best.h

#ifndef BEST_H_
#define BEST_H_

/* typedefs used by Fredrik's code, derived from BEST code */

/* struct for constraints (similar to Distance in BEST code, except
   that a bitfield is used to hold info on the taxon pair)  */
typedef struct {
    double      depth;
    BitsLong*   pairSet;
} Depth;

/* Declaration of functions that are called from MrBayes */
void    AllocateBestChainVariables (void);
int     FillSpeciesTreeParams (RandLong* seed, int from, int to);
void    FreeBestChainVariables (void);
int     IsSpeciesTreeConsistent (Tree *speciesTree, int chain);
double  LnSpeciesTreeProb (int chain);
double  LnJointGeneTreeSpeciesTreePr (Tree **geneTrees, int numGeneTrees, Tree *speciesTree, int chain);
int     Move_GeneTree1 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
int     Move_GeneTree2 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
int     Move_GeneTree3 (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
int     Move_NodeSliderGeneTree (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
int     Move_SpeciesTree (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp);
void    ShowUpperTriangMatrix (double *values, int squareSize);

/* NOTE: To add and set up more move functions, a struct needs to be added to SetUpMoveTypes in model.c */

#endif  /* BEST_H_ */