Merge branch 'development' of https://github.com/revbayes/revbayes in…

…to development

src/core/analysis/HillClimber.cpp

@@ -312,8 +312,8 @@ bool HillClimber::hasConverged(double min_acceptance_ratio)
 
     for (size_t i=0; i<moves.size() && converged == true; ++i)
     {
-        size_t num_tried    = moves[i].getNumberTried();
-        size_t num_accepted = moves[i].getNumberAccepted();
+        size_t num_tried    = moves[i].getNumberTriedCurrentPeriod();
+        size_t num_accepted = moves[i].getNumberAcceptedCurrentPeriod();
 
         if ( num_tried > 0)
         {

src/core/analysis/Model.cpp

@@ -29,7 +29,7 @@ Model::Model(const DagNode *source) : Parallelizable()
  * The entire model graph is copied and a map between the pointers to the original DAG nodes and
  * the copied DAG nodes is created for convenient access.
  *
- * \param[in]    sources    The set of DAG nodes from which the model graph is extracted.
+ * \param[in]    s    The set of DAG nodes from which the model graph is extracted.
  */
 Model::Model(const std::set<const DagNode*> &s) : Parallelizable(),
     sources() 
@@ -107,7 +107,7 @@ Model::~Model( void )
  * \todo Check that this copy constructor is good or if we should use a different mechanism for the map between the
  * original DAG nodes and the copied DAG nodes.
  *
- * \param[in]    m    The model object to copy.
+ * \param[in]    x    The model object to copy.
  */
 Model& Model::operator=(const Model &x) 
 {

src/core/analysis/MonteCarloAnalysis.cpp

@@ -4,6 +4,7 @@
 #include "AbstractFileMonitor.h"
 #include "DagNode.h"
 #include "MonteCarloAnalysis.h"
+#include "MonteCarloSampler.h"
 #include "RlUserInterface.h"
 
 #include <algorithm>
@@ -18,19 +19,22 @@ using namespace RevBayesCore;
  *
  * \param[in]    m    The monte carlo sampler.
  */
-MonteCarloAnalysis::MonteCarloAnalysis(MonteCarloSampler *m, size_t r) : Cloneable(), Parallelizable(),
-replicates( r ),
-runs(r,NULL)
+MonteCarloAnalysis::MonteCarloAnalysis(MonteCarloSampler *m, size_t r, MonteCarloAnalysisOptions::TraceCombinationTypes tc) : Cloneable(), Parallelizable(),
+    replicates( r ),
+    runs(r,NULL),
+    trace_combination( tc )
 {
 
     runs[0] = m;
     resetReplicates();
+
 }
 
 
 MonteCarloAnalysis::MonteCarloAnalysis(const MonteCarloAnalysis &a) : Cloneable(), Parallelizable(a),
-replicates( a.replicates ),
-runs(a.replicates,NULL)
+    replicates( a.replicates ),
+    runs(a.replicates,NULL),
+    trace_combination( a.trace_combination )
 {
 
     // create replicate Monte Carlo samplers
@@ -84,7 +88,8 @@ MonteCarloAnalysis& MonteCarloAnalysis::operator=(const MonteCarloAnalysis &a)
         }
         runs = std::vector<MonteCarloSampler*>(a.replicates,NULL);
 
-        replicates      = a.replicates;
+        replicates          = a.replicates;
+        trace_combination   = a.trace_combination;
 
         // create replicate Monte Carlo samplers
         for (size_t i=0; i < replicates; ++i)
@@ -636,7 +641,7 @@ void MonteCarloAnalysis::run( size_t kIterations, RbVector<StoppingRule> rules,
 
         if ( runs[i] != NULL )
         {
-            runs[i]->finishMonitors( replicates );
+            runs[i]->finishMonitors( replicates, trace_combination );
         }
 
     }

src/core/analysis/MonteCarloAnalysis.h

@@ -2,7 +2,7 @@
 #define MonteCarloAnalysis_H
 
 #include "Cloneable.h"
-#include "MonteCarloSampler.h"
+#include "MonteCarloAnalysisOptions.h"
 #include "Parallelizable.h"
 #include "RbVector.h"
 #include "StoppingRule.h"
@@ -17,6 +17,9 @@
 
 namespace RevBayesCore {
 
+    class Model;
+    class MonteCarloSampler;
+
     /**
      * @brief Monte Carlo analysis running and managing the MonteCarloSampler objects.
      *
@@ -32,7 +35,8 @@ namespace RevBayesCore {
     class MonteCarloAnalysis : public Cloneable, public Parallelizable {
 
     public:
-        MonteCarloAnalysis(MonteCarloSampler *m, size_t r);
+
+        MonteCarloAnalysis(MonteCarloSampler *m, size_t r, MonteCarloAnalysisOptions::TraceCombinationTypes ct);
         MonteCarloAnalysis(const MonteCarloAnalysis &m);
         virtual                                            ~MonteCarloAnalysis(void);                                       //!< Virtual destructor
 
@@ -63,7 +67,7 @@ namespace RevBayesCore {
 
         size_t                                              replicates;
         std::vector<MonteCarloSampler*>                     runs;
-
+        MonteCarloAnalysisOptions::TraceCombinationTypes    trace_combination;
     };
 
     // Global functions using the class

src/core/analysis/MonteCarloAnalysisOptions.h

@@ -0,0 +1,18 @@
+#ifndef MonteCarloAnalysisOptions_H
+#define MonteCarloAnalysisOptions_H
+
+
+namespace RevBayesCore {
+
+
+    struct MonteCarloAnalysisOptions {
+
+        enum TraceCombinationTypes { NONE, SEQUENTIAL, MIXED };
+
+    };
+
+
+}
+
+#endif
+

src/core/analysis/PowerPosteriorAnalysis.cpp

@@ -307,7 +307,7 @@ void PowerPosteriorAnalysis::runStone(size_t idx, size_t gen)
     outStream.close();
 
     // Monitor
-    sampler->finishMonitors( 1 );
+    sampler->finishMonitors( 1, MonteCarloAnalysisOptions::NONE );
 
 }
 

src/core/analysis/mcmc/Mcmc.cpp

@@ -196,7 +196,7 @@ Mcmc* Mcmc::clone( void ) const
 /**
  * Finish the monitors which will close the output streams.
  */
-void Mcmc::finishMonitors( size_t n_reps )
+void Mcmc::finishMonitors( size_t n_reps, MonteCarloAnalysisOptions::TraceCombinationTypes tc )
 {
 
     // iterate over all monitors
@@ -211,7 +211,7 @@ void Mcmc::finishMonitors( size_t n_reps )
             // combine results if we used more than one replicate
             if ( n_reps > 1 )
             {
-                monitors[i].combineReplicates( n_reps );
+                monitors[i].combineReplicates( n_reps, tc );
             }
 
         }

src/core/analysis/mcmc/Mcmc.h

@@ -34,7 +34,7 @@ namespace RevBayesCore {
         void                                                addMonitor(const Monitor &m);
         void                                                disableScreenMonitor(bool all, size_t rep);                                             //!< Disable/remove all screen monitors
         Mcmc*                                               clone(void) const;
-        void                                                finishMonitors(size_t n);                                                               //!< Finish the monitors
+        void                                                finishMonitors(size_t n, MonteCarloAnalysisOptions::TraceCombinationTypes ct);                 //!< Finish the monitors
         double                                              getChainLikelihoodHeat(void) const;                                                     //!< Get the heat for this chain
         double                                              getChainPosteriorHeat(void) const;                                                      //!< Get the heat for this chain
         size_t                                              getChainIndex(void) const;                                                              //!< Get the index of this chain

src/core/analysis/mcmc/Mcmcmc.cpp

@@ -16,15 +16,15 @@
 using namespace RevBayesCore;
 
 Mcmcmc::Mcmcmc(const Model& m, const RbVector<Move> &mv, const RbVector<Monitor> &mn, std::string sT, size_t nc, size_t si, double dt, size_t ntries) : MonteCarloSampler(),
-num_chains(nc),
-schedule_type(sT),
-current_generation(0),
-swap_interval(si),
-active_chain_index( 0 ),
-delta( dt ),
-generation( 0 ),
-numAttemptedSwaps( 0 ),
-numAcceptedSwaps( 0 )
+    num_chains(nc),
+    schedule_type(sT),
+    current_generation(0),
+    swap_interval(si),
+    active_chain_index( 0 ),
+    delta( dt ),
+    generation( 0 ),
+    num_attempted_swaps( 0 ),
+    num_accepted_swaps( 0 )
 {
 
     // initialize container sizes
@@ -53,8 +53,8 @@ Mcmcmc::Mcmcmc(const Mcmcmc &m) : MonteCarloSampler(m)
     schedule_type       = m.schedule_type;
     pid_per_chain       = m.pid_per_chain;
 
-    numAttemptedSwaps   = m.numAttemptedSwaps;
-    numAcceptedSwaps    = m.numAcceptedSwaps;
+    num_attempted_swaps = m.num_attempted_swaps;
+    num_accepted_swaps  = m.num_accepted_swaps;
     generation          = m.generation;
 
 
@@ -151,7 +151,7 @@ void Mcmcmc::disableScreenMonitor( bool all, size_t rep )
 /**
  * Start the monitors at the beginning of a run which will simply delegate this call to each chain.
  */
-void Mcmcmc::finishMonitors( size_t n_reps )
+void Mcmcmc::finishMonitors( size_t n_reps, MonteCarloAnalysisOptions::TraceCombinationTypes tc )
 {
 
     // Monitor
@@ -160,7 +160,7 @@ void Mcmcmc::finishMonitors( size_t n_reps )
 
         if ( chains[i] != NULL )
         {
-            chains[i]->finishMonitors( n_reps );
+            chains[i]->finishMonitors( n_reps, tc );
         }
     }
 
@@ -407,8 +407,8 @@ void Mcmcmc::reset( void )
 {
 
     // reset counters
-    numAcceptedSwaps = 0;
-    numAttemptedSwaps = 0;
+    num_accepted_swaps = 0;
+    num_attempted_swaps = 0;
 
     //    /* Reset the monitors */
     //    for (size_t i = 0; i < chainsPerProcess[pid].size(); ++i)
@@ -732,7 +732,7 @@ void Mcmcmc::swapNeighborChains(void)
     j = int(GLOBAL_RNG->uniform01() * (num_chains-1));
     k = j + 1;
 
-    ++numAttemptedSwaps;
+    ++num_attempted_swaps;
 
     // compute exchange ratio
     double bj = chain_heats[j];
@@ -813,7 +813,7 @@ void Mcmcmc::swapNeighborChains(void)
             }
         }
 
-        ++numAcceptedSwaps;
+        ++num_accepted_swaps;
     }
 
 
@@ -850,7 +850,7 @@ void Mcmcmc::swapRandomChains(void)
             while(j == k);
         }
 
-        ++numAttemptedSwaps;
+        ++num_attempted_swaps;
 
         // compute exchange ratio
         double bj = chain_heats[j];
@@ -899,7 +899,7 @@ void Mcmcmc::swapRandomChains(void)
             heat_ranks[j] = heat_ranks[k];
             heat_ranks[k] = tmp;
 
-            ++numAcceptedSwaps;
+            ++num_accepted_swaps;
         }
 
 
@@ -935,7 +935,7 @@ void Mcmcmc::swapRandomChains(void)
 void Mcmcmc::tune( void )
 {
 
-    double rate = numAcceptedSwaps / double(numAttemptedSwaps);
+    double rate = num_accepted_swaps / double(num_attempted_swaps);
 
     if ( rate > 0.44 )
     {

src/core/analysis/mcmc/Mcmcmc.h

@@ -29,35 +29,35 @@ namespace RevBayesCore {
     public:
         Mcmcmc(const Model& m, const RbVector<Move> &mv, const RbVector<Monitor> &mn, std::string sT="random", size_t nc=4, size_t si=100, double dt=0.1, size_t ntries=1000);
         Mcmcmc(const Mcmcmc &m);
-        virtual                                ~Mcmcmc(void);                                       //!< Virtual destructor
+        virtual                                ~Mcmcmc(void);                                                                   //!< Virtual destructor
 
         // public methods
         void                                    addFileMonitorExtension(const std::string &s, bool dir);
         void                                    addMonitor(const Monitor &m);
-        void                                    disableScreenMonitor(bool all, size_t rep);         //!< Disable/remove all screen monitors
+        void                                    disableScreenMonitor(bool all, size_t rep);                                     //!< Disable/remove all screen monitors
         Mcmcmc*                                 clone(void) const;
-        void                                    finishMonitors(size_t n);                           //!< Finish the monitors
+        void                                    finishMonitors(size_t n, MonteCarloAnalysisOptions::TraceCombinationTypes ct);  //!< Finish the monitors
         const Model&                            getModel(void) const;
         double                                  getModelLnProbability(bool likelihood_only);
         RbVector<Monitor>&                      getMonitors( void );
-        std::string                             getStrategyDescription(void) const;                 //!< Get the discription of the strategy used for this sampler.
-        void                                    initializeSampler(bool priorOnly=false);            //!< Initialize objects for mcmc sampling
+        std::string                             getStrategyDescription(void) const;                                             //!< Get the discription of the strategy used for this sampler.
+        void                                    initializeSampler(bool priorOnly=false);                                        //!< Initialize objects for mcmc sampling
         void                                    monitor(unsigned long g);
         void                                    nextCycle(bool advanceCycle);
         void                                    printOperatorSummary(void) const;
-        void                                    redrawStartingValues(void);                         //!< Redraw the starting values.
+        void                                    redrawStartingValues(void);                                                     //!< Redraw the starting values.
         void                                    removeMonitors(void);
-        void                                    reset(void);                                        //!< Reset the sampler for a new run.
-        void                                    setLikelihoodHeat(double h);                        //!< Set the heat of the likelihood function.
+        void                                    reset(void);                                                                    //!< Reset the sampler for a new run.
+        void                                    setLikelihoodHeat(double h);                                                    //!< Set the heat of the likelihood function.
         void                                    setModel(Model *m, bool redraw);
-        void                                    setNumberOfProcesses(size_t i);                     //!< Set the number of processes for this replication.
-        void                                    startMonitors(size_t numCycles, bool reopen);       //!< Start the monitors
-        void                                    tune(void);                                         //!< Tune the sampler and its moves.
-        void                                    writeMonitorHeaders(void);                          //!< Write the headers of the monitors.
+        void                                    setNumberOfProcesses(size_t i);                                                 //!< Set the number of processes for this replication.
+        void                                    startMonitors(size_t numCycles, bool reopen);                                   //!< Start the monitors
+        void                                    tune(void);                                                                     //!< Tune the sampler and its moves.
+        void                                    writeMonitorHeaders(void);                                                      //!< Write the headers of the monitors.
 
 
     protected:
-        void                                    setActivePIDSpecialized(size_t i, size_t n);                  //!< Set the number of processes for this class.
+        void                                    setActivePIDSpecialized(size_t i, size_t n);                                    //!< Set the number of processes for this class.
 
 
     private:
@@ -68,7 +68,7 @@ namespace RevBayesCore {
         void                                    synchronizeValues(bool likelihood_only);
         void                                    synchronizeHeats(void);
         void                                    updateChainState(size_t j);
-        double                                  computeBeta(double d, size_t i);                    // incremental temperature schedule
+        double                                  computeBeta(double d, size_t i);                                                // incremental temperature schedule
 
         size_t                                  num_chains;
         std::vector<size_t>                     heat_ranks;
@@ -87,8 +87,8 @@ namespace RevBayesCore {
         Mcmc*                                   base_chain;
 
         unsigned long                           generation;
-        unsigned long                           numAttemptedSwaps;
-        unsigned long                           numAcceptedSwaps;
+        unsigned long                           num_attempted_swaps;
+        unsigned long                           num_accepted_swaps;
     };
 
 }