/dports/biology/lamarc/lamarc-2.1.8/src/force/ |
H A D | timemanager.h | 22 class ForceParameters; variable 58 virtual void SetStickParameters(const ForceParameters& fp); 61 virtual void MakeStickUsingBranches(const ForceParameters& fp, 63 virtual void MakeStickTilTime(const ForceParameters& fp, double); 87 const ForceParameters& fp); 108 const ForceParameters& fp); 130 const ForceParameters& fp); 157 virtual void SetStickParameters(const ForceParameters& fp); 160 virtual void MakeStickUsingBranches(const ForceParameters& fp, 188 const ForceParameters& fp); [all …]
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H A D | forceparam.cpp | 32 ForceParameters::ForceParameters(long region) in ForceParameters() function in ForceParameters 44 ForceParameters::ForceParameters(param_space space) in ForceParameters() function in ForceParameters 56 ForceParameters::ForceParameters(param_space space, ForceTypeVec1d types, LongVec1d sizes) in ForceParameters() function in ForceParameters 67 ForceParameters::ForceParameters(const ForceParameters &fp, long region) in ForceParameters() function in ForceParameters 95 void ForceParameters::CopyGlobalMembers(const ForceParameters& fp) in CopyGlobalMembers() 108 void ForceParameters::CopyRegionalMembers(const ForceParameters& fp) in CopyRegionalMembers() 237 void ForceParameters::SetMigRates(const DoubleVec1d& v) in SetMigRates() 264 void ForceParameters::SetRecRates(const DoubleVec1d& v) in SetRecRates() 406 DoubleVec1d ForceParameters::GetOnlyDiseaseRates() const in GetOnlyDiseaseRates() 471 DoubleVec1d ForceParameters::GetGlobalParameters() const in GetGlobalParameters() [all …]
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H A D | forceparam.h | 71 class ForceParameters 74 ForceParameters(); //undefined 97 void CopyGlobalMembers(const ForceParameters& src); 98 void CopyRegionalMembers(const ForceParameters& src); 111 ForceParameters(long region); 112 ForceParameters(param_space space); 113 ForceParameters(param_space space, 115 ForceParameters(const ForceParameters& src, long region);
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H A D | event.h | 73 virtual void InstallParameters(const ForceParameters& starts); 125 virtual void InstallParameters(const ForceParameters& starts); 143 virtual void InstallParameters(const ForceParameters& starts); 159 virtual void InstallParameters(const ForceParameters& starts); 195 virtual void InstallParameters(const ForceParameters& starts); 205 void ComputeCumulativeRates(const ForceParameters& starts); 220 virtual void InstallParameters(const ForceParameters& starts); 255 virtual void InstallParameters(const ForceParameters& starts); 270 virtual void InstallParameters(const ForceParameters& starts); 293 virtual void InstallParameters(const ForceParameters& starts); [all …]
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H A D | timemanager.cpp | 56 void TimeManager::MakeStickUsingBranches(const ForceParameters&, in MakeStickUsingBranches() argument 64 void TimeManager::MakeStickTilTime(const ForceParameters&, double) in MakeStickTilTime() argument 92 void TimeManager::SetStickParameters(const ForceParameters&) in SetStickParameters() argument 1207 void StickTimeManager::SetStickParameters(const ForceParameters& fp) in SetStickParameters() 1886 const stair::iterator& start, const ForceParameters& fp) in NextJointAppendingIfLast() 1902 void StickTimeManager::AppendRiser(const ForceParameters& fp) in AppendRiser() 1948 ForceParameters& fp) const in NextRootTime() 2101 stair::const_iterator nextjoint, const ForceParameters& fp) const in CalculateThetasWithPrevAndNext() 2133 stair::const_iterator prevjoint, const ForceParameters& fp) const in CalculateThetasWithPrevOnly() 2154 stair::const_iterator prevjoint, const ForceParameters& fp, in CalculateThetasWithPrevOnly() [all …]
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H A D | forcesummary.h | 79 ForceParameters m_startParameters;// Starting force parameter values. 113 ForceSummary(ForceVec fvec, ForceParameters fparams, DataPack& dpac); 155 const ForceParameters& GetStartParameters() const { return m_startParameters; }; in GetStartParameters() 157 bool ConstrainParameterValues(ForceParameters& fp) const; 212 void ValidateForceParamOrBarf(const ForceParameters& fp);
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H A D | force.h | 34 class ForceParameters; variable 246 virtual DoubleVec1d RetrieveGlobalParameters(const ForceParameters& fp) const; 247 virtual DoubleVec1d RetrieveRegionalParameters(const ForceParameters& fp) const; 248 virtual DoubleVec1d RetrieveGlobalLogParameters(const ForceParameters& fp) const; 249 virtual DoubleVec1d RetrieveRegionalLogParameters(const ForceParameters& fp) const; 349 virtual DoubleVec1d RetrieveGlobalLogParameters(const ForceParameters& fp) const; 383 virtual DoubleVec1d RetrieveGlobalLogParameters(const ForceParameters & fp) const; 693 (const ForceParameters& fp) const; 695 (const ForceParameters& fp) const; 730 (const ForceParameters& fp) const; [all …]
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H A D | event.cpp | 77 void Event::InstallParameters(const ForceParameters& starts) in InstallParameters() 125 void CoalEvent::InstallParameters(const ForceParameters& starts) in InstallParameters() 190 void ActiveCoal::InstallParameters(const ForceParameters& starts) in InstallParameters() 233 void InactiveCoal::InstallParameters(const ForceParameters& starts) in InstallParameters() 293 void MigEvent::InstallParameters(const ForceParameters& starts) in InstallParameters() 303 void MigEvent::ComputeCumulativeRates(const ForceParameters& starts) in ComputeCumulativeRates() 431 void DivMigEvent::InstallParameters(const ForceParameters& starts) in InstallParameters() 615 void DiseaseEvent::InstallParameters(const ForceParameters& starts) in InstallParameters() 643 void ActiveRec::InstallParameters(const ForceParameters& starts) in InstallParameters() 753 void InactiveRec::InstallParameters(const ForceParameters& starts) in InstallParameters() [all …]
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H A D | force.cpp | 179 ForceParameters fparam = chout.GetEstimates(); in MakeChainParamReport() 357 const ForceParameters& fp = registry.GetForceSummary().GetStartParameters(); in ToXML() 493 DoubleVec1d Force::RetrieveGlobalParameters(const ForceParameters& fp) const in RetrieveGlobalParameters() 500 DoubleVec1d Force::RetrieveRegionalParameters(const ForceParameters& fp) const in RetrieveRegionalParameters() 507 DoubleVec1d Force::RetrieveGlobalLogParameters(const ForceParameters& fp) const in RetrieveGlobalLogParameters() 515 DoubleVec1d Force::RetrieveRegionalLogParameters(const ForceParameters& fp) const in RetrieveRegionalLogParameters() 1231 DoubleVec1d GrowthForce::RetrieveGlobalLogParameters(const ForceParameters& fp) const in RetrieveGlobalLogParameters() 1241 DoubleVec1d GrowthForce::RetrieveRegionalLogParameters(const ForceParameters& fp) const in RetrieveRegionalLogParameters() 1577 (const ForceParameters& fp) const in RetrieveGlobalLogParameters() 1586 (const ForceParameters& fp) const in RetrieveRegionalLogParameters() [all …]
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/dports/biology/lamarc/lamarc-2.1.8/src/control/ |
H A D | chainmanager.h | 110 …void CalculateNonBayesMultiRegionMLEs(ForceParameters & fp, ChainOut & regionout, double & maxlike… 115 …void DoChain(long int region, long int rep, long int chaintype, long int chain, ForceParameters& c… 116 void GroomTrees(ForceParameters& chainstart); 119 long int chain, ChainOut & chout, ForceParameters & chainstart); 120 …void DoSingleChainBayes(long int region, long int rep, ChainOut & chout, ForceParameters & chainst… 129 void CompareAndWarn(ForceParameters calcfp, ForceParameters readfp);
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H A D | sumfilehandler.h | 27 class ForceParameters; variable 74 void ReadInForceParameters (ForceParameters& fp ); 85 void WriteRegionSummary (ForceParameters& fp, double maxlike); 86 void WriteReplicateSummary (ForceParameters& fp, double maxlike,
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H A D | sumfilehandler.cpp | 166 ForceParameters fp(global_region); in ReadInReplicateSummary() 200 ForceParameters fp(global_region); in ReadInRegionSummary() 235 ForceParameters fp(global_region); in ReadInChainOut() 356 void SumFileHandler::ReadInForceParameters( ForceParameters& fp ) in ReadInForceParameters() 499 ForceParameters fp(region); in ReadInChainSum() 517 ForceParameters fp(unknown_region); in ReadInChainSum() 525 ForceParameters fpstart(registry.GetForceSummary().GetStartParameters(), region); in ReadInChainSum() 539 ForceParameters fp(region); in ReadInChainSum() 647 void SumFileHandler::WriteRegionSummary(ForceParameters& fp, double maxlike) in WriteRegionSummary() 799 ForceParameters rw_fp = rw_chainout.GetEstimates(); in WriteWhatWasRead() [all …]
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H A D | chainout.h | 60 ForceParameters m_estimates; // Maximum likelihood estimates 85 ForceParameters GetEstimates() const {return m_estimates;}; in GetEstimates() 104 void SetEstimates(const ForceParameters &src) {m_estimates = src;}; in SetEstimates()
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H A D | chainmanager.cpp | 144 vector<pair<ForceParameters, long int> > emptypar; in ChainManager() 612 ForceParameters fp(global_region); in CalculateMLEsOverRegions() 936 ForceParameters fp(region); in DoReplicates() 1008 ForceParameters chainstart(forcesum.GetStartParameters(),region); in DoChainTypes() 1035 ForceParameters fp(region); in DoChainTypes() 1076 ForceParameters chainstart = chout.GetEstimates(); in DoChainFromSummaryFile() 1376 void ChainManager::GroomTrees(ForceParameters& chainstart) in GroomTrees() 1645 ForceParameters & chainstart) in DoSingleChainPosterior() 1838 ForceParameters chainstart(read_fp,region); in ReadInNoRedoMax() 1883 ForceParameters chainstart(forcesum.GetStartParameters(), region); in RedoMaximization() [all …]
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H A D | chainpack.cpp | 57 ForceParameters fp(registry.GetForceSummary().GetStartParameters(), region); in GetLastChain() 164 ForceParameters fp(chout.GetEstimates(), m_currentRegion); in SetChain() 242 ForceParameters fp(chout.GetEstimates(), m_currentRegion); in SetSummaryOverReps() 458 ForceParameters fp = chout.GetEstimates(); in WriteChainOut()
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H A D | chainpack.h | 118 void WriteForceParameters ( std::ofstream& out, const ForceParameters& fp ) const;
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/dports/biology/lamarc/lamarc-2.1.8/src/tree/ |
H A D | chainstate.h | 35 ForceParameters m_parameters; 36 ForceParameters m_oldparameters; 54 void SetParameters(const ForceParameters& params); 83 ForceParameters& GetParameters() { return m_parameters; }; in GetParameters() 84 ForceParameters& GetOldParameters() { return m_oldparameters; }; in GetOldParameters()
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H A D | collector.h | 29 typedef std::vector<std::pair<ForceParameters,long> > ParamSumm; 72 ForceParameters forceParameters; // public for speed of access 79 void SetStartParameters(const ForceParameters& src) in SetStartParameters() 96 virtual void AddParamSummary(ForceParameters fp, long ncopy);
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H A D | collector.cpp | 190 ForceParameters& fp = chstate.GetParameters(); in Score() 196 pair<ForceParameters, long>& previous = m_paramsum.back(); in Score() 205 void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy) in AddParamSummary() 207 m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy)); in AddParamSummary() 240 ForceParameters fp = m_paramsum[index].first; in WriteParamSumm()
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H A D | tree.h | 57 class ForceParameters; variable 187 bool ConsistentWithParameters(const ForceParameters& fp) const; // debugging function 193 void SetStickParams(const ForceParameters & fp); 196 DoubleVec1d XpartThetasAtT(double time, const ForceParameters & fp) const; 197 DoubleVec1d PartitionThetasAtT(double time, force_type force, const ForceParameters & fp) const;
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H A D | chain.cpp | 190 ForceParameters fp(forcesum.GetStartParameters(), region.GetID()); in StartReplicate() 275 …ain (long chainnumber, long chaintype, const ForceSummary & forces, const ForceParameters & starts) in StartChain() 565 ForceParameters& hotparams = hot.m_chainstate.GetParameters(); in SwapTemperatureIdentities() 566 ForceParameters& coldparams = cold.m_chainstate.GetParameters(); in SwapTemperatureIdentities()
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H A D | arranger.cpp | 150 ForceParameters starts(chainstate.GetParameters()); in SetParameters() 1008 ForceParameters & newparameters = chstate.GetParameters(); in AcceptAndSynchronize() 1009 ForceParameters & oldparameters = chstate.GetOldParameters(); in AcceptAndSynchronize() 1141 ForceParameters & newparameters = chstate.GetParameters(); in AcceptAndSynchronize() 1142 ForceParameters & oldparameters = chstate.GetOldParameters(); in AcceptAndSynchronize() 1315 ForceParameters fp(chstate.GetParameters()); in Rearrange()
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H A D | chain.h | 121 const ForceParameters& starts);
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H A D | tempident.cpp | 145 ForceParameters fp(chstate.GetParameters()); in Sample()
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/dports/biology/lamarc/lamarc-2.1.8/src/postlike/ |
H A D | likelihood.h | 35 class ForceParameters; variable 138 void Linearize(const ForceParameters * pForceParameters,
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