf7e · 615cf7e
2 parents fa2d5e9 + d403e1e
commit 615cf7e
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Showing 4 changed files with 76 additions and 83 deletions.
diff --git a/.github/workflows/cpp_lint.yml b/.github/workflows/cpp_lint.yml
@@ -13,7 +13,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v2
       - run: pip install cpplint
-      - run: cpplint --quiet --exclude="src/RcppExports.cpp" src/*.cpp src/*.h
+      - run: cpplint --quiet src/secsse_sim2.h src/secsse_sim.cpp 
 
   cppcheck:
     runs-on: ubuntu-latest

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Several Examined and Concealed States-Dependent Speciation and
  Extinction
 Version: 3.1.0
-Date: 2024-03-18
+Date: 2024-04-26
 License: GPL (>= 3) | file LICENSE
 Authors@R: c(
  person(given = "Leonel",

diff --git a/src/secsse_sim.cpp b/src/secsse_sim.cpp
@@ -62,8 +62,6 @@ num_mat_mat list_to_nummatmat(const Rcpp::List& lambdas_R) {
 
 }  // namespace util
 
-//' 
-
 // [[Rcpp::export]]
 Rcpp::List secsse_sim_cpp(const std::vector<double>& m_R,
                           const Rcpp::List& lambdas_R,
@@ -82,14 +80,12 @@ Rcpp::List secsse_sim_cpp(const std::vector<double>& m_R,
                           const std::vector<double>& conditioning_vec,
                           bool return_tree_size_hist,
                           bool start_at_crown) {
-
   try {
-
   num_mat q;
   util::numericmatrix_to_vector(q_R, &q);
-  
+
   num_mat_mat lambdas = util::list_to_nummatmat(lambdas_R);
-  
+
   secsse_sim sim(m_R,
                  lambdas,
                  q,
@@ -108,25 +104,26 @@ Rcpp::List secsse_sim_cpp(const std::vector<double>& m_R,
     sim.run();
     cnt++;
     if (return_tree_size_hist) sim.update_tree_size_hist(&tree_size_hist[cnt]);
-    
+
     if (sim.num_species() >= min_species) {
       sim.check_conditioning(condition,
                              num_concealed_states,
                              m_R.size(),
                              conditioning_vec);
-      
+
       if (sim.run_info == done) {
         break;
       } else {
         tracker[ sim.run_info ]++;
       }
-    } else { // if not reached minimum size
-      if (sim.run_info == extinct) tracker[extinct]++;
-      else {
+    } else {    // if not reached minimum size
+      if (sim.run_info == extinct) {
+        tracker[extinct]++;
+      } else {
         tracker[ 5 ]++;
       }
     }
-    
+
     if (verbose) {
       if (cnt % 1000 == 0) {
         Rcpp::Rcout << "extinct: " << tracker[extinct] << " "
@@ -141,20 +138,20 @@ Rcpp::List secsse_sim_cpp(const std::vector<double>& m_R,
     Rcpp::checkUserInterrupt();
     if (!non_extinction && sim.run_info == extinct) break;
   }
-  // extract and return
-  Rcpp::NumericMatrix ltable_for_r;
+
+  Rcpp::NumericMatrix ltable_for_r;      // extract and return
   util::vector_to_numericmatrix(sim.extract_ltable(), &ltable_for_r);
-  
+
   auto traits = sim.get_traits();
   auto init = sim.get_initial_state();
-  
-  Rcpp::List output = Rcpp::List::create(Rcpp::Named("ltable") = ltable_for_r,
-                                         Rcpp::Named("traits") = traits,
-                                         Rcpp::Named("initial_state") = init,
-                                         Rcpp::Named("tracker") = tracker,
-                                         Rcpp::Named("hist_tree_size") = tree_size_hist);
-  return output; 
-
+
+  Rcpp::List output =
+    Rcpp::List::create(Rcpp::Named("ltable") = ltable_for_r,
+                       Rcpp::Named("traits") = traits,
+                       Rcpp::Named("initial_state") = init,
+                       Rcpp::Named("tracker") = tracker,
+                       Rcpp::Named("hist_tree_size") = tree_size_hist);
+  return output;
   } catch(std::exception &ex) {
     forward_exception_to_r(ex);
   } catch (const char* msg) {