/dports/biology/mrbayes/MrBayes-3.2.7/src/ |
H A D | proposal.h | 4 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 5 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 6 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 8 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 9 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 10 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 13 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 19 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 22 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 36 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); [all …]
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H A D | best.h | 20 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 21 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 22 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 23 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); 24 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
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H A D | proposal.c | 99 *lnProposalRatio = 0.0; in Move_Aamodel() 367 *lnProposalRatio = 0.0; in Move_Adgamma() 1616 *lnProposalRatio = 0.0; in Move_Extinction() 1727 *lnProposalRatio = 0.0; in Move_Fossilization() 7512 *lnProposalRatio = 0.0; in Move_MixtureRates_Slider() 8453 *lnProposalRatio = 0.0; in Move_Omega() 8892 *lnProposalRatio = 0.0; in Move_OmegaM3() 8959 *lnProposalRatio = 0.0; in Move_OmegaNeu() 9057 *lnProposalRatio = 0.0; in Move_OmegaPos() 9141 *lnProposalRatio = 0.0; in Move_OmegaPur() [all …]
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H A D | best.c | 1160 Move_ExtSPRClock(param, chain, seed, lnPriorRatio, lnProposalRatio, mvp); in Move_GeneTree1() 1198 (*lnProposalRatio) += (backwardLnProposalProb - forwardLnProposalProb); in Move_GeneTree1() 1264 Move_NNIClock(param, chain, seed, lnPriorRatio, lnProposalRatio, mvp); in Move_GeneTree2() 1302 (*lnProposalRatio) += (backwardLnProposalProb - forwardLnProposalProb); in Move_GeneTree2() 1368 Move_ParsSPRClock(param, chain, seed, lnPriorRatio, lnProposalRatio, mvp); in Move_GeneTree3() 1406 (*lnProposalRatio) += (backwardLnProposalProb - forwardLnProposalProb); in Move_GeneTree3() 1551 (*lnProposalRatio) = 0.0; in Move_NodeSliderGeneTree() 1568 … (*lnProposalRatio) += nEvents[p->left->index ] * log (p->left->length / oldLeftLength); in Move_NodeSliderGeneTree() 1572 (*lnProposalRatio) += nEvents[p->index] * log (p->length / oldPLength); in Move_NodeSliderGeneTree() 1664 oldDepth, newDepth, (*lnPriorRatio), (*lnProposalRatio)); in Move_NodeSliderGeneTree() [all …]
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H A D | bayes.h | 879 …ram *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
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H A D | mcmc.c | 16027 …MrBFlt r=0.0, lnLikelihoodRatio, lnPriorRatio, lnProposalRatio, lnLike=0.0, lnPrior=0.0, f=0.… in RunChain() local 16790 lnProposalRatio = 0.0; in RunChain() 16816 …if ((theMove->moveFxn)(theMove->parm, chn, seed, &lnPriorRatio, &lnProposalRatio, theMove->tuningP… in RunChain() 16866 if (lnProposalRatio != lnProposalRatio) in RunChain() 16904 if (lnLikelihoodRatio + lnPriorRatio + lnProposalRatio < -100.0) in RunChain() 16906 else if (lnLikelihoodRatio + lnPriorRatio + lnProposalRatio > 0.0) in RunChain() 16909 r = exp(lnLikelihoodRatio + lnPriorRatio + lnProposalRatio); in RunChain()
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H A D | model.c | 18192 MrBFlt lnPriorRatio = 0.0, lnProposalRatio = 0.0; in SetModelParams() local
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