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Searched refs:ForceParameters (Results 1 – 25 of 37) sorted by relevance

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/dports/biology/lamarc/lamarc-2.1.8/src/force/
H A Dtimemanager.h22 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);
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H A Dforceparam.cpp32 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()
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H A Dforceparam.h71 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);
H A Devent.h73 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);
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H A Dtimemanager.cpp56 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()
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H A Dforcesummary.h79 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);
H A Dforce.h34 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;
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H A Devent.cpp77 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()
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H A Dforce.cpp179 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()
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/dports/biology/lamarc/lamarc-2.1.8/src/control/
H A Dchainmanager.h110 …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);
H A Dsumfilehandler.h27 class ForceParameters; variable
74 void ReadInForceParameters (ForceParameters& fp );
85 void WriteRegionSummary (ForceParameters& fp, double maxlike);
86 void WriteReplicateSummary (ForceParameters& fp, double maxlike,
H A Dsumfilehandler.cpp166 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()
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H A Dchainout.h60 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()
H A Dchainmanager.cpp144 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()
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H A Dchainpack.cpp57 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()
H A Dchainpack.h118 void WriteForceParameters ( std::ofstream& out, const ForceParameters& fp ) const;
/dports/biology/lamarc/lamarc-2.1.8/src/tree/
H A Dchainstate.h35 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()
H A Dcollector.h29 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);
H A Dcollector.cpp190 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()
H A Dtree.h57 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;
H A Dchain.cpp190 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()
H A Darranger.cpp150 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()
H A Dchain.h121 const ForceParameters& starts);
H A Dtempident.cpp145 ForceParameters fp(chstate.GetParameters()); in Sample()
/dports/biology/lamarc/lamarc-2.1.8/src/postlike/
H A Dlikelihood.h35 class ForceParameters; variable
138 void Linearize(const ForceParameters * pForceParameters,

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