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
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
#include<fstream>
using namespace std;
#include "GibbsParameters.h"
#include "common.h"
#define DEBUGGP(x)
#define Sof(x) (long)x.size()
void gibbsParameters::getAllParameters(){
message("Parameters:\n burnIn: %ld\
\n samplesN: %ld\n samplesSave: %ld\
\n samplesNmax: %ld\n chainsN: %ld\
\n targetScaleReduction: %lf\n dirAlpha: %lf\
\n dirBeta: %lf\n betaAlpha: %lf\n betaBeta: %lf\n",
gs_burnIn,gs_samplesN,gs_samplesSave,gs_samplesNmax,gs_chainsN,gs_targetScaleReduction,dirP.alpha,dirP.beta,betaP.alpha,betaP.beta);
}
bool gibbsParameters::setParameters(string paramFileName){
this->paramFileName = paramFileName;
return readParameters();
}
bool gibbsParameters::setParameters(ArgumentParser &args){
if(args.isSet("MCMC_burnIn"))gs_burnIn=args.getL("MCMC_burnIn");
if(args.isSet("MCMC_samplesN"))gs_samplesN=args.getL("MCMC_samplesN");
if(args.isSet("MCMC_samplesSave"))gs_samplesSave=args.getL("MCMC_samplesSave");
if(args.isSet("MCMC_samplesNmax"))gs_samplesNmax=args.getL("MCMC_samplesNmax");
if(args.isSet("MCMC_chainsN"))gs_chainsN=args.getL("MCMC_chainsN");
if(args.isSet("MCMC_scaleReduction"))gs_targetScaleReduction=args.getD("MCMC_scaleReduction");
if(args.isSet("MCMC_dirAlpha"))dirP.alpha=args.getD("MCMC_dirAlpha");
return true;
}
bool gibbsParameters::readParameters(){
ifstream pFile;
string param;
double val;
char tmp[256];
pFile.open(paramFileName.c_str());
while((pFile.is_open())&&(! pFile.eof())){
if((! (pFile>>param)) || (Sof(param)==0) || (param[0]=='#')){
pFile.getline(tmp,256);
continue;
}
pFile>>val;
if(pFile.good()){
DEBUGGP(message("# DEBUG gPar ||%s==%lf||\n",(param).c_str(),val);)
if(param=="burnIn")parameter("burnIn",gs_burnIn,val);
if(param=="samplesN")parameter("samplesN",gs_samplesN,val);
if(param=="samplesSave")parameter("samplesSave",gs_samplesSave,val);
if(param=="samplesNmax")parameter("samplesNmax",gs_samplesNmax,val);
if(param=="chainsN")parameter("chainsN",gs_chainsN,val);
if(param=="targetScaleReduction")parameter("targetScaleReduction",gs_targetScaleReduction,val);
if(param=="dirAlpha")parameter("dirAlpha",dirP.alpha,val);
if(param=="dirBeta")parameter("dirBeta",dirP.beta,val);
if(param=="betaAlpha")parameter("betaAlpha",betaP.alpha,val);
if(param=="betaBeta")parameter("betaBeta",betaP.beta,val);
}
pFile.getline(tmp,256);
}
pFile.close();
return true;
}
void gibbsParameters::parameter(string name, double &variable, double value){
bool output=false;
if(verbose && (variable != value))output = true;
variable = value;
if(output){
message("### %s: %lf\n",(name).c_str(),variable);
}
}
void gibbsParameters::parameter(string name, long &variable, double value){
bool output=false;
if(verbose && (variable != (long) value))output = true;
variable = (long) value;
if(output){
message("### %s: %ld\n",(name).c_str(),variable);
}
}
void gibbsParameters::parameter(string name, bool &variable, double value){
bool output=false;
if(verbose && (variable !=(bool)((long) value)))output = true;
variable = (bool)((long)value);
if(output){
message("### %s: %d\n",(name).c_str(),variable);
}
}
gibbsParameters::gibbsParameters(bool verbose){
this->verbose = verbose;
gs_burnIn=1000;
gs_samplesN=1000;
gs_samplesNmax=50000;
gs_samplesSave=500;
gs_chainsN=4;
gs_targetScaleReduction=1.2;
dirP.alpha=1;
dirP.beta=1;
betaP.alpha=10;
betaP.beta=2;
gs_samplesFile="gibbs_log.rpkmS";
gs_meansFile="gibbs_log.thetaMeans";
}
|
