4 /**************** typedefs used by Fredrik's code, derived from BEST code *******************/
6 /* struct for constraints (similar to Distance in BEST code, except
7 that a bitfield is used to hold info on the taxon pair) */
13 /**************** Declaration of functions that are called from MrBayes **************/
14 void AllocateBestChainVariables (void);
15 int FillSpeciesTreeParams (RandLong* seed, int from, int to);
16 void FreeBestChainVariables (void);
17 int IsSpeciesTreeConsistent (Tree *speciesTree, int chain);
18 double LnSpeciesTreeProb (int chain);
19 double LnJointGeneTreeSpeciesTreePr (Tree **geneTrees, int numGeneTrees, Tree *speciesTree, int chain);
20 int Move_GeneTree1 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
21 int Move_GeneTree2 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
22 int Move_GeneTree3 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
23 int Move_NodeSliderGeneTree (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
24 int Move_SpeciesTree (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
25 void ShowUpperTriangMatrix (double *values, int squareSize);
27 /* NOTE: To add and set up more move functions, a struct needs to be added to SetUpMoveTypes in model.c */
29 #endif /* __BEST_H__ */