1
int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol);
2
int ChangeNumRuns (int from, int to);
3
int ChangeNumChains (int from, int to);
5
int DoesTreeSatisfyConstraints(Tree *t);
7
int DoLinkParm (char *parmName, char *tkn);
9
int DoLsetParm (char *parmName, char *tkn);
11
int DoPropsetParm (char *parmName, char *tkn);
13
int DoPrsetParm (char *parmName, char *tkn);
15
int DoReportParm (char *parmName, char *tkn);
16
int DoShowMcmcTrees (void);
17
int DoShowModel (void);
18
int DoShowMoves (void);
19
int DoShowmovesParm (char *parmName, char *tkn);
20
int DoShowParams (void);
21
int DoStartvals (void);
22
int DoStartvalsParm (char *parmName, char *tkn);
24
int FillNormalParams (SafeLong *seed, int fromChain, int toChain);
25
int FillRelPartsString (Param *p, char **relPartString);
26
void FillStdStateFreqs(int chfrom, int chto, SafeLong *seed);
27
int FillTopologySubParams (Param *param, int chn, int state, SafeLong *seed);
28
int FillTreeParams (SafeLong *seed, int fromChain, int toChain);
30
int GetEmpiricalFreqs (int *relParts, int nRelParts);
31
int GetNumDivisionChars (void);
32
int *GetParamIntVals (Param *parm, int chain, int state);
33
MrBFlt *GetParamStdStateFreqs (Param *parm, int chain, int state);
34
MrBFlt *GetParamSubVals (Param *parm, int chain, int state);
35
MrBFlt *GetParamVals (Param *parm, int chain, int state);
36
Tree *GetTree (Param *parm, int chain, int state);
37
Tree *GetTreeFromIndex (int index, int chain, int state);
38
int InitializeLinks (void);
39
int InitializeTreeCalibrations (Tree *t);
41
int SetAARates (void);
42
int SetLocalTaxa (void);
43
int SetModelDefaults (void);
45
int SetUpAnalysis (SafeLong *seed);
46
void SetUpMoveTypes (void);
49
int UpdateTK02EvolLengths (Param *param, Tree *t, int chain);
50
int UpdateClockRate(MrBFlt clockRate, int chain);
51
int UpdateCppEvolLengths (Param *param, TreeNode *p, int chain);
52
int UpdateIgrBranchRates (Param *param, Tree *t, int chain);