1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
/*
* treetest.h
*
*
* Part of TREE-PUZZLE 5.2 (July 2004)
*
* (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
* (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
* M. Vingron, and Arndt von Haeseler
* (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
*
* All parts of the source except where indicated are distributed under
* the GNU public licence. See http://www.opensource.org for details.
*
* ($Id$)
*
*/
#ifndef TREETEST_H
#define TREETEST_H
#include <util.h>
/* minimum log-lh difference to best log-lh to be different */
#define MINKHDIFF 0.005
/*****************************************************************************/
/* ELW/SR Test (Expected Likelihood Weights, Strimmer & Rambaut, 2002) */
/*****************************************************************************/
void elw_test(ivector Alias,
dmatrix allsites,
int numutrees,
int numsites,
double siglevel,
int numboots,
ivector *elw_test_passed,
dvector *elw_Support);
/*****************************************************************************/
/* SH Test (Shimodaira & Hasegawa, 1999) */
/*****************************************************************************/
void sh_test(ivector Alias, /* site pattern translat array */
dmatrix allsites, /* tree site log-likelihoods */
int numutrees, /* number of trees */
int numsites, /* number of sites */
double siglevel, /* significance level to test */
int numboots, /* number of bootstraps to draw */
ivector *sh_test_passed, /* has tree passed tests */
dvector *sh_Pval); /* and p-value */
/* print tree statistics */
void printtreestats(FILE *ofp,
dvector ulkl,
dvector ulklc,
int numutrees,
dmatrix allsites, /* tree site log-likelihoods */
dmatrix allsitesc, /* tree site log-likelihoods */
ivector Alias, /* link site -> corresponding site pattern */
int Maxsite,
int Numptrn,
ivector Weight,
int compclock);
#endif /* TREETEST_H */
|
