bpp-phyl  2.2.0
bpp::OptimizationTools Member List

This is the complete list of members for bpp::OptimizationTools, including all inherited members.

buildDistanceTree(DistanceEstimation &estimationMethod, AgglomerativeDistanceMethod &reconstructionMethod, const ParameterList &parametersToIgnore, bool optimizeBrLen=false, const std::string &param=DISTANCEMETHOD_INIT, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *profiler=0, OutputStream *messenger=0, unsigned int verbose=0)bpp::OptimizationToolsstatic
DISTANCEMETHOD_INITbpp::OptimizationToolsstatic
DISTANCEMETHOD_ITERATIONSbpp::OptimizationToolsstatic
DISTANCEMETHOD_PAIRWISEbpp::OptimizationToolsstatic
estimateDistanceMatrix(DistanceEstimation &estimationMethod, const ParameterList &parametersToIgnore, const std::string &param=DISTANCEMETHOD_INIT, unsigned int verbose=0)bpp::OptimizationToolsstatic
OPTIMIZATION_BFGSbpp::OptimizationToolsstatic
OPTIMIZATION_BRENTbpp::OptimizationToolsstatic
OPTIMIZATION_GRADIENTbpp::OptimizationToolsstatic
OPTIMIZATION_NEWTONbpp::OptimizationToolsstatic
OptimizationTools()bpp::OptimizationTools
optimizeBranchLengthsParameters(DiscreteRatesAcrossSitesTreeLikelihood *tl, const ParameterList &parameters, OptimizationListener *listener=0, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)bpp::OptimizationToolsstatic
optimizeNumericalParameters(DiscreteRatesAcrossSitesTreeLikelihood *tl, const ParameterList &parameters, OptimizationListener *listener=0, unsigned int nstep=1, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON, const std::string &optMethodModel=OPTIMIZATION_BRENT)bpp::OptimizationToolsstatic
optimizeNumericalParameters2(DiscreteRatesAcrossSitesTreeLikelihood *tl, const ParameterList &parameters, OptimizationListener *listener=0, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, bool reparametrization=false, bool useClock=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)bpp::OptimizationToolsstatic
optimizeNumericalParametersWithGlobalClock(DiscreteRatesAcrossSitesClockTreeLikelihood *cl, const ParameterList &parameters, OptimizationListener *listener=0, unsigned int nstep=1, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_GRADIENT)bpp::OptimizationToolsstatic
optimizeNumericalParametersWithGlobalClock2(DiscreteRatesAcrossSitesClockTreeLikelihood *cl, const ParameterList &parameters, OptimizationListener *listener=0, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_GRADIENT)bpp::OptimizationToolsstatic
optimizeTreeNNI(NNIHomogeneousTreeLikelihood *tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, unsigned int nStep=1, const std::string &nniMethod=NNITopologySearch::PHYML)bpp::OptimizationToolsstatic
optimizeTreeNNI(DRTreeParsimonyScore *tp, unsigned int verbose=1)bpp::OptimizationToolsstatic
optimizeTreeNNI2(NNIHomogeneousTreeLikelihood *tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, const std::string &nniMethod=NNITopologySearch::PHYML)bpp::OptimizationToolsstatic
optimizeTreeScale(TreeLikelihood *tl, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1)bpp::OptimizationToolsstatic
~OptimizationTools()bpp::OptimizationToolsvirtual