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matvec::Fpmm Class Reference

#include <fpmm.h>

List of all members.

Public Methods

 Fpmm (void)
 Fpmm (Fpmm &F)
 Fpmm (int nl, double frq, double vr)
void initial (int nl, double frq, double vr)
void setup_trm (int nl, double frq)
void setup_genval (double vr)
double getpr (int fpgn, int mpgn, int opgn)
Vector< double > getgv (void)
Vector< double > getgenfreq (void)
void print_trm (void)
void print_genval (void)
void print_genfreq (void)
int get_dim (void)
int display (void)

Public Attributes

double var

Protected Attributes

Dblock trm
int ndim
Vector< double > genval
Vector< double > genfreq
double freq

Constructor & Destructor Documentation

matvec::Fpmm::Fpmm (  void    )  [inline]
 

Definition at line 52 of file fpmm.h.

References freq, ndim, and var. 

00052 {ndim=0;freq=0.5;var=1.0;}

matvec::Fpmm::Fpmm (  Fpmm &    F ) 
 

Definition at line 26 of file fpmm.cpp.

References freq, genfreq, genval, ndim, and trm. 

00026                  {
00027  trm  = F.trm;
00028  ndim = F.ndim;
00029  genval = F.genval;
00030  genfreq = F.genfreq;
00031  freq = F.freq;
00032 }

matvec::Fpmm::Fpmm (  int    nl,
double    frq,
double    vr
)  [inline]
 

Definition at line 54 of file fpmm.h.

References setup_genval(), and setup_trm(). 

00054                                           {
00055         setup_trm(nl, frq);
00056         setup_genval(vr);
00057       }

Member Function Documentation

int matvec::Fpmm::display (  void    ) 
 

Definition at line 157 of file fpmm.cpp.

References genval. 

00157                      {
00158   std::cout << "Fpmm Object: Polygenic Values" << std::endl;
00159   std::cout << genval << std::endl;
00160   return 1;
00161 }

int matvec::Fpmm::get_dim (  void    )  [inline]
 

Definition at line 73 of file fpmm.h.

References ndim.

Referenced by matvec::Population::multipoint_init_parm(). 

00073 {return ndim;}

Vector<double> matvec::Fpmm::getgenfreq (  void    )  [inline]
 

Definition at line 69 of file fpmm.h.

Referenced by matvec::Population::multipoint_init_parm(). 

00069 {return genfreq;}

Vector<double> matvec::Fpmm::getgv (  void    )  [inline]
 

Definition at line 68 of file fpmm.h.

Referenced by matvec::Population::multipoint_init_parm(). 

00068 {return genval;}

double matvec::Fpmm::getpr (  int    fpgn,
int    mpgn,
int    opgn
)  [inline]
 

Definition at line 67 of file fpmm.h.

Referenced by matvec::NuFamily::multi_anterior(), and matvec::NuFamily::multi_fullsibs_prob(). 

00067 {return trm[fpgn][mpgn][opgn];};

void matvec::Fpmm::initial (  int    nl,
double    frq,
double    vr
)  [inline]
 

Definition at line 59 of file fpmm.h.

References setup_genval(), and setup_trm(). 

00059                                                   {
00060 //        cout << "inside Fpmm.initial" << endl;
00061         setup_trm(nl, frq);
00062         setup_genval(vr);
00063       //  cout << "exiting Fpmm.initial" << endl;
00064       }

void matvec::Fpmm::print_genfreq (  void    )  [inline]
 

Definition at line 72 of file fpmm.h. 

00072 {std::cout << genfreq;}

void matvec::Fpmm::print_genval (  void    )  [inline]
 

Definition at line 71 of file fpmm.h. 

00071 {std::cout << genval;}

void matvec::Fpmm::print_trm (  void    )  [inline]
 

Definition at line 70 of file fpmm.h. 

00070 {std::cout << trm;}

void matvec::Fpmm::setup_genval (  double    vr ) 
 

Definition at line 133 of file fpmm.cpp.

References genfreq, genval, ndim, matvec::Vector< double >::resize(), and var.

Referenced by Fpmm(), and initial(). 

00133                                 {
00134   var = vr;  
00135   int gen;
00136   double mean=0.0, vart=0.0,scale;
00137 
00138   genval.resize(ndim);
00139   if (ndim == 1) {
00140     // no polygenic component
00141     genval[0]=0.0;
00142   }
00143   else {
00144     for (gen=0; gen<ndim; gen++){
00145       mean += gen*genfreq[gen];
00146     }
00147     for (gen=0; gen<ndim; gen++){
00148       vart += (gen - mean)*(gen - mean)*genfreq[gen];
00149     }
00150     scale = std::sqrt(var/vart);
00151     for (gen=0; gen<ndim; gen++){
00152       genval[gen] = (gen - mean)*scale;
00153     }
00154   }
00155 }

void matvec::Fpmm::setup_trm (  int    nl,
double    frq
) 
 

Definition at line 34 of file fpmm.cpp.

References freq, genfreq, ndim, matvec::Vector< double >::resize(), matvec::Dblock::resize(), and trm.

Referenced by Fpmm(), and initial(). 

00034                                      {
00035 
00036   int locus,m, f, o,m1, f1, o1;
00037   int ndimt;
00038   Vector<double> gf(3); // genotypic freqs for 1 locus
00039   double sum;
00040   Dblock trmt;  // temporary transmission matrix; used to update trm
00041   Dblock trm1;  // transmission matrix for one locus
00042  
00043   freq = 1 - fq; // to be consistent with SALP freq is the frequency of the bad allele
00044   ndim=2*nl+1;
00045 
00046   trm.resize(ndim,ndim,ndim);
00047   genfreq.resize(ndim);
00048   if (ndim == 1) {
00049     // We have no polygenic component so ndim=ncol=nrow=1 so that
00050     // trm is 1 and genfreq=1
00051     trm[0][0][0]=1.0;
00052     genfreq[0]=1.0;
00053   }
00054   else {
00055   trmt.resize(ndim,ndim,ndim);
00056   trm1.resize(3,3,3);
00057  
00058   gf(1) = (1-freq)*(1-freq);
00059   gf(2) = 2*freq*(1-freq);
00060   gf(3) = freq*freq;
00061 
00062   // transition probs; father, mother, child
00063   double A[3][3][3] = 
00064 {1.0, 0.0, 0.0,   0.5,  0.5, 0.0,    0.0, 1.0, 0.0,
00065  0.5, 0.5, 0.0,   0.25, 0.5, 0.25,   0.0, 0.5, 0.5,
00066  0.0, 1.0, 0.0,   0.0,  0.5, 0.5,    0.0,0.0,1.0};
00067 
00068 // calculating trm1
00069 
00070  for (f=0;f<3;f++){
00071     for (m=0;m<3;m++){
00072        for (o=0;o<3;o++){
00073          trm1[f][m][o] = A[f][m][o]*gf[f]*gf[m];
00074          trmt[f][m][o] = trm1[f][m][o];
00075          trm[f][m][o] = trm1[f][m][o];
00076        }
00077     }
00078  }
00079 
00080  for (locus=2; locus<=nl; locus++){
00081    // inittialize trm to zero
00082    ndimt = 2*locus + 1;
00083     for (f=0;f<ndimt;f++){
00084       for (m=0;m<ndimt;m++){
00085        for (o=0;o<ndimt;o++){
00086          trm[f][m][o] = 0.0;
00087        }
00088       }
00089     }
00090    // go through all combinations of trmt
00091     ndimt = 2*(locus-1) + 1;
00092     for (f=0;f<ndimt;f++){
00093       for (m=0;m<ndimt;m++){
00094        for (o=0;o<ndimt;o++){
00095        // make appropriate contributions for each comb. of trm1
00096          for (f1=0;f1<3;f1++){
00097            for (m1=0;m1<3;m1++){
00098              for (o1=0;o1<3;o1++){
00099                trm[f+f1][m+m1][o+o1] += trmt[f][m][o]*trm1[f1][m1][o1];
00100              }
00101            }
00102          }
00103        }
00104       }
00105     }
00106     ndimt = 2*locus + 1;
00107     for (f=0;f<ndimt;f++){
00108       for (m=0;m<ndimt;m++){
00109        for (o=0;o<ndimt;o++){
00110          trmt[f][m][o] = trm[f][m][o];
00111        }
00112       }
00113     }
00114  }
00115     for (f=0;f<ndim;f++){
00116       genfreq[f] = 0.0;
00117       for (m=0;m<ndim;m++){
00118         sum = 0.0;
00119         for (o=0;o<ndim;o++){ 
00120           sum += trm[f][m][o];
00121         }
00122         genfreq[f] += sum;
00123         for (o=0;o<ndim;o++){ 
00124           trm[f][m][o] /= sum;
00125         }
00126       }
00127     }
00128   }
00129   //  std::cout << genfreq;
00130 
00131 }

Member Data Documentation

double matvec::Fpmm::freq [protected]
 

Definition at line 47 of file fpmm.h.

Referenced by Fpmm(), and setup_trm().

Vector<double> matvec::Fpmm::genfreq [protected]
 

Definition at line 46 of file fpmm.h.

Referenced by Fpmm(), setup_genval(), and setup_trm().

Vector<double> matvec::Fpmm::genval [protected]
 

Definition at line 45 of file fpmm.h.

Referenced by display(), Fpmm(), and setup_genval().

int matvec::Fpmm::ndim [protected]
 

Definition at line 43 of file fpmm.h.

Referenced by Fpmm(), get_dim(), setup_genval(), and setup_trm().

Dblock matvec::Fpmm::trm [protected]
 

Definition at line 42 of file fpmm.h.

Referenced by Fpmm(), and setup_trm().

double matvec::Fpmm::var
 

Definition at line 58 of file fpmm.h.

Referenced by Fpmm(), matvec::Individual::initial_multi_m_anterior(), matvec::NuFamily::multi_m_anterior(), matvec::Population::multi_m_log_likelihood_peeling(), matvec::NuFamily::multi_sumint_offspring(), matvec::Model::multipoint_estimate_PolyV(), and setup_genval().

The documentation for this class was generated from the following files:
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