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
|
/*
* simpson.cpp
* Dotur
*
* Created by Sarah Westcott on 1/7/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "simpson.h"
/***********************************************************************/
EstOutput Simpson::getValues(SAbundVector* rank){
try {
//vector<double> simpsonData(3,0);
data.resize(3,0);
double simpson = 0.0000;
double ci = 0;
double maxRank = (double)rank->getMaxRank();
double sampled = (double)rank->getNumSeqs();
double sobs = (double)rank->getNumBins();
double firstTerm = 0;
double secondTerm = 0;
if(sobs != 0){
double simnum=0.0000;
for(unsigned long long i=1;i<=maxRank;i++){
simnum += (double)(rank->get(i)*i*(i-1));
}
simpson = simnum / (sampled*(sampled-1));
for(unsigned long long i=1;i<=maxRank;i++){
double piI = (double) i / (double)sampled;
firstTerm += rank->get(i) * pow(piI, 3);
secondTerm += rank->get(i) * pow(piI, 2);
}
double var = (4.0 / sampled) * (firstTerm - secondTerm*secondTerm);
ci = 1.95 * pow(var, 0.5);
}
double simpsonlci = simpson - ci;
double simpsonhci = simpson + ci;
data[0] = simpson;
data[1] = simpsonlci;
data[2] = simpsonhci;
if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
return data;
}
catch(exception& e) {
m->errorOut(e, "Simpson", "getValues");
exit(1);
}
}
/***********************************************************************/
|
