mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 06:50:25 +08:00
67 lines
1.9 KiB
C++
67 lines
1.9 KiB
C++
#include "KH_calculation.h"
|
|
|
|
namespace KH_calculation {
|
|
|
|
double get_phi (double z)
|
|
{
|
|
// constants
|
|
double a1 = 0.254829592;
|
|
double a2 = -0.284496736;
|
|
double a3 = 1.421413741;
|
|
double a4 = -1.453152027;
|
|
double a5 = 1.061405429;
|
|
double p = 0.3275911;
|
|
|
|
// Save the sign of z
|
|
int sign = 1;
|
|
if (z < 0)
|
|
{
|
|
sign = -1;
|
|
}
|
|
z = fabs(z)/sqrt(2.0);
|
|
|
|
// A&S formula 7.1.26
|
|
double t = 1.0/(1.0 + p*z);
|
|
double y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-z*z);
|
|
|
|
return 0.5*(1.0 + sign*y);
|
|
}
|
|
|
|
|
|
double calc_p_value_kh (const Vdouble & LogLikePerPositionA, const Vdouble & LogLikePerPositionB)
|
|
{
|
|
//calc esteemated variance of delta of KH (Assessing the Uncertainty in Phylogenetic Inference, Nielsen, pg 484)
|
|
//delta(X) = LL(A) - LL(B)
|
|
//H0: E(delta(X)) <= 0 ---> tree B is either better or equal to tree A
|
|
//H1: E(delta(X)) > 0 ---> tree A is better than tree B
|
|
int num_pos = LogLikePerPositionA.size();
|
|
double varDeltaX = 0;
|
|
double sum_diffs = 0;
|
|
double avg_diff = 0;
|
|
for (int i=0; i < num_pos; ++i)
|
|
{
|
|
sum_diffs += (LogLikePerPositionA[i] - LogLikePerPositionB[i]);
|
|
}
|
|
avg_diff = sum_diffs / num_pos;
|
|
|
|
double sum_squares = 0;
|
|
double sqr_diff = 0;
|
|
for (int i=0; i < num_pos; ++i)
|
|
{
|
|
sqr_diff = pow (LogLikePerPositionA[i] - LogLikePerPositionB[i] - avg_diff, 2);
|
|
sum_squares += sqr_diff;
|
|
}
|
|
varDeltaX = (num_pos / (num_pos - 1)) * sum_squares;
|
|
//end calc esteemated variance of delta of KH (Assessing the Uncertainty in Phylogenetic Inference, Nielsen, pg 484)
|
|
|
|
//obtain the standard test statistic, z:
|
|
double stdDeltaX = sqrt (varDeltaX);
|
|
double z = sum_diffs / stdDeltaX; //let's hope stdDeltaX is not a zero
|
|
|
|
double phi_of_z = get_phi (z);
|
|
double p_value = 1 - phi_of_z; //one-sided test to see if A is better than B
|
|
|
|
return p_value;
|
|
}
|
|
|
|
}; |