TTDeletMutBitstrSH Class Reference

The StatHandler for TTDeletMutations_bitstring. More...

#include <ttdeletmutations_bitstring.h>

Inheritance diagram for TTDeletMutBitstrSH:

Collaboration diagram for TTDeletMutBitstrSH:

Public Member Functions
	TTDeletMutBitstrSH (TProtoDeletMutations_bitstring *TP)
virtual	~TTDeletMutBitstrSH ()
virtual bool	setStatRecorders (std::string &token)
void	setStatsForDeletMutations (age_t AGE)
void	setViabStats (age_t AGE)
void	setDeletStats (age_t AGE)
void	setLethalEquivalents (age_t AGE)
void	setFst (age_t AGE)
void	setAdultDeletStats ()
void	setOffsprgDeletStats ()
void	setViability (age_idx agex)
void	setAdultViab ()
void	setOffsprgViab ()
void	setMeanViability (age_idx agex)
double	getMeanFecWithPatchMate (bool HOME)
double	getBtheta ()
double	getBalpha ()
double	getHeterosis ()
double	getLoad ()
double	getPatchLoad (unsigned int i)
double	getDeletAllFreq ()
double	getDeletAllHmz ()
double	getDeletAllHtz ()
double	getFixedDeletLoci ()
double	getFixedDeletLociPerPatch ()
double	getSegregatingDeletLoci ()
double	getSegregatingDeletLociPerPatch ()
double	getDeletAllPerGenome ()
double	getHs ()
double	getHt ()
double	getFst ()
double	getLethalEquivalents ()
double	getAdultsLetheq ()
double	getOffsprgLetheq ()
double	getViability (unsigned int v)
double	getMeanViability ()
double	getMeanViability (unsigned int a)
double	getSibProportions (unsigned int i)
Public Member Functions inherited from TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >
	TraitStatHandler (TProtoDeletMutations_bitstring *trait_proto)
virtual	~TraitStatHandler ()
Public Member Functions inherited from StatHandler< SH >
	StatHandler ()
virtual	~StatHandler ()
virtual void	clear ()
	Empties the _recorders list, they are destroyed in StatHandlerBase::reset(). More...
virtual StatRecorder< SH > *	add (std::string Title, std::string Name, age_t AGE, unsigned int ARG1, unsigned int ARG2, double(SH::*getStatNoArg)(void), double(SH::*getStatOneArg)(unsigned int), double(SH::*getStatTwoArg)(unsigned int, unsigned int), void(SH::*setStat)(void))
	Adds a StatRecorder to the list, it is also added to the StatHandlerBase::_stats list. More...
Public Member Functions inherited from StatHandlerBase
	StatHandlerBase ()
virtual	~StatHandlerBase ()
virtual void	reset ()
	Empties the _stats list and calls clear() (defined in the derived class). More...
Metapop *	get_pop_ptr ()
void	set_service (StatServices *srv)
StatServices *	get_service ()
unsigned int	getOccurrence ()
unsigned int	getNumOccurrences ()
unsigned int	getCurrentOccurrence ()
unsigned int	getNbRecorders ()
std::list< StatRecBase * > &	getStats ()
virtual void	add (StatRecBase *rec)
virtual void	init ()
virtual void	update ()
	This function is left empty as the StatServices calls StatRecorder::setVal directly. More...
Public Member Functions inherited from Handler
virtual	~Handler ()

Private Attributes
double	fecWithHomePatchMate
double	fecWithOtherPatchMate
double	_SibProps [5]
double	_viability [5]
double	_meanViab
double	_deletHtzLoci
double	_deletHmzLoci
double	_fixLocPerPatch
double	_segrLocPerPatch
double	_Ho
double	_Hs
double	_Ht
double	_Fst
double	_Hmz
double	_deletAllCount
double	_freq
double	_fixloc
double	_segrloc
double	_letheq
double *	_deletFreqTable
bool	_isContinuousEffect

Additional Inherited Members
Protected Types inherited from StatHandler< SH >
typedef std::list< StatRecorder< SH > * >::iterator	REC_IT
Protected Attributes inherited from TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >
TProtoDeletMutations_bitstring *	_SHLinkedTrait
	Pointer to a TraitProtoype object. More...
int	_SHLinkedTraitIndex
	Index of the trait in the Individual::Traits table. More...
Protected Attributes inherited from StatHandler< SH >
std::list< StatRecorder< SH > * >	_recorders
	The list of stat recorders. More...
Protected Attributes inherited from StatHandlerBase
Metapop *	_pop
	Link to the current population, set through the link to the StatService. More...

Detailed Description

The StatHandler for TTDeletMutations_bitstring.

Constructor & Destructor Documentation

TTDeletMutBitstrSH()

TTDeletMutBitstrSH::TTDeletMutBitstrSH ( TProtoDeletMutations_bitstring *  TP )

inline

  : TraitStatHandler<TProtoDeletMutations_bitstring, TTDeletMutBitstrSH> ( TP ), _deletFreqTable(0)
  { _isContinuousEffect = TP->get_iscontinuous(); }

References _isContinuousEffect, and TProtoDeletMutations_bitstring::get_iscontinuous().

~TTDeletMutBitstrSH()

virtual TTDeletMutBitstrSH::~TTDeletMutBitstrSH ( )

inlinevirtual

{if(_deletFreqTable != 0) delete [] _deletFreqTable;}

References _deletFreqTable.

Member Function Documentation

getAdultsLetheq()

double TTDeletMutBitstrSH::getAdultsLetheq ( )

inline

{setDeletStats(ADULTS);  return _letheq;}

References _letheq, ADULTS, and setDeletStats().

getBalpha()

double TTDeletMutBitstrSH::getBalpha ( )

inline

{return fecWithOtherPatchMate;}

References fecWithOtherPatchMate.

getBtheta()

double TTDeletMutBitstrSH::getBtheta ( )

inline

{return fecWithHomePatchMate;}

References fecWithHomePatchMate.

getDeletAllFreq()

double TTDeletMutBitstrSH::getDeletAllFreq ( )

inline

{return _freq;}

References _freq.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getDeletAllHmz()

double TTDeletMutBitstrSH::getDeletAllHmz ( )

inline

{return _Hmz;}

References _Hmz.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getDeletAllHtz()

double TTDeletMutBitstrSH::getDeletAllHtz ( )

inline

{return _Ho;}

References _Ho.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getDeletAllPerGenome()

double TTDeletMutBitstrSH::getDeletAllPerGenome ( )

inline

{return _deletAllCount;}

References _deletAllCount.

getFixedDeletLoci()

double TTDeletMutBitstrSH::getFixedDeletLoci ( )

inline

{return _fixloc;}

References _fixloc.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getFixedDeletLociPerPatch()

double TTDeletMutBitstrSH::getFixedDeletLociPerPatch ( )

inline

{return _fixLocPerPatch;}

References _fixLocPerPatch.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getFst()

double TTDeletMutBitstrSH::getFst ( )

inline

{return _Fst;}

References _Fst.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getHeterosis()

double TTDeletMutBitstrSH::getHeterosis

(

)

{
  double Btheta = getMeanFecWithPatchMate(true);
  double Balpha = getMeanFecWithPatchMate(false);
 
  return (Balpha != 0 ? (1 - (Btheta/Balpha)): nanf("NULL"));
}

References getMeanFecWithPatchMate().

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getHs()

double TTDeletMutBitstrSH::getHs ( )

inline

{return _Hs;}

References _Hs.

getHt()

double TTDeletMutBitstrSH::getHt ( )

inline

{return _Ht;}

References _Ht.

getLethalEquivalents()

double TTDeletMutBitstrSH::getLethalEquivalents ( )

inline

{return _letheq;}

References _letheq.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getLoad()

double TTDeletMutBitstrSH::getLoad

(

)

{
  unsigned int nb_patch=0;
  double mean_load=0;
 
  for(unsigned int i = 0; i<_pop->getPatchNbr(); i++){
    
    if(_pop->getPatch(i)->size(FEM, ADLTx) != 0) {
 
      mean_load += getPatchLoad(i);
 
      nb_patch++;
    }
  }
 
 return (nb_patch != 0 ? mean_load/nb_patch : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, FEM, Metapop::getPatch(), getPatchLoad(), Metapop::getPatchNbr(), and Patch::size().

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getMeanFecWithPatchMate()

double TTDeletMutBitstrSH::getMeanFecWithPatchMate

(

bool

HOME

)

{
  double m_fec = 0;
  unsigned int nbfem = 0;
  Patch* patch;
  Individual* fem;
  
  if(HOME) {
    for(unsigned int i = 0, pnb = _pop->getPatchNbr(); i < pnb; ++i) {
      patch = _pop->getPatch(i);
      for(unsigned int j = 0, size = patch->size(FEM, ADLTx); j < size; ++j) {
        fem = patch->get(FEM, ADLTx, j);
        m_fec += fem->getFecWithHomePatchMate();
        nbfem += (fem->getLocalMatings() != 0);
      }
    }
  } else {
    for(unsigned int i = 0, pnb = _pop->getPatchNbr(); i < pnb; ++i) {
      patch = _pop->getPatch(i);
      for(unsigned int j = 0, size = _pop->getPatch(i)->size(FEM, ADLTx); j < size; ++j) {
        fem = patch->get(FEM, ADLTx, j);
        m_fec += fem->getFecWithOtherPatchMate();
        nbfem += (fem->getMatings(0) != 0);
      }
    }
  }
  return (nbfem != 0 ? (double) m_fec/nbfem : 0.0);
}

References StatHandlerBase::_pop, ADLTx, FEM, Patch::get(), Individual::getFecWithHomePatchMate(), Individual::getFecWithOtherPatchMate(), Individual::getLocalMatings(), Individual::getMatings(), Metapop::getPatch(), Metapop::getPatchNbr(), and Patch::size().

Referenced by getHeterosis().

Here is the caller graph for this function:

getMeanViability() [1/2]

double TTDeletMutBitstrSH::getMeanViability ( )

inline

{return _meanViab;}

References _meanViab.

Referenced by setStatRecorders(), and setViabStats().

Here is the caller graph for this function:

getMeanViability() [2/2]

double TTDeletMutBitstrSH::getMeanViability ( unsigned int  a )

inline

{setMeanViability(static_cast<age_idx> (a)); return _meanViab;}

References _meanViab, and setMeanViability().

getOffsprgLetheq()

double TTDeletMutBitstrSH::getOffsprgLetheq ( )

inline

{setDeletStats(OFFSPRG); return _letheq;}

References _letheq, OFFSPRG, and setDeletStats().

getPatchLoad()

double TTDeletMutBitstrSH::getPatchLoad

(

unsigned int

i

)

{
  Individual *ind;
  double fec, matings;
  double rel_fec, max_fec = 0, mean_patch_fec = 0;
  
  for(unsigned int j = 0, size = _pop->getPatch(i)->size(FEM, ADLTx); j < size; j++) {
    ind = _pop->getPatch(i)->get(FEM, ADLTx, j);
    fec = (double)ind->getTotRealizedFecundity();
    matings = (double)ind->getTotMatings();
    rel_fec = (matings != 0 ? fec/matings : 0.0);
    mean_patch_fec += rel_fec;
    if(rel_fec > max_fec) max_fec = rel_fec;
  }
  
  mean_patch_fec /= _pop->getPatch(i)->size(FEM, ADLTx);
  
  return ( max_fec != 0 ? (max_fec - mean_patch_fec)/max_fec : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, FEM, Patch::get(), Metapop::getPatch(), Individual::getTotMatings(), Individual::getTotRealizedFecundity(), and Patch::size().

Referenced by getLoad().

Here is the caller graph for this function:

getSegregatingDeletLoci()

double TTDeletMutBitstrSH::getSegregatingDeletLoci ( )

inline

{return _segrloc;}

References _segrloc.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getSegregatingDeletLociPerPatch()

double TTDeletMutBitstrSH::getSegregatingDeletLociPerPatch ( )

inline

{return _segrLocPerPatch;}

References _segrLocPerPatch.

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

getSibProportions()

double TTDeletMutBitstrSH::getSibProportions ( unsigned int  i )

inline

{return _SibProps[i];}

References _SibProps.

Referenced by setViabStats().

Here is the caller graph for this function:

getViability()

double TTDeletMutBitstrSH::getViability ( unsigned int  v )

inline

{return _viability[v];}

References _viability.

Referenced by setViabStats().

Here is the caller graph for this function:

setAdultDeletStats()

void TTDeletMutBitstrSH::setAdultDeletStats ( )

inline

{setDeletStats(ADULTS);}

References ADULTS, and setDeletStats().

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

setAdultViab()

void TTDeletMutBitstrSH::setAdultViab ( )

inline

{setViability(ADLTx);}

References ADLTx, and setViability().

Referenced by setViabStats().

Here is the caller graph for this function:

setDeletStats()

void TTDeletMutBitstrSH::setDeletStats

(

age_t

AGE

)

{
  unsigned int i, j, k, nb_ind = 0, nb_patch = 0;
  unsigned int nb_locus = _SHLinkedTrait->get_nb_locus();
  unsigned int psize=0;
  TTDeletMutations_bitstring* trait;
  Patch* current_patch;
  age_idx agex = (AGE == ADULTS ? ADLTx : OFFSx);
 
  _deletHtzLoci = 0;
  _deletHmzLoci = 0;
  _deletAllCount = 0;
  _Hs = 0;
  _Ht = 0;
  _fixLocPerPatch = 0;
  _segrLocPerPatch = 0;
 
  if(_deletFreqTable != NULL)
    delete [] _deletFreqTable;
 
  _deletFreqTable = new double [nb_locus];
 
  double* patch_freqbylocus = new double[nb_locus];
 
  for(i = 0; i < nb_locus; ++i)
    _deletFreqTable[i] = 0;
 
 
  for(i = 0; i < _pop->getPatchNbr(); ++i) {
 
    current_patch = _pop->getPatch(i);
 
    if( (psize = current_patch->size(AGE)) == 0) continue;
 
    nb_patch++;
 
    nb_ind += psize;
 
    for(j = 0; j < nb_locus; ++j)
      patch_freqbylocus[j] = 0;
    
    //Females
    for(j = 0; j < current_patch->size(FEM, agex); ++j) {
 
      trait = static_cast< TTDeletMutations_bitstring* > ( current_patch->get( FEM, agex, j )->getTrait( _SHLinkedTraitIndex ) );
 
      _deletHmzLoci += trait->get_nb_hmz_mutations();
 
      _deletHtzLoci += trait->get_nb_htz_mutations();
 
      //sparse iteration over set bits in both chromosomes
      bitstring** seq = (bitstring**)trait->get_sequence();
      for (unsigned int c = 0; c < 2; ++c) {
        for (size_t w = 0; w < seq[c]->nb_words(); ++w) {
          auto word = *seq[c]->getword_atIdx(w);
          while (word) {
            unsigned int bit = __builtin_ctzl(word);
            patch_freqbylocus[w * BITS_PER_WORD + bit] += 1;
            word &= word - 1;
          }
        }
      }
 
    }//end for females
 
    //Males
    for(j = 0; j < current_patch->size(MAL, agex); ++j) {
 
      trait = static_cast< TTDeletMutations_bitstring* > ( current_patch->get( MAL, agex, j )->getTrait( _SHLinkedTraitIndex ) );
 
      _deletHmzLoci += trait->get_nb_hmz_mutations();
 
      _deletHtzLoci += trait->get_nb_htz_mutations();
 
      //sparse iteration over set bits in both chromosomes
      bitstring** seq = (bitstring**)trait->get_sequence();
      for (unsigned int c = 0; c < 2; ++c) {
        for (size_t w = 0; w < seq[c]->nb_words(); ++w) {
          auto word = *seq[c]->getword_atIdx(w);
          while (word) {
            unsigned int bit = __builtin_ctzl(word);
            patch_freqbylocus[w * BITS_PER_WORD + bit] += 1;
            word &= word - 1;
          }
        }
      }
 
    }//end for males
    
    double dipl_size = psize*2.0;
    for(j = 0; j < nb_locus; ++j) {
      //aggregate for the pop freq by locus:
      _deletFreqTable[j] += patch_freqbylocus[j];
      //aggregate mut nbr for the population tot mut nbr:
      _deletAllCount += patch_freqbylocus[j];
      //get the local Patch mut freq by locus:
      patch_freqbylocus[j] /= dipl_size;
      //compute the expected local htz = 2pq:
      _Hs += patch_freqbylocus[j] * (1.0 - patch_freqbylocus[j]);
    }
 
    for(j = 0; j < nb_locus; ++j) {
      //segregating and fixed loci in the Patch:
      if(patch_freqbylocus[j] == 1.0)
        _fixLocPerPatch++;
      else if(patch_freqbylocus[j] != 0)
        _segrLocPerPatch++;
    }
 
  }//end for Patch
 
  double dipl_size = nb_ind*2.0;
  
  _freq = 0;
  _fixloc = _segrloc = 0;
  
  for(i = 0; i < nb_locus; ++i){
    
    _deletFreqTable[i] /= dipl_size;
    
    _Ht += _deletFreqTable[i] * (1.0 - _deletFreqTable[i]);//2pq: expected htz
      
    _freq += _deletFreqTable[i];
    
    _fixloc += (_deletFreqTable[i] == 1);
    
    _segrloc += (_deletFreqTable[i] < 1 && _deletFreqTable[i] != 0);
  }
  
  //factorization not done in previous loops:
  _Hs *= 2;
  _Ht *= 2;
  
  _deletAllCount /= nb_ind;
  _freq /= nb_locus;
  _Hs /= nb_locus * nb_patch;
  _Ht /= nb_locus;
  _Ho = _deletHtzLoci / (nb_ind * nb_locus);
  _Hmz = _deletHmzLoci/ (nb_ind * nb_locus);
  _fixLocPerPatch /= nb_patch;
  _segrLocPerPatch /= nb_patch;
 
  setLethalEquivalents(AGE);
  
  setFst(AGE);
  
  delete [] patch_freqbylocus;
  delete [] _deletFreqTable;
  _deletFreqTable = 0;
}

References _deletAllCount, _deletFreqTable, _deletHmzLoci, _deletHtzLoci, _fixloc, _fixLocPerPatch, _freq, _Hmz, _Ho, _Hs, _Ht, StatHandlerBase::_pop, _segrloc, _segrLocPerPatch, TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >::_SHLinkedTrait, TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >::_SHLinkedTraitIndex, ADLTx, ADULTS, BITS_PER_WORD, FEM, Patch::get(), TTDeletMutations_bitstring::get_nb_hmz_mutations(), TTDeletMutations_bitstring::get_nb_htz_mutations(), TProtoDeletMutations_bitstring::get_nb_locus(), TTDeletMutations_bitstring::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), bitstring::getword_atIdx(), MAL, bitstring::nb_words(), OFFSx, setFst(), setLethalEquivalents(), and Patch::size().

Referenced by getAdultsLetheq(), getOffsprgLetheq(), setAdultDeletStats(), and setOffsprgDeletStats().

Here is the caller graph for this function:

setFst()

void TTDeletMutBitstrSH::setFst

(

age_t

AGE

)

{
  unsigned i, nbpatch = 0;
  double Hsnei, Htnei, harmonic = 0, size;
  Patch* current_patch;
 
  for (i = 0; i < _pop->getPatchNbr(); ++i){
 
    current_patch = _pop->getPatch(i);
 
    if( (size = (double)current_patch->size(AGE)) != 0){
      nbpatch++;
      harmonic += 1.0/size;
    }
  }
 
  harmonic = (double)nbpatch/harmonic;
 
  Hsnei = harmonic/(harmonic-1.0)*(_Hs - ( _Ho/(2.0*harmonic) ) );
  Htnei = _Ht + ( Hsnei/(harmonic*nbpatch) ) - ( _Ho/(2.0*harmonic*nbpatch) );
 
  _Fst = 1.0 - (Hsnei/Htnei);
}

References _Fst, _Ho, _Hs, _Ht, StatHandlerBase::_pop, Metapop::getPatch(), Metapop::getPatchNbr(), and Patch::size().

Referenced by setDeletStats().

Here is the caller graph for this function:

setLethalEquivalents()

void TTDeletMutBitstrSH::setLethalEquivalents

(

age_t

AGE

)

{
  _letheq = 0;
  
  if(_deletFreqTable == 0) 
    fatal("allele frequency table not set when computing lethal equivalents\n");
  
  if(_isContinuousEffect) {
    float* s = _SHLinkedTrait->get_s_continous();
    for(int i = 0, nloc = _SHLinkedTrait->get_nb_locus(); i < nloc; i++)
      _letheq += _deletFreqTable[i] * s[i];
  } else
    _letheq = ((_deletHtzLoci/2 + _deletHmzLoci) * _SHLinkedTrait->get_strength())
              / _pop->size(AGE);
}

References _deletFreqTable, _deletHmzLoci, _deletHtzLoci, _isContinuousEffect, _letheq, StatHandlerBase::_pop, TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >::_SHLinkedTrait, fatal(), TProtoDeletMutations_bitstring::get_nb_locus(), TProtoDeletMutations_bitstring::get_s_continous(), TProtoDeletMutations_bitstring::get_strength(), and Metapop::size().

Referenced by setDeletStats().

Here is the caller graph for this function:

setMeanViability()

void TTDeletMutBitstrSH::setMeanViability

(

age_idx

agex

)

{
  unsigned int ind_cnt = 0;
  Patch *patch;
  _meanViab = 0;
  for(unsigned int i = 0; i<_pop->getPatchNbr(); ++i) {
    patch = _pop->getPatch(i);
    for(unsigned int j = 0, size = patch->size(FEM, agex); j < size; ++j) {
      _meanViab += *(double*)patch->get(FEM, ADLTx, j)->getTraitValue(_SHLinkedTraitIndex);
      ind_cnt++;
    }
    for(unsigned int j = 0, size = patch->size(MAL, agex); j < size; ++j) {
      _meanViab += *(double*)patch->get(MAL, ADLTx, j)->getTraitValue(_SHLinkedTraitIndex);
      ind_cnt++;
    }
  }
  
  _meanViab = ( ind_cnt != 0 ? _meanViab/ind_cnt : nanf("NULL"));
}

References _meanViab, StatHandlerBase::_pop, TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >::_SHLinkedTraitIndex, ADLTx, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTraitValue(), MAL, and Patch::size().

Referenced by getMeanViability().

Here is the caller graph for this function:

setOffsprgDeletStats()

void TTDeletMutBitstrSH::setOffsprgDeletStats ( )

inline

{setDeletStats(OFFSPRG);}

References OFFSPRG, and setDeletStats().

Referenced by setStatsForDeletMutations().

Here is the caller graph for this function:

setOffsprgViab()

void TTDeletMutBitstrSH::setOffsprgViab ( )

inline

{setViability(OFFSx);}

References OFFSx, and setViability().

Referenced by setViabStats().

Here is the caller graph for this function:

setStatRecorders()

bool TTDeletMutBitstrSH::setStatRecorders ( std::string &  token )

virtual

Implements StatHandlerBase.

{
#ifdef _DEBUG_
  message("-TTDeletMutBitstrSH::setStatRecorders ");
#endif
  if(token.compare("delet") == 0) {
    
    setStatsForDeletMutations(ALL);
    
  }else if(token.compare("adlt.delet") == 0) {
    
    setStatsForDeletMutations(ADULTS);
    
    
  }else if(token.compare("off.delet") == 0) {
    
    setStatsForDeletMutations(OFFSPRG);
    
    
  } else if(token.compare("viability") == 0) {
    
    setViabStats(ALL);
    
  } else if(token.compare("off.viability") == 0) {
    
    setViabStats(OFFSPRG);
    
  } else if(token.compare("adlt.viability") == 0) {
    
    setViabStats(ADULTS);
    
  } else if(token.compare("meanviab") == 0) {
    
    add("Offspring Viability","off.viab",OFFSPRG, static_cast<unsigned int> (OFFSx),
        0,0,&TTDeletMutBitstrSH::getMeanViability,0,0);
    add("Adults Viability","adlt.viab",ADULTS, static_cast<unsigned int> (ADLTx),
        0,0,&TTDeletMutBitstrSH::getMeanViability,0,0);
    
  } else
    return false;
  
  return true;
}

References StatHandler< SH >::add(), ADLTx, ADULTS, ALL, getMeanViability(), message(), OFFSPRG, OFFSx, setStatsForDeletMutations(), and setViabStats().

setStatsForDeletMutations()

void TTDeletMutBitstrSH::setStatsForDeletMutations

(

age_t

AGE

)

{
  if(AGE == ALL) {
    setStatsForDeletMutations(OFFSPRG); setStatsForDeletMutations(ADULTS);
    return;
  }
  
  string prefix = (AGE == ADULTS ? "adlt." : "off.");
  void (TTDeletMutBitstrSH::* setter) () = (AGE == ADULTS ?
                                            &TTDeletMutBitstrSH::setAdultDeletStats :
                                            &TTDeletMutBitstrSH::setOffsprgDeletStats);
  
  add("Frequency of deleterious alleles", prefix + "delfreq",   AGE,0,0,
      &TTDeletMutBitstrSH::getDeletAllFreq,0,0,
      setter);
  
  add("Homozygosity of delet. allele", prefix + "delhmz",   AGE,0,0,
      &TTDeletMutBitstrSH::getDeletAllHmz,0,0,0);
  
  add("Heterozygosity of delet. allele", prefix + "delhtz",   AGE,0,0,
      &TTDeletMutBitstrSH::getDeletAllHtz,0,0,0);
  
  add("Fixed Delet Mutations - Global", prefix + "delfix",   AGE,0,0,
      &TTDeletMutBitstrSH::getFixedDeletLoci,0,0,0);
  
  add("Fixed Delet Mutations - Local", prefix + "delfixp",   AGE,0,0,
      &TTDeletMutBitstrSH::getFixedDeletLociPerPatch,0,0,0);
  
  add("Segregating Delet Mutations - Global", prefix + "delsegr",   AGE,0,0,
      &TTDeletMutBitstrSH::getSegregatingDeletLoci,0,0,0);
  
  add("Segregating Delet Mutations - Local",  prefix + "delsegrp",   AGE,0,0,
      &TTDeletMutBitstrSH::getSegregatingDeletLociPerPatch,0,0,0);
  
  add("Delet Fst", prefix + "delfst",   AGE,0,0,
      &TTDeletMutBitstrSH::getFst,0,0,0);
  
  add("Lethal Equivalents", prefix + "lethequ",   AGE,0,0,
      &TTDeletMutBitstrSH::getLethalEquivalents,0,0,0);
  
  add("Heterosis", "heterosis",   ADULTS,0,0,
      &TTDeletMutBitstrSH::getHeterosis,0,0,0);
  
  add("Genetic Load", "load",   ADULTS,0,0,
      &TTDeletMutBitstrSH::getLoad,0,0,0);
  
}

References StatHandler< SH >::add(), ADULTS, ALL, getDeletAllFreq(), getDeletAllHmz(), getDeletAllHtz(), getFixedDeletLoci(), getFixedDeletLociPerPatch(), getFst(), getHeterosis(), getLethalEquivalents(), getLoad(), getSegregatingDeletLoci(), getSegregatingDeletLociPerPatch(), OFFSPRG, setAdultDeletStats(), and setOffsprgDeletStats().

Referenced by setStatRecorders().

Here is the caller graph for this function:

setViability()

void TTDeletMutBitstrSH::setViability

(

age_idx

agex

)

{
  Individual *ind;
  unsigned int ped_class;
  Patch *patch;
  
  for(unsigned i = 0; i < 5; i++) {
    _viability[i] = 0;
    _SibProps[i] = 0;
  }
  
  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
    
    patch = _pop->getPatch(i);
    
    for(unsigned int j = 0, size = patch->size(MAL, agex); j < size; ++j) {
      
      ind = patch->get(MAL, agex, j);
      
      ped_class = ind->getPedigreeClass();
      
      _viability[ped_class] += *(double*)ind->getTrait(_SHLinkedTraitIndex)->getValue();
      
      _SibProps[ped_class]++;
    }
    
    for(unsigned int j = 0, size = patch->size(FEM, agex); j < size; ++j) {
      
      ind = patch->get(FEM, agex, j);
      
      ped_class = ind->getPedigreeClass();
      
      _viability[ped_class] += *(double*)ind->getTrait(_SHLinkedTraitIndex)->getValue();
      
      _SibProps[ped_class]++;
    }
    
  }
  
  double tot_ind = _SibProps[0] + _SibProps[1] + _SibProps[2] + _SibProps[3] + _SibProps[4];
  _meanViab = _viability[0] + _viability[1] + _viability[2] + _viability[3] + _viability[4];
  _meanViab /= tot_ind;
  
  for(unsigned i = 0; i < 5; i++)
    _viability[i] = (_SibProps[i] != 0 ? _viability[i] / _SibProps[i] : nanf("NULL"));
  
  for(unsigned i = 0; i < 5; i++)
    _SibProps[i] /= tot_ind;
 
}

References _meanViab, StatHandlerBase::_pop, TraitStatHandler< TProtoDeletMutations_bitstring, TTDeletMutBitstrSH >::_SHLinkedTraitIndex, _SibProps, _viability, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getPedigreeClass(), Individual::getTrait(), TTrait::getValue(), MAL, and Patch::size().

Referenced by setAdultViab(), and setOffsprgViab().

Here is the caller graph for this function:

setViabStats()

void TTDeletMutBitstrSH::setViabStats

(

age_t

AGE

)

{
  if(AGE == ALL) {
    setViabStats(OFFSPRG); setViabStats(ADULTS);
    return;
  }
  
  string prefix = (AGE == ADULTS ? "adlt." : "off.");
  void (TTDeletMutBitstrSH::* setter) () = (AGE == ADULTS ?
                                            &TTDeletMutBitstrSH::setAdultViab :
                                            &TTDeletMutBitstrSH::setOffsprgViab);
  
  add("Average Viability",       prefix + "viab",  AGE, 0, 0,
      &TTDeletMutBitstrSH::getMeanViability,0,0,
      setter);
  
  add("Outbreds Viability",      prefix + "viab.outb",  AGE, 0,0,0,
      &TTDeletMutBitstrSH::getViability,0,0);
  
  add("Inbreds Viability",       prefix + "viab.outw",  AGE, 1,0,0,
      &TTDeletMutBitstrSH::getViability,0,0);
  
  add("Half Sibs Viability",     prefix + "viab.hsib",  AGE, 2,0,0,
      &TTDeletMutBitstrSH::getViability,0,0);
  
  add("Full Sibs Viability",     prefix + "viab.fsib",  AGE, 3,0,0,
      &TTDeletMutBitstrSH::getViability,0,0);
  
  add("Selfed Viability",        prefix + "viab.self",  AGE, 4,0,0,
      &TTDeletMutBitstrSH::getViability,0,0);
  
  add("Outbred btw Proportion",  prefix + "prop.outb",  AGE, 0,0,0,
      &TTDeletMutBitstrSH::getSibProportions,0,0);
  
  add("Outbred wtn Proportion",  prefix + "prop.outw",  AGE, 1,0,0,
      &TTDeletMutBitstrSH::getSibProportions,0,0);
  
  add("Half Sibs Proportion",    prefix + "prop.hsibs",  AGE, 2,0,0,
      &TTDeletMutBitstrSH::getSibProportions,0,0);
  
  add("Full Sibs Proportion",    prefix + "prop.fsibs",  AGE, 3,0,0,
      &TTDeletMutBitstrSH::getSibProportions,0,0);
  
  add("Selfed Proportion",       prefix + "prop.self",  AGE, 4,0,0,
      &TTDeletMutBitstrSH::getSibProportions,0,0);
}

References StatHandler< SH >::add(), ADULTS, ALL, getMeanViability(), getSibProportions(), getViability(), OFFSPRG, setAdultViab(), and setOffsprgViab().

Referenced by setStatRecorders().

Here is the caller graph for this function:

Member Data Documentation

_deletAllCount

double TTDeletMutBitstrSH::_deletAllCount

private

Referenced by getDeletAllPerGenome(), and setDeletStats().

_deletFreqTable

double* TTDeletMutBitstrSH::_deletFreqTable

private

Referenced by setDeletStats(), setLethalEquivalents(), and ~TTDeletMutBitstrSH().

_deletHmzLoci

double TTDeletMutBitstrSH::_deletHmzLoci

private

Referenced by setDeletStats(), and setLethalEquivalents().

_deletHtzLoci

double TTDeletMutBitstrSH::_deletHtzLoci

private

Referenced by setDeletStats(), and setLethalEquivalents().

_fixloc

double TTDeletMutBitstrSH::_fixloc

private

Referenced by getFixedDeletLoci(), and setDeletStats().

_fixLocPerPatch

double TTDeletMutBitstrSH::_fixLocPerPatch

private

Referenced by getFixedDeletLociPerPatch(), and setDeletStats().

_freq

double TTDeletMutBitstrSH::_freq

private

Referenced by getDeletAllFreq(), and setDeletStats().

_Fst

double TTDeletMutBitstrSH::_Fst

private

Referenced by getFst(), and setFst().

_Hmz

double TTDeletMutBitstrSH::_Hmz

private

Referenced by getDeletAllHmz(), and setDeletStats().

_Ho

double TTDeletMutBitstrSH::_Ho

private

Referenced by getDeletAllHtz(), setDeletStats(), and setFst().

_Hs

double TTDeletMutBitstrSH::_Hs

private

Referenced by getHs(), setDeletStats(), and setFst().

_Ht

double TTDeletMutBitstrSH::_Ht

private

Referenced by getHt(), setDeletStats(), and setFst().

_isContinuousEffect

bool TTDeletMutBitstrSH::_isContinuousEffect

private

Referenced by setLethalEquivalents(), and TTDeletMutBitstrSH().

_letheq

double TTDeletMutBitstrSH::_letheq

private

Referenced by getAdultsLetheq(), getLethalEquivalents(), getOffsprgLetheq(), and setLethalEquivalents().

_meanViab

double TTDeletMutBitstrSH::_meanViab

private

Referenced by getMeanViability(), setMeanViability(), and setViability().

_segrloc

double TTDeletMutBitstrSH::_segrloc

private

Referenced by getSegregatingDeletLoci(), and setDeletStats().

_segrLocPerPatch

double TTDeletMutBitstrSH::_segrLocPerPatch

private

Referenced by getSegregatingDeletLociPerPatch(), and setDeletStats().

_SibProps

double TTDeletMutBitstrSH::_SibProps[5]

private

Referenced by getSibProportions(), and setViability().

_viability

double TTDeletMutBitstrSH::_viability[5]

private

Referenced by getViability(), and setViability().

fecWithHomePatchMate

double TTDeletMutBitstrSH::fecWithHomePatchMate

private

Referenced by getBtheta().

fecWithOtherPatchMate

double TTDeletMutBitstrSH::fecWithOtherPatchMate

private

Referenced by getBalpha().

---

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

• ttdeletmutations_bitstring.h
• stats_delet_bitstring.cc
• ttdeletmutations_bitstring.cc