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Searched refs:MrBFlt (Results 1 – 19 of 19) sorted by relevance

/dports/biology/mrbayes/MrBayes-3.2.7/src/
H A D	proposal.h	4 …Aamodel (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 5 …dBranch (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 6 …Adgamma (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 7 …PPEvent (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 8 …ve_Beta (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 9 …_Beta_M (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 10 …e_BrLen (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 11 …kRate_M (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 13 …CPPRate (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 19 …_ExtSPR (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… [all …]
H A D	utils.h	219 MrBFlt BetaQuantile (MrBFlt alpha, MrBFlt beta, MrBFlt x); 250 MrBFlt LnProbRatioFix (MrBFlt newX, MrBFlt oldX, MrBFlt *params); 265 MrBFlt LnProbGamma (MrBFlt alpha, MrBFlt beta, MrBFlt x); 266 MrBFlt LnProbTruncGamma (MrBFlt alpha, MrBFlt beta, MrBFlt x, MrBFlt min, MrBFlt max); 267 MrBFlt LnProbLogNormal (MrBFlt exp, MrBFlt sd, MrBFlt x); 268 MrBFlt LnRatioLogNormal (MrBFlt exp, MrBFlt sd, MrBFlt xNew, MrBFlt xOld); 269 MrBFlt LnProbTK02LogNormal (MrBFlt mean, MrBFlt var, MrBFlt x); 270 MrBFlt LnRatioTK02LogNormal (MrBFlt exp, MrBFlt sd, MrBFlt xNew, MrBFlt xOld); 280 MrBFlt QuantileGamma (MrBFlt x, MrBFlt alfa, MrBFlt beta); 282 MrBFlt QuantileLogNormal (MrBFlt prob, MrBFlt mu, MrBFlt sigma); [all …]
H A D	mcmc.h	5 void AutotuneDirichlet (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt alphaPi, Mr… 6 void AutotuneMultiplier (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt lambda, Mr… 7 void AutotuneSlider (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt width, MrBFlt … 18 MrBFlt GetParsimonyLength (Tree t, int chain); 20 MrBFlt GetRate (int division, int chain); 21 int LnBirthDeathPriorPr (Tree t, MrBFlt clockRate, MrBFlt prob, MrBFlt sR, MrBFlt eR, char s… 22 int LnCoalescencePriorPr (Tree t, MrBFlt prob, MrBFlt theta, MrBFlt growth); 23 MrBFlt LnUniformPriorPr (Tree t, MrBFlt clockRate); 24 …t LnFossilizationPriorPr (Tree t, MrBFlt clockRate, MrBFlt prob, MrBFlt sR, MrBFlt eR, MrB… 27 MrBFlt LogOmegaPrior (MrBFlt w1, MrBFlt w2, MrBFlt w3); [all …]
H A D	bayes.h	487 typedef MrBFlt (LnPriorProbFxn)(MrBFlt val, MrBFlt priorParams); 490 typedef MrBFlt (LnPriorRatioFxn)(MrBFlt newVal, MrBFlt oldVal, MrBFlt priorParams); 499 MrBFlt *pair; 566 MrBFlt brlens; 879 …MoveFxn)(Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 885 …pedef void (AutotuneFxn)(MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt *tuningParame… 1014 MrBFlt omegaFix; 1042 MrBFlt shapeFix; 1044 MrBFlt shapeExp; 1049 MrBFlt corrFix; [all …]
H A D	best.h	20 …neTree1 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 21 …neTree2 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 22 …neTree3 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 23 …eneTree (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… 24 …iesTree (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M…
H A D	utils.c	75 MrBFlt BetaCf (MrBFlt a, MrBFlt b, MrBFlt x); 76 MrBFlt BetaQuantile (MrBFlt alpha, MrBFlt beta, MrBFlt x); 77 MrBFlt CdfBinormal (MrBFlt h1, MrBFlt h2, MrBFlt r); 84 void ComplexDivision2 (MrBFlt ar, MrBFlt ai, MrBFlt br, MrBFlt bi, MrBFlt cr, MrBFlt ci); 97 MrBFlt D_sign (MrBFlt a, MrBFlt b); 110 MrBFlt LBinormal (MrBFlt h1, MrBFlt h2, MrBFlt r); 126 MrBFlt Tha (MrBFlt h1, MrBFlt h2, MrBFlt a1, MrBFlt a2); 132 MrBFlt LogNormalPoint (MrBFlt x, MrBFlt mu, MrBFlt sigma); 9562 MrBFlt BetaCf (MrBFlt a, MrBFlt b, MrBFlt x) in BetaCf() 13035 MrBFlt LnProbTruncGamma (MrBFlt alpha, MrBFlt beta, MrBFlt x, MrBFlt min, MrBFlt max) in LnProbTruncGamma() [all …]
H A D	likelihood.h	115 void LaunchLogLikeForBeagleMultiPartition(int chain, MrBFlt* lnL); 117 void LaunchLogLikeForDivision (int chain, int d, MrBFlt* lnL); 118 int Likelihood_Adgamma (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 119 int Likelihood_Gen (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 121 int Likelihood_Gen_SSE (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 124 int Likelihood_NUC4 (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 135 int Likelihood_NY98 (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 139 int Likelihood_Pars (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 140 int Likelihood_ParsStd (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); 141 int Likelihood_Res (TreeNode p, int division, int chain, MrBFlt lnL, int whichSitePats); [all …]
H A D	model.h	`4 int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol); 39 MrBFlt GetParamStdStateFreqs (Param parm, int chain, int state); 40 MrBFlt GetParamSubVals (Param parm, int chain, int state); 41 MrBFlt GetParamVals (Param parm, int chain, int state); 55 int UpdateClockRate (MrBFlt clockRate, int chain);`
H A D	mcmc.c	174 MrBFlt LnP0 (MrBFlt t, MrBFlt l, MrBFlt m); 175 MrBFlt LnP0Subsample (MrBFlt t, MrBFlt l, MrBFlt m, MrBFlt f); 176 MrBFlt LnP1 (MrBFlt t, MrBFlt l, MrBFlt m); 177 MrBFlt LnP1Subsample (MrBFlt t, MrBFlt l, MrBFlt m, MrBFlt f); 178 MrBFlt LnP0_fossil (MrBFlt t, MrBFlt lambda, MrBFlt mu, MrBFlt psi, MrBFlt c1, MrBFlt c2); 179 MrBFlt LnP1_fossil (MrBFlt t, MrBFlt rho, MrBFlt c1, MrBFlt c2); 180 MrBFlt LnQi_fossil (MrBFlt t, MrBFlt t_f, int sl, MrBFlt c1, MrBFlt c2); 181 MrBFlt LnPi_fossil (MrBFlt t, MrBFlt t_f, int sl, MrBFlt c1, MrBFlt c2, MrBFlt *lambda, MrBFl… 8610 MrBFlt LnP0 (MrBFlt t, MrBFlt b, MrBFlt d) in LnP0() 8640 MrBFlt LnP1 (MrBFlt t, MrBFlt b, MrBFlt d) in LnP1() [all …]
H A D	mbbeagle.h	`13 void LaunchBEAGLELogLikeForDivision (int chain, int d, ModelInfo* m, Tree* tree, MrBFlt* lnL); 15 MrBFlt LaunchLogLikeForAllDivisionsInParallel (int chain); 23 int TreeLikelihood_Beagle (Tree t, int division, int chain, MrBFlt lnL, int whichSitePats); 29 void LaunchBEAGLELogLikeMultiPartition(int* divisions, int divisionCount, int chain, MrBFlt* lnL); 34 int TreeLikelihood_BeagleMultiPartition (int* divisions, int divisionCount, int chain, MrBFlt *l…`
H A D	proposal.c	65 …Aamodel (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_Aamodel() 173 …PPEvent (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_AddDeleteCPPEvent() 322 …Adgamma (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_Adgamma() 389 …ve_Beta (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_Beta() 505 …e_BrLen (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_BrLen() 609 …kRate_M (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_ClockRate_M() 868 …CPPRate (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_CPPRate() 1111 …dBranch (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_AddBranch() 2268 …_ExtSPR (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_ExtSPR() 7538 …ove_NNI (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_NNI() [all …]
H A D	sumpt.c	55 MrBFlt *age; 111 void CalculateTreeToTreeDistance (Tree tree1, Tree tree2, MrBFlt d1, MrBFlt d2, MrBFlt d3); 127 …bleLine (int numRuns, int rowCount, Stat theStats, MrBFlt numPSRFSamples, MrBFlt maxPSRF, MrBF… 129 void Range (MrBFlt vals, int nVals, MrBFlt min, MrBFlt max); 1632 MrBFlt tempD; in ExamineSumpFile() 2190 prob = (MrBFlt ) SafeCalloc (6nElements, sizeof(MrBFlt)); in PrintModelStats() 2214 f = (MrBFlt) modelCounts[j2] / (MrBFlt) nSamples; in PrintModelStats() 2631 int PrintPlot (MrBFlt xVals, MrBFlt yVals, int numVals) in PrintPlot() 2784 MrBFlt tempD; in ReadParamSamples() 3139 void CalculateTreeToTreeDistance (Tree tree1, Tree tree2, MrBFlt d1, MrBFlt d2, MrBFlt d3) in CalculateTreeToTreeDistance() [all …]
H A D	sumpt.h	`24 MrBFlt *values; 37 int PrintPlot (MrBFlt xVals, MrBFlt *yVals, int nSamples);`
H A D	model.c	94 … UpdateCppEvolLength (int nEvents, MrBFlt pos, MrBFlt rateMult, MrBFlt evolLength, TreeN… 471 p->position = (MrBFlt **) SafeCalloc (2numGlobalChains, sizeof (MrBFlt )); in AllocateCppEvents() 475 p->rateMult = (MrBFlt ) SafeCalloc (2numGlobalChains, sizeof (MrBFlt *)); in AllocateCppEvents() 639 paramValues = (MrBFlt ) SafeCalloc (nOfParams, sizeof(MrBFlt)); in AllocateNormalParams() 1082 int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol) in AreDoublesEqual() 3938 MrBFlt tempD; in DoPlotParm() 4459 MrBFlt tempD, sum; in DoPrsetParm() 11663 MrBFlt clockRate; in FillTopologySubParams() 20031 MrBFlt values; in SetPopSizeParam() 24553 int UpdateCppEvolLength (int nEvents, MrBFlt pos, MrBFlt rateMult, MrBFlt *evolLength, TreeNod… in UpdateCppEvolLength() [all …]
H A D	best.c	1115 …neTree1 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_GeneTree1() 1219 …neTree2 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_GeneTree2() 1323 …neTree3 (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_GeneTree3() 1422 …eneTree (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_NodeSliderGeneTree() 1425 MrBFlt window, minDepth, maxDepth, oldDepth, newDepth, in Move_NodeSliderGeneTree() 1679 …iesTree (Param param, int chain, RandLong seed, MrBFlt lnPriorRatio, MrBFlt lnProposalRatio, M… in Move_SpeciesTree()
H A D	mbbeagle.c	44 void LaunchLogLikeForDivision(int chain, int d, MrBFlt* lnL); 84 … m->logLikelihoods = (MrBFlt ) SafeCalloc ((numLocalChains)m->numChars, sizeof(MrBFlt)); in InitBeagleInstance() 85 m->inRates = (MrBFlt ) SafeCalloc (m->numRateCats, sizeof(MrBFlt)); in InitBeagleInstance() 86 m->branchLengths = (MrBFlt ) SafeCalloc (2numLocalTaxa, sizeof(MrBFlt)); in InitBeagleInstance() 88 … m->inWeights = (MrBFlt ) SafeCalloc (m->numRateCatsm->nCijkParts, sizeof(MrBFlt)); in InitBeagleInstance() 1375 MrBFlt correctionFactor, theRate, baseRate, catRate, length; in TreeTiProbs_Beagle() 1561 m->branchLengths = (MrBFlt ) SafeCalloc (sizePD2numLocalTaxa, sizeof(MrBFlt)); in InitBeagleMultiPartitionInstance() 1577 m->inRates = (MrBFlt ) SafeCalloc (m->numRateCats, sizeof(MrBFlt)); in InitBeagleMultiPartitionInstance() 1578 … m->inWeights = (MrBFlt ) SafeCalloc (m->numRateCatsm->nCijkParts, sizeof(MrBFlt)); in InitBeagleMultiPartitionInstance() 1588 m->logLikelihoodsAll = (MrBFlt ) SafeCalloc ((numLocalChains)m->numCharsAll, sizeof(MrBFlt)); in InitBeagleMultiPartitionInstance() [all …]
H A D	likelihood.c	74 int SetNucQMatrix (MrBFlt *a, int n, int whichChain, int division, MrBFlt rateMult, MrBFlt … 75 int SetStdQMatrix (MrBFlt *a, int nStates, MrBFlt bs, int cType); 76 int SetProteinQMatrix (MrBFlt *a, int n, int whichChain, int division, MrBFlt rateMult); 5642 MrBFlt like, rP; in Likelihood_Adgamma() 8229 int SetNucQMatrix (MrBFlt *a, int n, int whichChain, int division, MrBFlt rateMult, MrBFlt rA, Mr… in SetNucQMatrix() 8237 MrBFlt trans; in SetNucQMatrix() 8271 rateValues = (MrBFlt ) SafeCalloc (6, sizeof(MrBFlt)); in SetNucQMatrix() 8283 rateValues = (MrBFlt ) SafeCalloc (6, sizeof(MrBFlt)); in SetNucQMatrix() 8828 int SetProteinQMatrix (MrBFlt a, int n, int whichChain, int division, MrBFlt rateMult) in SetProteinQMatrix() 9285 int SetStdQMatrix (MrBFlt a, int nStates, MrBFlt *bs, int cType) in SetStdQMatrix() [all …]
H A D	command.c	155 MrBFlt WhichCont (int x); 1202 MrBFlt tempD; in DoCalibrateParm() 2566 MrBFlt tempD; in DoConstraintParm() 5257 MrBFlt charValue; in DoMatrixParm() 8152 MrBFlt tempD; in DoTreeParm() 8344 … t->position[t->nESets-1] = (MrBFlt *) SafeCalloc (2(size_t)numTaxa, sizeof(MrBFlt )); in DoTreeParm() 8390 t->popSize = (MrBFlt ) SafeCalloc (2numTranslates, sizeof(MrBFlt)); in DoTreeParm() 8392 t->popSize = (MrBFlt ) SafeCalloc (2numLocalTaxa, sizeof(MrBFlt)); in DoTreeParm() 14309 tempNum = (MrBFlt ) SafeRealloc ((void ) tempNum, 6 sizeof(MrBFlt)); in SetPartition() 15105 MrBFlt WhichCont (int x) in WhichCont() [all …]
H A D	bayes.c	`104 MrBFlt myStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of me … 105 MrBFlt partnerStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of partner …`