[algorithm.initial_rates] dispersal and extinction

src/BioGeoTree.cpp

@@ -970,12 +970,12 @@ double BioGeoTree::getSim_E()
 	return sim_E;
 }
 
-void BioGeoTree::setSim_D(double & disp)
+void BioGeoTree::setSim_D(const double disp)
 {
 	sim_D = disp;
 }
 
-void BioGeoTree::setSim_E(double & ext)
+void BioGeoTree::setSim_E(const double ext)
 {
 	sim_E = ext;
 }

src/BioGeoTree.h

@@ -129,8 +129,8 @@ class BioGeoTree{
 	void simulate(Node & node);
 	double getSim_D();
 	double getSim_E();
-	void setSim_D(double & disp);
-	void setSim_E(double & ext);
+	void setSim_D(const double disp);
+	void setSim_E(const double ext);
 
 	void read_true_states(string truestatesfile);
 	vector<int> * get_true_state(int num);

src/main.cpp

@@ -118,6 +118,32 @@ int main(int argc, char* argv[]){
 
   config.step_up();
 
+  // Algorithm table (optional) ------------------------------------------------
+  // Default values here, possibly overwritten with configuration.
+  double D{0.1};
+  double E{0.1};
+  int M{1000};
+  double S{0.0001};
+
+  if (config.seek_table("algorithm", true).has_value()) {
+    const auto& m{config.seek_integer("max_iterations", false)};
+    const auto& s{config.seek_float("stopping_precision", false)};
+    if (m.has_value()) { M = *m; }
+    if (s.has_value()) { S = *s; }
+    if (config.seek_table("initial_rates", true).has_value()) {
+      const auto& d{config.seek_float("dispersal", false)};
+      const auto& e{config.seek_float("extinction", false)};
+      if (d.has_value()) { D = *d; }
+      if (e.has_value()) { E = *e; }
+      config.step_up();
+    }
+    config.step_up();
+  }
+  const double dispersal{D};
+  const double extinction{E};
+  const int maxiterations{M};
+  const double stoppingprecision{S};
+
   // Geographical parameters ---------------------------------------------------
   config.require_table("areas", true);
 
@@ -223,11 +249,6 @@ int main(int argc, char* argv[]){
 		bool LHOODS = false;
 		bool NodeLHOODS = false;
 
-		int maxiterations = 1000;
-		double stoppingprecision = 0.0001;
-
-		double dispersal = 0.1;
-		double extinction = 0.1;
 		bool estimate = true;
 		bool simulate = false;
 		int simNum = 1;
@@ -349,26 +370,6 @@ int main(int argc, char* argv[]){
 						if(tokens.size() > 1){
 							numreps = atoi(tokens[1].c_str());
 						}
-					}else if ((!strcmp(tokens[0].c_str(), "dispersal")) || (!strcmp(tokens[0].c_str(), "sim_dispersal"))){
-						if(tokens.size() > 1){
-							dispersal = atof(tokens[1].c_str());
-							cout << "setting dispersal: " << dispersal << endl;
-							if (!strcmp(tokens[0].c_str(), "sim_dispersal"))
-								estimate = false;
-						}
-					}else if ((!strcmp(tokens[0].c_str(), "extinction")) || (!strcmp(tokens[0].c_str(), "sim_extinction"))){
-						if(tokens.size() > 1){
-							extinction = atof(tokens[1].c_str());
-							cout << "setting extinction: " << extinction << endl;
-							if (!strcmp(tokens[0].c_str(), "sim_extinction"))
-								estimate = false;
-						}
-					}else if(!strcmp(tokens[0].c_str(), "maxiterations")){
-						maxiterations = atoi(tokens[1].c_str());
-						cout << "setting maxiterations: " << maxiterations << endl;
-					}else if(!strcmp(tokens[0].c_str(), "stoppingprecision")){
-						stoppingprecision = atof(tokens[1].c_str());
-						cout << "setting stoppingprecision: " << stoppingprecision << endl;
 					}else if(!strcmp(tokens[0].c_str(), "simbiogeotree")){
 						simulate = true;
 						if(tokens.size() > 1)

tests/input/input/config.toml

@@ -16,6 +16,14 @@ rapid_anagenesis = false
 
 durations = [5.33, 17.7, 10.87, 22.1, 14.0]
 
+[algorithm]
+max_iterations = 1000
+stopping_precision = 0.0001
+
+[algorithm.initial_rates]
+dispersal = 0.1
+extinction = 0.1
+
 # --- Geographical parameters --------------------------------------------------
 [areas]
 # names = ["WP", "EP", "WN", "EN", "CA", "SA", "AF", "MD", "IN", "WA", "AU"]

tests/input/specs/config.clib

@@ -138,8 +138,8 @@ test: No areas table.
 edit (config.toml):
     PREFIX (#1) [areas]
 failure (1):: EOE
-    Configuration error: table contains unexpected parameter 'names'.
-    ('parameters' line 11, column 1 of 'config.toml')
+    Configuration error: 'names' is required, but not given.
+    ('areas' line 32, column 1 of 'config.toml')
 EOE
 
 # Distributions ================================================================
@@ -151,7 +151,7 @@ edit (config.toml):
 failure (1):: EOE
     Unknown area name in distribution: 'wrong'.
     (known areas: 'WP' 'EP' 'WN' 'EN' 'CA' 'SA' 'AF' 'MD' 'IN' 'WA' 'AU')
-    ('areas:distributions:set:1' line 28, column 3 of 'config.toml')
+    ('areas:distributions:set:1' line 36, column 3 of 'config.toml')
 EOE
 
 test: Catch missing area in binary distribution.
@@ -161,7 +161,7 @@ edit (config.toml):
 failure (1):: EOE
     Invalid binary specification of a distribution:
     '1101011010' contains 10 digits but there are 11 areas.
-    ('areas:distributions:set:3' line 30, column 3 of 'config.toml')
+    ('areas:distributions:set:3' line 38, column 3 of 'config.toml')
 EOE
 
 test: Catch extra area in binary distribution.
@@ -171,7 +171,7 @@ edit (config.toml):
 failure (1):: EOE
     Invalid binary specification of a distribution:
     '110101101011' contains 12 digits but there are 11 areas.
-    ('areas:distributions:set:3' line 30, column 3 of 'config.toml')
+    ('areas:distributions:set:3' line 38, column 3 of 'config.toml')
 EOE
 
 test: Catch the ambiguous case.
@@ -184,7 +184,7 @@ failure (1):: EOE
     Ambiguous distribution specification:
     '101' could either represent the single area '101' or a binary set of other areas..
     Now be honest: you did that on purpose, right?
-    ('areas:distributions:set:1' line 28, column 3 of 'config.toml')
+    ('areas:distributions:set:1' line 36, column 3 of 'config.toml')
 EOE
 
 # MRCAs ========================================================================
@@ -194,7 +194,7 @@ edit (config.toml):
     REPLACE (age = 15.8) BY r'# \1'
 failure (1):: EOE
     Configuration error: 'age' is required, but not given.
-    ('mrca:Gavialidae' line 36, column 1 of 'config.toml')
+    ('mrca:Gavialidae' line 44, column 1 of 'config.toml')
 EOE
 
 test: Catch invalid area.
@@ -203,7 +203,7 @@ edit (config.toml):
     ~    'area = "wrong"'
 failure (1):: EOE
     Unknown area 'wrong' provided.
-    ('mrca:Gavialidae:area' line 39, column 8 of 'config.toml')
+    ('mrca:Gavialidae:area' line 47, column 8 of 'config.toml')
 EOE
 
 test: Catch invalid MRCA type specification.
@@ -213,7 +213,7 @@ edit (config.toml):
 failure (1):: EOE
     Unknown MRCA type: 'fixed branch'.
     Supported types are 'fixed node', 'fossil node' and 'fossil branch'.
-    ('mrca:Caiman:type' line 43, column 8 of 'config.toml')
+    ('mrca:Caiman:type' line 51, column 8 of 'config.toml')
 EOE
 
 # Clear for later tests specs.