4 int AddToPrintString (char *tempStr);
5 void AutotuneDirichlet (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt *alphaPi, MrBFlt minTuning, MrBFlt maxTuning);
6 void AutotuneMultiplier (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt *lambda, MrBFlt minTuning, MrBFlt maxTuning);
7 void AutotuneSlider (MrBFlt acceptanceRate, MrBFlt targetRate, int batch, MrBFlt *width, MrBFlt minTuning, MrBFlt maxTuning);
10 int DoMcmcParm (char *parmName, char *tkn);
13 int DoSsParm (char *parmName, char *tkn);
14 int ExhaustiveParsimonySearch (Tree *t, int chain, TreeInfo *tInfo);
15 MrBFlt GetParsDP (Tree *t, TreeNode *p, int chain);
16 void GetParsFP (Tree *t, TreeNode *p, int chain);
17 int GetParsimonyBrlens (Tree *t, int chain, MrBFlt *brlens);
18 MrBFlt GetParsimonyLength (Tree *t, int chain);
19 void GetParsimonySubtreeRootstate (Tree *t, TreeNode *root, int chain);
20 MrBFlt GetRate (int division, int chain);
21 int LnBirthDeathPriorPr (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt sR, MrBFlt eR, char *sS, MrBFlt sF);
22 int LnCoalescencePriorPr (Tree *t, MrBFlt *prob, MrBFlt theta, MrBFlt growth);
23 MrBFlt LnUniformPriorPr (Tree *t, MrBFlt clockRate);
24 int LnFossilizationPriorPr (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt *sR, MrBFlt *eR, MrBFlt sF, MrBFlt *fR, char *sS);
25 int LogClockTreePriorRatio (Param *param, int chain, MrBFlt *lnPriorRatio);
26 MrBFlt LogDirPrior (Tree *t, ModelParams *mp, int PV);
27 MrBFlt LogOmegaPrior (MrBFlt w1, MrBFlt w2, MrBFlt w3);
28 FILE *OpenNewMBPrintFile (char *fileName);
29 int ResetScalersPartition (int *isScalerNode, Tree* t, unsigned rescaleFreq);
30 int SafeSprintf (char **target, int *targetLen, char *fmt, ...);
31 int SetFilePositions (int samplePos);
32 MrBFlt TreeLength (Param *param, int chain);
34 #endif /* __MCMC_H__ */