TTNeutralGenesSH Class Reference

The stat handler for neutral markers. More...

#include <ttneutralgenes.h>

Inheritance diagram for TTNeutralGenesSH:

Collaboration diagram for TTNeutralGenesSH:

Public Member Functions
	TTNeutralGenesSH (TProtoNeutralGenes *TP)
virtual	~TTNeutralGenesSH ()
virtual void	init ()
virtual bool	setStatRecorders (std::string &token)
void	setFreqRecorders (age_t AGE)
void	setFreqRecordersPerPatch (age_t AGE)
void	setFstatRecorders (age_t AGE)
void	setFstat2Recorders (age_t AGE)
void	setFstatWCRecorders (age_t AGE)
void	setCoaMatrixRecorders (age_t AGE, unsigned char dim)
void	setFstMatrixRecorders (age_t AGE, unsigned char dim)
void	setNeiGeneticDistanceRecorders (age_t AGE, bool pairwise)
void	setDxyRecorders (age_t AGE, bool patchwise)
Allele and genotype frequencies:
void	setAdultAlleleFreq ()
void	setOffspringAlleleFreq ()
void	setHeterozygosity (age_t AGE)
void	setAdultHeterozygosity ()
void	setOffspringHeterozygosity ()
double	getGlobalAlleleFreq (unsigned int loc, unsigned int all)
double	getHeterozygosity (unsigned int loc)
F-stats:
void	setAlleleTables (age_t AGE)
void	setHeteroTable (age_t AGE)
void	allocateTables (unsigned int loci, unsigned int all)
DataTable< double > *	getAlleleFreqTable ()
	Accessor to the table of allele frequencies, per patch. More...
DataTable< unsigned int > *	getAlleleCountTable ()
DataTable< double > *	getHeteroTable ()
TMatrix *	getGlobalFreqs ()
	Accessor to the table of allele frequencies in the whole population. More...
void	setFstMatrix (age_t AGE, unsigned char dim)
	Computes the weighted within and between patch Fst's as well as the overall Fst (Theta). More...
void	setAdultsFstMatrix ()
void	setAdultsFstWithin ()
void	setAdultsFstBetween ()
void	setOffsprgFstMatrix ()
void	setOffsprgFstWithin ()
void	setOffsprgFstBetween ()
double	getWeightedFst ()
	Returns the weighted Fst using Weir & Hill (2002) method. More...
double	getFst_ij (unsigned int i)
	Accessor to the Fst matrix as set by setFstMatrix(). More...
void	setFst_li (unsigned int N, unsigned int L, double **array)
	Computes the per-locus per-patch Fst values using Weir&Hill 2002 approach. More...
void	setFstat (age_t AGE)
	Computes the F-statistics following Nei & Chesser (1983). More...
void	setOffsprgFstat ()
void	setAdultsFstat ()
double	setHo (age_idx age_pos)
double	setHs (age_idx age_pos)
double	setHt (age_idx age_pos)
double	getHsnei ()
double	getHtnei ()
double	getHo ()
double	getHs ()
double	getHt ()
double	getFst ()
double	getFis ()
double	getFit ()
void	setFstat2 (age_t AGE)
	New version of Nei & Chesser. More...
void	setOffsprgFstat2 ()
void	setAdultsFstat2 ()
deque< double >	setHo2 (age_idx age_pos)
deque< double >	setHs2 (age_idx age_pos)
deque< double >	setHt2 (age_idx age_pos)
void	setFstatWeirCockerham (age_t AGE)
	Computes the Weir & Cockerham (1984) Fstat values (Theta, F, and f). More...
void	setFstatWeirCockerham_MS (age_t AGE)
void	setOffspringFstatWeirCockerham ()
void	setAdultsFstatWeirCockerham ()
double	getFstWC ()
double	getFisWC ()
double	getFitWC ()
void	setLociDivCounter (age_t AGE)
	Sets the allelic diversity counters. More...
double	getNbAllLocal ()
double	getNbAllGlobal ()
double	getFixLocLocal ()
double	getFixLocGlobal ()
Coancestries
double	Coancestry (void **ind1, void **ind2, unsigned int nb_locus)
	Gives the coancestry (probability of identity by state) of two gene sequences. More...
void	setCoaMatrix (age_idx age_pos, unsigned char dim)
	Computes the within and between patches coancestry coefficients. More...
void	setAdultsCoaMatrix ()
void	setOffsprgCoaMatrix ()
void	setAdultsCoaWithin ()
void	setOffsprgCoaWithin ()
void	setAdultsCoaBetween ()
void	setOffsprgCoaBetween ()
void	setAdults_Theta ()
double	getCoa (unsigned int i)
	Gets the given coancestry coefficient from the coancestry matrix. More...
double	getMeanTheta ()
double	getMeanAlpha ()
double	getTheta_FF ()
	Gives the mean within females coancestry coefficient. More...
double	getTheta_MM ()
	Gives the mean within males coancestry coefficient. More...
double	getTheta_FM ()
	Gives the mean between males and females coancestry coefficient. More...
void	setSibStats ()
void	setSibCoa (Individual *I1, Individual *I2)
double	getSibProportions (unsigned int i)
double	getSibCoaMeans (unsigned int i)
Nei's genetic distance:
void	setAdltNeiGeneticDistance ()
void	setOffsprgNeiGeneticDistance ()
void	setNeiGeneticDistance (age_t AGE)
double	getNeiGeneticDistance (unsigned int i)
double	getMeanNeiGeneticDistance ()
Sequence divergence: Dxy (Nei & Li 1979; Nei 1987)
double	getDxyOffspringPerPatch (unsigned int patch1, unsigned patch2)
double	getDxyAdultPerPatch (unsigned int patch1, unsigned patch2)
double	getDxyPerPatch (age_idx age, unsigned int patch1, unsigned patch2)
double	getDxy (unsigned int age_class)
Public Member Functions inherited from TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >
	TraitStatHandler (TProtoNeutralGenes *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	update ()
	This function is left empty as the StatServices calls StatRecorder::setVal directly. More...
Public Member Functions inherited from Handler
virtual void	init ()=0
	Inits state. More...
virtual void	update ()=0
	Updates the handler state. More...
virtual	~Handler ()

Private Attributes
DataTable< unsigned int >	_alleleCountTable
DataTable< double >	_alleleFreqTable
DataTable< double >	_heteroTable
TMatrix	_globalAlleleFreq
unsigned int	_table_set_gen
unsigned int	_table_set_age
unsigned int	_table_set_repl
double	Theta_FF
double	Theta_MM
double	Theta_FM
double	_mean_theta
double	_mean_alpha
TMatrix *	_coa_matrix
double	_sib_prop [4]
	Kinship classes proportions. More...
double	_sib_coa [4]
double	_ho
	F-statistics. More...
double	_hs
double	_ht
double	_hsnei
double	_htnei
double	_nb_all_local
double	_nb_all_global
double	_fst
double	_fis
double	_fit
double	_fix_loc_local
double	_fix_loc_global
double	_fst_WH
	Weir & Hill (2002) F-stat estimates. More...
double	_fst_WC
	Weir & Cockerham (1984) F-stat estimates. More...
double	_fis_WC
double	_fit_WC
double *	_fst_WC_loc
	Per-locus F-stats (Weir&Cockerham). More...
double *	_fis_WC_loc
double *	_fit_WC_loc
double	_fst_W1
double	_fst_W2
TMatrix *	_fst_matrix
	Pairwise Fst matrix. More...
TMatrix *	_D
double	_meanD

Additional Inherited Members
Protected Types inherited from StatHandler< SH >
typedef std::list< StatRecorder< SH > * >::iterator	REC_IT
Protected Attributes inherited from TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >
TProtoNeutralGenes *	_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 stat handler for neutral markers.

Constructor & Destructor Documentation

TTNeutralGenesSH()

TTNeutralGenesSH::TTNeutralGenesSH ( TProtoNeutralGenes *  TP )

inline

    : TraitStatHandler<TProtoNeutralGenes, TTNeutralGenesSH>(TP), _table_set_gen(0), _table_set_age(0),
    _table_set_repl(0), _coa_matrix(0), _fst_WC_loc(0), _fis_WC_loc(0), _fit_WC_loc(0), _fst_matrix(0),
        _D(0)
        { }

~TTNeutralGenesSH()

virtual TTNeutralGenesSH::~TTNeutralGenesSH ( )

inlinevirtual

  {
    if(_coa_matrix != NULL) delete _coa_matrix;
    if(_fst_matrix != NULL) delete _fst_matrix;
    if(_fst_WC_loc) delete[]_fst_WC_loc;
    if(_fis_WC_loc) delete[]_fis_WC_loc;
    if(_fit_WC_loc) delete[]_fit_WC_loc;
    if(_D != NULL) delete _D;
  }

References _coa_matrix, _D, _fis_WC_loc, _fit_WC_loc, _fst_matrix, and _fst_WC_loc.

Member Function Documentation

allocateTables()

void TTNeutralGenesSH::allocateTables	(	unsigned int	loci,
		unsigned int	all
	)

{
  unsigned int nb_patch = _pop->getPatchNbr();
  unsigned int **sizes;
  
  sizes = new unsigned int * [nb_patch];
  
  for(unsigned int i = 0; i < nb_patch; ++i) {
    sizes[i] = new unsigned int [loci];
    for(unsigned int j = 0; j < loci; ++j)
      sizes[i][j] = all;
  }
  
  _alleleCountTable.allocate(nb_patch, loci, sizes);
  
  _alleleFreqTable.allocate(nb_patch, loci, sizes);
  
  _globalAlleleFreq.reset(loci, all);
  
  for(unsigned int i = 0; i < nb_patch; ++i)
    delete [] sizes[i];
  delete [] sizes;
  
  //reset the time info, to force recalculation after allocate
  _table_set_age = NONE;
  _table_set_gen = 0;
  _table_set_repl = 0;
}

References _alleleCountTable, _alleleFreqTable, _globalAlleleFreq, StatHandlerBase::_pop, _table_set_age, _table_set_gen, _table_set_repl, DataTable< T >::allocate(), Metapop::getPatchNbr(), NONE, and TMatrix::reset().

Referenced by init(), setAlleleTables(), setFstat(), setFstat2(), TTNeutralGenesFH::write_Fst_i(), and TTNeutralGenesFH::write_varcompWC().

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Coancestry()

double TTNeutralGenesSH::Coancestry	(	void **	ind1,
		void **	ind2,
		unsigned int	nb_locus
	)

Gives the coancestry (probability of identity by state) of two gene sequences.

The probability returned is the average probability of having two identical alleles at a locus between the two sequences.

Parameters

ind1	first _sequence, treated as of type (unsigned char**)
ind2	second _sequence, treated as of type (unsigned char**)
nb_locus	number of loci present in each _sequence

{
  unsigned int p = 0;
  unsigned char **seq1, **seq2;
  
  seq1 = (unsigned char**)ind1;
  seq2 = (unsigned char**)ind2;
  
  for (unsigned int k = 0; k < nb_locus; ++k)
    p += !(seq1[0][k]^seq2[0][k]) + !(seq1[0][k]^seq2[1][k]) + !(seq1[1][k]^seq2[0][k]) + !(seq1[1][k]^seq2[1][k]);
  
  return (double)p/(4.0*nb_locus);
}

Referenced by setAdults_Theta(), setCoaMatrix(), and setSibCoa().

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getAlleleCountTable()

DataTable< unsigned int > * TTNeutralGenesSH::getAlleleCountTable ( )

inline

{return &_alleleCountTable;}

References _alleleCountTable.

Referenced by TTNeutralGenesFH::write_varcompWC().

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getAlleleFreqTable()

DataTable< double > * TTNeutralGenesSH::getAlleleFreqTable ( )

inline

Accessor to the table of allele frequencies, per patch.

{return &_alleleFreqTable;}

References _alleleFreqTable.

Referenced by TTNeutralGenesFH::write_varcompWC().

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getCoa()

double TTNeutralGenesSH::getCoa ( unsigned int  i )

inline

Gets the given coancestry coefficient from the coancestry matrix.

Parameters

i	combination of the row and column indexes (see setCoaMatrixRecorders()).

Note

the upper half and the diagonal of the matrix are filled, other positions are set to 0.

  {
    unsigned int scale = (unsigned int)pow( 10.0, (int)log10((float)_coa_matrix->getNbCols()) + 1 );
    return _coa_matrix->get(i/scale, i%scale);
  }

References _coa_matrix, TMatrix::get(), and TMatrix::getNbCols().

Referenced by setCoaMatrixRecorders().

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getDxy()

double TTNeutralGenesSH::getDxy

(

unsigned int

age_class

)

{
  double D = 0;
  unsigned int p = 0;
  
  age_t AGE = (static_cast<age_idx>(age_class) == OFFSx ? OFFSPRG : ADULTS);
  
  for (unsigned int p1 = 0; p1 < _pop->getPatchNbr(); ++p1) {
    
    if( !_pop->size( AGE , p1) ) continue;
      
    for (unsigned int p2 = p1 + 1; p2 < _pop->getPatchNbr(); ++p2) {
      
      if( !_pop->size( AGE , p2) ) continue;
 
      D += getDxyPerPatch(static_cast<age_idx>(age_class), p1, p2);
    
      p++;
    }
  }
  
  return (p != 0 ? D/p : nanf("NULL"));
}

References StatHandlerBase::_pop, ADULTS, getDxyPerPatch(), Metapop::getPatchNbr(), OFFSPRG, OFFSx, and Metapop::size().

Referenced by setDxyRecorders().

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getDxyAdultPerPatch()

double TTNeutralGenesSH::getDxyAdultPerPatch ( unsigned int  patch1, unsigned  patch2  )

inline

{return getDxyPerPatch(ADLTx, patch1, patch2);}

References ADLTx, and getDxyPerPatch().

Referenced by setDxyRecorders().

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getDxyOffspringPerPatch()

double TTNeutralGenesSH::getDxyOffspringPerPatch ( unsigned int  patch1, unsigned  patch2  )

inline

{return getDxyPerPatch(OFFSx, patch1, patch2);}

References getDxyPerPatch(), and OFFSx.

Referenced by setDxyRecorders().

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getDxyPerPatch()

double TTNeutralGenesSH::getDxyPerPatch	(	age_idx	age,
		unsigned int	patch1,
		unsigned	patch2
	)

{
  double D = 0;
  Patch* patch_1 = _pop->getPatchPtr(patch1);
  Patch* patch_2 = _pop->getPatchPtr(patch2);
  unsigned int size_1 = patch_1->size(FEM, age);
  unsigned int size_2 = patch_2->size(FEM, age);
  unsigned int N = 0;//4*size_1 * size_2;// (2N)^2, tot num of haplotype comparisons
  
  
  unsigned int num_loc = _SHLinkedTrait->get_locus_num();
  
  unsigned char **seq_1, **seq_2;
  
  //females:
  for (unsigned int i = 0; i < size_1; ++i) {
    
    seq_1 = (unsigned char**)patch_1->get(FEM, age, i)->getTrait(_SHLinkedTraitIndex)->get_sequence();
    
    for (unsigned int j = 0; j < size_2; ++j) {
      
      seq_2 = (unsigned char**)patch_2->get(FEM, age, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < num_loc; ++l) {
        D += (seq_1[0][l] != seq_2[0][l]);
        D += (seq_1[1][l] != seq_2[1][l]);
        D += (seq_1[0][l]!=seq_2[1][l]);
        D += (seq_1[1][l]!=seq_2[0][l]);
      } 
      N += 4;
    }
    
    for (unsigned int j = 0; j < patch_2->size(MAL, age); ++j) {
      
      seq_2 = (unsigned char**)patch_2->get(MAL, age, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < num_loc; ++l) {
        D += (seq_1[0][l]!=seq_2[0][l]);
        D += (seq_1[1][l]!=seq_2[1][l]);
        D += (seq_1[0][l]!=seq_2[1][l]);
        D += (seq_1[1][l]!=seq_2[0][l]);
      } 
      N += 4;
      
    }
  }
  
  //same for the males:
  size_1 = patch_1->size(MAL, age);
  size_2 = patch_2->size(MAL, age);
  
//  N += 4 * size_1 * size_2;
  
//  if( N == 0) return 0; //needless to go further
  
  for (unsigned int i = 0; i < size_1; ++i) {
    
    seq_1 = (unsigned char**)patch_1->get(MAL, age, i)->getTrait(_SHLinkedTraitIndex)->get_sequence();
    
    for (unsigned int j = 0; j < size_2; ++j) {
      
      seq_2 = (unsigned char**)patch_2->get(MAL, age, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < num_loc; ++l) {
        D += seq_1[0][l]!=seq_2[0][l];
        D += seq_1[1][l]!=seq_2[1][l];
        D += seq_1[0][l]!=seq_2[1][l];
        D += seq_1[1][l]!=seq_2[0][l];
      } 
      N += 4;
    }
    
    for (unsigned int j = 0; j < patch_2->size(FEM, age); ++j) {
      
      seq_2 = (unsigned char**)patch_2->get(FEM, age, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < num_loc; ++l) {
        D += seq_1[0][l]!=seq_2[0][l];
        D += seq_1[1][l]!=seq_2[1][l];
        D += seq_1[0][l]!=seq_2[1][l];
        D += seq_1[1][l]!=seq_2[0][l];
      } 
      N += 4;
      
    }
  }
  
  if( N == 0) return 0;
 
  return D/N;
}

References StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, FEM, Patch::get(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatchPtr(), Individual::getTrait(), MAL, and Patch::size().

Referenced by getDxy(), getDxyAdultPerPatch(), and getDxyOffspringPerPatch().

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getFis()

double TTNeutralGenesSH::getFis ( )

inline

{return _fis;}

References _fis.

Referenced by setFstatRecorders().

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getFisWC()

double TTNeutralGenesSH::getFisWC ( )

inline

{return _fis_WC;}

References _fis_WC.

Referenced by setFstatWCRecorders().

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getFit()

double TTNeutralGenesSH::getFit ( )

inline

{return _fit;}

References _fit.

Referenced by setFstatRecorders().

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getFitWC()

double TTNeutralGenesSH::getFitWC ( )

inline

{return _fit_WC;}

References _fit_WC.

Referenced by setFstatWCRecorders().

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getFixLocGlobal()

double TTNeutralGenesSH::getFixLocGlobal ( )

inline

{return _fix_loc_global;}

References _fix_loc_global.

Referenced by setFstatRecorders().

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getFixLocLocal()

double TTNeutralGenesSH::getFixLocLocal ( )

inline

{return _fix_loc_local;}

References _fix_loc_local.

Referenced by setFstatRecorders().

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getFst()

double TTNeutralGenesSH::getFst ( )

inline

{return _fst;}

References _fst.

Referenced by setFstat2Recorders(), and setFstatRecorders().

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getFst_ij()

double TTNeutralGenesSH::getFst_ij ( unsigned int  i )

inline

Accessor to the Fst matrix as set by setFstMatrix().

  {
    unsigned int scale = (unsigned int)pow( 10.0, (int)log10((float)_fst_matrix->getNbCols()) + 1 );
    return _fst_matrix->get(i/scale, i%scale);
  }

References _fst_matrix, TMatrix::get(), and TMatrix::getNbCols().

Referenced by setFstMatrixRecorders().

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getFstWC()

double TTNeutralGenesSH::getFstWC ( )

inline

{return _fst_WC;}

References _fst_WC.

Referenced by setFstatWCRecorders().

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getGlobalAlleleFreq()

double TTNeutralGenesSH::getGlobalAlleleFreq ( unsigned int  loc, unsigned int  all  )

inline

                                                                  {
    return _globalAlleleFreq.get(loc, all);
  }

References _globalAlleleFreq, and TMatrix::get().

Referenced by setFreqRecorders().

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getGlobalFreqs()

TMatrix * TTNeutralGenesSH::getGlobalFreqs ( )

inline

Accessor to the table of allele frequencies in the whole population.

{return &_globalAlleleFreq;}

References _globalAlleleFreq.

Referenced by TTNeutralGenesFH::write_varcompWC().

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getHeteroTable()

DataTable< double > * TTNeutralGenesSH::getHeteroTable ( )

inline

{return &_heteroTable;}

References _heteroTable.

Referenced by TTNeutralGenesFH::write_varcompWC().

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getHeterozygosity()

double TTNeutralGenesSH::getHeterozygosity ( unsigned int  loc )

inline

                                              {
    double het = 0;
    for(unsigned int i = 0; i < _heteroTable.getNumGroups(); ++i )
      het += _heteroTable.get(i, loc, 0);
    return het/_heteroTable.getNumGroups(); //mean per patch heterozygosity
  }

References _heteroTable, DataTable< T >::get(), and DataTable< T >::getNumGroups().

Referenced by setFreqRecorders().

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getHo()

double TTNeutralGenesSH::getHo ( )

inline

{return _ho;}

References _ho.

Referenced by setFstat2Recorders(), and setFstatRecorders().

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getHs()

double TTNeutralGenesSH::getHs ( )

inline

{return _hs;}

References _hs.

getHsnei()

double TTNeutralGenesSH::getHsnei ( )

inline

{return _hsnei;}

References _hsnei.

Referenced by setFstat2Recorders(), and setFstatRecorders().

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getHt()

double TTNeutralGenesSH::getHt ( )

inline

{return _ht;}

References _ht.

getHtnei()

double TTNeutralGenesSH::getHtnei ( )

inline

{return _htnei;}

References _htnei.

Referenced by setFstat2Recorders(), and setFstatRecorders().

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getMeanAlpha()

double TTNeutralGenesSH::getMeanAlpha ( )

inline

{return _mean_alpha;}

References _mean_alpha.

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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getMeanNeiGeneticDistance()

double TTNeutralGenesSH::getMeanNeiGeneticDistance ( )

inline

{return _meanD;}

References _meanD.

Referenced by setNeiGeneticDistanceRecorders().

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getMeanTheta()

double TTNeutralGenesSH::getMeanTheta ( )

inline

{return _mean_theta;}

References _mean_theta.

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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getNbAllGlobal()

double TTNeutralGenesSH::getNbAllGlobal ( )

inline

{return _nb_all_global;}

References _nb_all_global.

Referenced by setFstatRecorders().

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getNbAllLocal()

double TTNeutralGenesSH::getNbAllLocal ( )

inline

{return _nb_all_local;}

References _nb_all_local.

Referenced by setFstatRecorders().

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getNeiGeneticDistance()

double TTNeutralGenesSH::getNeiGeneticDistance ( unsigned int  i )

inline

  { 
    unsigned int scale = (unsigned int)pow( 10.0, (int)log10((float)_D->getNbCols()) + 1 );
    return _D->get(i/scale,i%scale);
  }

References _D, TMatrix::get(), and TMatrix::getNbCols().

Referenced by setNeiGeneticDistanceRecorders().

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getSibCoaMeans()

double TTNeutralGenesSH::getSibCoaMeans ( unsigned int  i )

inline

{return _sib_coa[i];}

References _sib_coa.

Referenced by setStatRecorders().

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getSibProportions()

double TTNeutralGenesSH::getSibProportions ( unsigned int  i )

inline

{return _sib_prop[i];}

References _sib_prop.

Referenced by setStatRecorders().

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getTheta_FF()

double TTNeutralGenesSH::getTheta_FF ( )

inline

Gives the mean within females coancestry coefficient.

{return Theta_FF;}

References Theta_FF.

Referenced by setStatRecorders().

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getTheta_FM()

double TTNeutralGenesSH::getTheta_FM ( )

inline

Gives the mean between males and females coancestry coefficient.

{return Theta_FM;}

References Theta_FM.

Referenced by setStatRecorders().

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getTheta_MM()

double TTNeutralGenesSH::getTheta_MM ( )

inline

Gives the mean within males coancestry coefficient.

{return Theta_MM;}

References Theta_MM.

Referenced by setStatRecorders().

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getWeightedFst()

double TTNeutralGenesSH::getWeightedFst ( )

inline

Returns the weighted Fst using Weir & Hill (2002) method.

This Fst is set by a previous call to setFstMatrix().

{return _fst_WH;}

References _fst_WH.

Referenced by setFstMatrixRecorders().

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init()

void TTNeutralGenesSH::init ( )

virtual

Reimplemented from StatHandlerBase.

{
  StatHandler<TTNeutralGenesSH>::init();
 
  allocateTables(_SHLinkedTrait->get_locus_num(),_SHLinkedTrait->get_allele_num());
}

References TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, allocateTables(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), and Handler::init().

setAdltNeiGeneticDistance()

void TTNeutralGenesSH::setAdltNeiGeneticDistance ( )

inline

{setNeiGeneticDistance(ADULTS);}

References ADULTS, and setNeiGeneticDistance().

Referenced by setNeiGeneticDistanceRecorders().

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setAdultAlleleFreq()

void TTNeutralGenesSH::setAdultAlleleFreq ( )

inline

{setAlleleTables(ADULTS);}

References ADULTS, and setAlleleTables().

Referenced by setFreqRecorders().

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setAdultHeterozygosity()

void TTNeutralGenesSH::setAdultHeterozygosity ( )

inline

{setHeterozygosity(ADULTS);}

References ADULTS, and setHeterozygosity().

Referenced by setFreqRecorders().

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setAdults_Theta()

void TTNeutralGenesSH::setAdults_Theta

(

)

{
  unsigned int Fsize,Msize,i,j,k, FFsize, MMsize, FMsize;
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  Patch *P1;
  double mean = 0, grand_mean = 0;
  
  Theta_FF = 0;
  Theta_MM = 0;
  Theta_FM = 0;
  
  _mean_theta = 0;
  
  for(i = 0; i < patchNbr; ++i) {
    
    P1 = _pop->getPatch(i);
    Fsize = P1->size(FEM, ADLTx);
    Msize = P1->size(MAL, ADLTx);
    
    FFsize = Fsize*(Fsize-1)/2;
    MMsize = Msize*(Msize-1)/2;
    FMsize = Fsize*Msize;
    
    grand_mean = 0;
    
    if(Fsize != 0 || Msize != 0) {
      
      if(Fsize != 0) {
        mean = 0;
        for(j = 0; j < Fsize-1;++j)
          for(k = j+1; k < Fsize;++k)
            mean += Coancestry(P1->get(FEM, ADLTx, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               P1->get(FEM, ADLTx, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               nb_locus);
        Theta_FF += mean/FFsize;
        grand_mean += mean;
      }
            
      if(Msize != 0) {
        mean = 0;
        for(j = 0; j < Msize-1;++j)
          for(k = j+1; k < Msize;++k)
            mean += Coancestry(P1->get(MAL, ADLTx, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               P1->get(MAL, ADLTx, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               nb_locus);
        Theta_MM += mean/MMsize;
        grand_mean += mean;
      }
      
      
      if(Fsize != 0 && Msize != 0) {
        mean = 0;
        for(j = 0; j < Fsize;++j)
          for(k = 0; k < Msize;++k)
            mean += Coancestry(P1->get(FEM, ADLTx, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               P1->get(MAL, ADLTx, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                               nb_locus);
        Theta_FM += mean/FMsize;
        grand_mean += mean;
      }
      _mean_theta += grand_mean / (FFsize + MMsize + FMsize);
    }
  }
  
  _mean_theta /= patchNbr;
  Theta_FF /= patchNbr;
  Theta_MM /= patchNbr;
  Theta_FM /= patchNbr;
}

References _mean_theta, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, ADLTx, Coancestry(), FEM, Patch::get(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), MAL, Patch::size(), Theta_FF, Theta_FM, and Theta_MM.

Referenced by setStatRecorders().

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setAdultsCoaBetween()

void TTNeutralGenesSH::setAdultsCoaBetween ( )

inline

{setCoaMatrix(ADLTx, 2);}

References ADLTx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setAdultsCoaMatrix()

void TTNeutralGenesSH::setAdultsCoaMatrix ( )

inline

{setCoaMatrix(ADLTx, 3);}

References ADLTx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setAdultsCoaWithin()

void TTNeutralGenesSH::setAdultsCoaWithin ( )

inline

{setCoaMatrix(ADLTx, 1);}

References ADLTx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setAdultsFstat()

void TTNeutralGenesSH::setAdultsFstat ( )

inline

{setFstat(ADULTS);}

References ADULTS, and setFstat().

Referenced by setFstatRecorders().

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setAdultsFstat2()

void TTNeutralGenesSH::setAdultsFstat2 ( )

inline

{setFstat2(ADULTS);}

References ADULTS, and setFstat2().

Referenced by setFstat2Recorders().

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setAdultsFstatWeirCockerham()

void TTNeutralGenesSH::setAdultsFstatWeirCockerham ( )

inline

{setFstatWeirCockerham(ADULTS);}

References ADULTS, and setFstatWeirCockerham().

Referenced by setFstatWCRecorders().

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setAdultsFstBetween()

void TTNeutralGenesSH::setAdultsFstBetween ( )

inline

{setFstMatrix(ADULTS, 2);}

References ADULTS, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setAdultsFstMatrix()

void TTNeutralGenesSH::setAdultsFstMatrix ( )

inline

{setFstMatrix(ADULTS, 3);}

References ADULTS, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setAdultsFstWithin()

void TTNeutralGenesSH::setAdultsFstWithin ( )

inline

{setFstMatrix(ADULTS, 1);}

References ADULTS, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setAlleleTables()

void TTNeutralGenesSH::setAlleleTables

(

age_t

AGE

)

{  
  
  if(_table_set_age == AGE 
     && _table_set_gen == _pop->getCurrentGeneration()
     && _table_set_repl == _pop->getCurrentReplicate())
    return;
  
  unsigned char** genes;
  unsigned int nb_locus = _SHLinkedTrait->get_locus_num(), nb_allele = _SHLinkedTrait->get_allele_num();
  unsigned int patch_size, patchNbr = _pop->getPatchNbr();
  age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
  Patch* crnt_patch;
  
  //check if the population size has changed:
  if(_alleleCountTable.getNumGroups() != patchNbr)
    allocateTables(_SHLinkedTrait->get_locus_num(), _SHLinkedTrait->get_allele_num());
  
  _alleleCountTable.init(0);
 
  //counting the copies of each allele present in each patch:
  for(unsigned int k = 0; k < patchNbr; ++k) {
 
    crnt_patch = _pop->getPatch(k);
 
    for(unsigned int i = 0, size = crnt_patch->size(FEM, age_pos); i < size; ++i) {
 
      genes = (unsigned char**)crnt_patch->get(FEM, age_pos, i)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int j = 0; j < nb_locus; ++j)
        _alleleCountTable.increment(k, j, genes[0][j]);
      
      for (unsigned int j = 0; j < nb_locus; ++j)
        _alleleCountTable.increment(k, j, genes[1][j]);
      
    } 
    
    for(unsigned int i = 0, size = crnt_patch->size(MAL, age_pos); i < size; ++i) {
      
      genes = (unsigned char**)crnt_patch->get(MAL, age_pos, i)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int j = 0; j < nb_locus; ++j)
        _alleleCountTable.increment(k, j, genes[0][j]);
      
      for (unsigned int j = 0; j < nb_locus; ++j)
        _alleleCountTable.increment(k, j, genes[1][j]);
      
    }
  }
  
  //allelic frequencies:
  for (unsigned int i = 0; i < patchNbr; ++i) {
    
    patch_size = _pop->getPatch(i)->size(age_pos) * 2;
    
    if (patch_size) {
      
    for (unsigned int l = 0; l < nb_locus; ++l)
      for (unsigned int u = 0; u < nb_allele; ++u)
        _alleleFreqTable.set(i, l, u, (double)_alleleCountTable.get(i, l, u) / (double)patch_size);
    
    } else {
      for (unsigned int l = 0; l < nb_locus; ++l)
        for (unsigned int u = 0; u < nb_allele; ++u)
          _alleleFreqTable.set(i, l, u, 0 );
    }
 
  }
 
  //population-wide allelic frequencies:  
  unsigned int tot_size = _pop->size(AGE) * 2;
 
  _globalAlleleFreq.assign(0);
  
  for(unsigned int i = 0; i < patchNbr; i++)
    for (unsigned int l = 0; l < nb_locus; ++l)
      for (unsigned int u = 0; u < nb_allele; ++u)
        _globalAlleleFreq.plus(l, u, _alleleCountTable.get(i, l, u));
  
  for (unsigned int l = 0; l < nb_locus; ++l)
    for (unsigned int u = 0; u < nb_allele; ++u)
      _globalAlleleFreq.divide(l, u, tot_size);
  
  _table_set_age = AGE;
  
  _table_set_gen = _pop->getCurrentGeneration();
  
  _table_set_repl = _pop->getCurrentReplicate();
}

References _alleleCountTable, _alleleFreqTable, _globalAlleleFreq, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, _table_set_age, _table_set_gen, _table_set_repl, ADLTx, ADULTS, allocateTables(), TMatrix::assign(), TMatrix::divide(), FEM, Patch::get(), DataTable< T >::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getCurrentGeneration(), Metapop::getCurrentReplicate(), DataTable< T >::getNumGroups(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), DataTable< T >::increment(), DataTable< T >::init(), MAL, OFFSx, TMatrix::plus(), DataTable< T >::set(), Metapop::size(), and Patch::size().

Referenced by setAdultAlleleFreq(), setFst_li(), setFstat(), setFstat2(), setFstatWeirCockerham(), setFstatWeirCockerham_MS(), setFstMatrix(), setNeiGeneticDistance(), setOffspringAlleleFreq(), and TTNeutralGenesFH::write_varcompWC().

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setCoaMatrix()

void TTNeutralGenesSH::setCoaMatrix	(	age_idx	age_pos,
		unsigned char	dim
	)

Computes the within and between patches coancestry coefficients.

Parameters

age_pos	the age class index
dim	the dimension of the matrix to fill: 1 = the diagonal (i.e. the wihtin patch coancestries or theta's) 2 = the upper half (i.e. the between patch coancestries or alpha's) 3 = both

{
  unsigned int Fsize,Msize,tot_size,size_i,size_l, wt;
  unsigned int nb_coeff = 0;
  unsigned int i, j, k, l;
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  Patch *P1, *P2;
  
  if(_coa_matrix == NULL)
    
    _coa_matrix = new TMatrix(patchNbr, patchNbr);
  
  else if( _coa_matrix->length() != patchNbr * patchNbr)
    
    _coa_matrix->reset(patchNbr, patchNbr);
  
  _coa_matrix->assign(0);
  
  if(dim & 1) {
    
    _mean_theta = 0;
    
    wt = 0;
    
    //first fill the diagonale: within deme coancestry (theta)
    for(i = 0; i < patchNbr; ++i) {
      
      P1 = _pop->getPatch(i);
      Fsize = P1->size(FEM, age_pos);
      Msize = P1->size(MAL, age_pos);
      
      tot_size = Fsize + Msize;
      
      if(tot_size != 0) {
        
        //fem-fem coa
          for(j = 0; j < Fsize; ++j)
            for(k = j+1; k < Fsize; ++k)
              _coa_matrix->plus(i, i, Coancestry(P1->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 P1->get(FEM, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 nb_locus));
        //mal-mal coa
        for(j = 0; j < Msize; ++j)
          for(k = j+1; k < Msize; ++k)
            _coa_matrix->plus(i, i, Coancestry(P1->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                               P1->get(MAL, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                               nb_locus));
        //fem-mal coa
        for(j = 0; j < Fsize; ++j)
          for(k = 0; k < Msize; ++k)
            _coa_matrix->plus(i, i, Coancestry(P1->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                               P1->get(MAL, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                               nb_locus));
        
        _coa_matrix->divide(i, i, tot_size*(tot_size -1)/2.0); 
      }//end if
      
      _mean_theta += tot_size * _coa_matrix->get(i, i);
      
      wt += tot_size;
      
    }//end for patchNbr
    
    //weighted average:
    _mean_theta /= wt;
    
  } //end if diag
  
  if(dim & 2) {
    //fill the first upper half of the matrix: between deme coancestry (alpha)
    
    _mean_alpha = 0;
    
    wt = 0;
    
    for(i = 0; i < patchNbr-1; ++i) {
      
      P1 = _pop->getPatch(i);
      
      for(l = i+1; l < patchNbr; ++l) {
        
        P2 = _pop->getPatch(l);
        
        tot_size = P1->size(age_pos) * P2->size(age_pos);
        
        if(tot_size != 0) {
          //females i vs. females l
          size_i = P1->size(FEM, age_pos);
          size_l = P2->size(FEM, age_pos);
          nb_coeff = size_i * size_l;
          
          for(j = 0; j < size_i; ++j)
            for(k = 0; k < size_l; ++k)
              _coa_matrix->plus(i, l, Coancestry(P1->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 P2->get(FEM, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 nb_locus));
          //females i vs. males l
          size_l = P2->size(MAL, age_pos);
          nb_coeff += size_i * size_l;
          
          for(j = 0; j < size_i; ++j)
            for(k = 0; k < size_l; ++k)
              _coa_matrix->plus(i, l, Coancestry(P1->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 P2->get(MAL, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 nb_locus));
          //males i vs. males l
          size_i = P1->size(MAL, age_pos);
          size_l = P2->size(MAL, age_pos);
          nb_coeff += size_i * size_l;
          
          for(j = 0; j < size_i; ++j)
            for(k = 0; k < size_l; ++k)
              _coa_matrix->plus(i, l, Coancestry(P1->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 P2->get(MAL, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 nb_locus));
          //males i vs. females l
          size_l = P2->size(FEM, age_pos);
          nb_coeff += size_i * size_l;
          
          for(j = 0; j < size_i; ++j)
            for(k = 0; k < size_l; ++k)
              _coa_matrix->plus(i, l, Coancestry(P1->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 P2->get(FEM, age_pos, k)->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                                                 nb_locus));
          _coa_matrix->divide(i, l, nb_coeff);
        }//endif
        
        _mean_alpha += tot_size * _coa_matrix->get(i, l);
        
        wt += tot_size;
        
      }//end for P2
    }//end for P1 
    
    //weighted average:
    _mean_alpha /= wt;
    
  }//end if upper half
  
}

References _coa_matrix, _mean_alpha, _mean_theta, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, TMatrix::assign(), Coancestry(), TMatrix::divide(), FEM, Patch::get(), TMatrix::get(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), TMatrix::length(), MAL, TMatrix::plus(), TMatrix::reset(), and Patch::size().

Referenced by setAdultsCoaBetween(), setAdultsCoaMatrix(), setAdultsCoaWithin(), setOffsprgCoaBetween(), setOffsprgCoaMatrix(), and setOffsprgCoaWithin().

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setCoaMatrixRecorders()

void TTNeutralGenesSH::setCoaMatrixRecorders	(	age_t	AGE,
		unsigned char	dim
	)

{
  std::ostringstream name, sub_name;
 
  void (TTNeutralGenesSH::* setter) () = (AGE == ADULTS ?
      ( dim & 3 ? &TTNeutralGenesSH::setAdultsCoaMatrix :
          dim & 2 ? &TTNeutralGenesSH::setAdultsCoaBetween :
              &TTNeutralGenesSH::setAdultsCoaWithin ) :
              ( dim & 3 ? &TTNeutralGenesSH::setOffsprgCoaMatrix :
                  dim & 2 ? &TTNeutralGenesSH::setOffsprgCoaBetween :
                      &TTNeutralGenesSH::setOffsprgCoaWithin) );
 
  const char *prefix = (AGE == ADULTS ? "adlt." : "off.");
 
  unsigned int nbpatch =  _pop->getPatchNbr();
  unsigned int scale = (unsigned int)pow(10.0, (int)log10((float)nbpatch) + 1);
 
  if(dim & 1) {
    name<<"Wtn Patch Coancestry ("<<prefix<<")";
    sub_name<< prefix << "theta";
    add(name.str(), sub_name.str(),  AGE,0, 0, &TTNeutralGenesSH::getMeanTheta, 0, 0, setter);
    name.str("");
    sub_name.str("");
  }
  if(dim & 2){
    name<<"Btn Patch Coancestry ("<<prefix<<")";
    sub_name<< prefix << "alpha";
    add(name.str(), sub_name.str(),  AGE, 0, 0, &TTNeutralGenesSH::getMeanAlpha, 0, 0, (!(dim&1) ? setter : 0) );
    name.str("");
    sub_name.str("");
  }
  if(dim & 1) {
    for(unsigned int i = 0; i < nbpatch; ++i) {
      name<<"coancestry "<<i+1<<"."<<i+1;
      sub_name<< prefix << "coa" << i+1 << "." << i+1;
      add(name.str(), sub_name.str(),  AGE, i*scale + i, 0, 0, &TTNeutralGenesSH::getCoa, 0, 0);
      name.str("");
      sub_name.str("");
    }
  }
  if(dim & 2){
    for(unsigned int i = 0; i < nbpatch; ++i) {
      for(unsigned int j = i+1; j < nbpatch; ++j) {
        name<<"coancestry "<<i+1<< "." <<j+1;
        sub_name<< prefix << "coa" << i+1 << "." << j+1;
        add(name.str(), sub_name.str(),  AGE, i*scale + j, 0, 0, &TTNeutralGenesSH::getCoa, 0, 0);
        name.str("");
        sub_name.str("");
      }
    }
  }
 
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADULTS, getCoa(), getMeanAlpha(), getMeanTheta(), Metapop::getPatchNbr(), setAdultsCoaBetween(), setAdultsCoaMatrix(), setAdultsCoaWithin(), setOffsprgCoaBetween(), setOffsprgCoaMatrix(), and setOffsprgCoaWithin().

Referenced by setStatRecorders().

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setDxyRecorders()

void TTNeutralGenesSH::setDxyRecorders	(	age_t	AGE,
		bool	patchwise
	)

{
  string prefix = (AGE == OFFSPRG ? "off." : "adlt.");
  age_idx age = (AGE == OFFSPRG ? OFFSx : ADLTx );
  string name = "Sequence divergence - Dxy";
  string sub_name = "Dxy";
 
 
  if (!patchwise) {
 
    add(name, prefix + sub_name, AGE, (unsigned int)age, 0, 0, &TTNeutralGenesSH::getDxy, 0, 0);
 
  } else {
 
    for (unsigned int p1 = 0; p1 < _pop->getPatchNbr(); ++p1) {
      for (unsigned int p2 = p1 + 1; p2 < _pop->getPatchNbr(); ++p2) {
        add(name, prefix + sub_name + ".p" + tstring::int2str(p1+1) + "p" + tstring::int2str(p2+1),
            AGE, p1, p2,
            0, 0, (AGE == OFFSPRG ? &TTNeutralGenesSH::getDxyOffspringPerPatch :
                &TTNeutralGenesSH::getDxyAdultPerPatch),
                0);
      }
    }
 
  }
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADLTx, getDxy(), getDxyAdultPerPatch(), getDxyOffspringPerPatch(), Metapop::getPatchNbr(), tstring::int2str(), OFFSPRG, and OFFSx.

Referenced by setStatRecorders().

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setFreqRecorders()

void TTNeutralGenesSH::setFreqRecorders

(

age_t

AGE

)

{
  string prefix = (AGE == OFFSPRG ? "off." : "adlt.");
 
  void (TTNeutralGenesSH::* setter) () = (AGE == ADULTS ? &TTNeutralGenesSH::setAdultAlleleFreq :
      &TTNeutralGenesSH::setOffspringAlleleFreq );
 
  unsigned int nb_allele = _SHLinkedTrait->get_allele_num();
  unsigned int nb_locus = _SHLinkedTrait->get_locus_num();
 
  for (unsigned int l = 0; l < nb_locus; ++l) {
    for (unsigned int u = 0; u < nb_allele-1; ++u) {
      add("", prefix + "ntrl.l" + tstring::int2str(l+1) + ".a" + tstring::int2str(u+1), AGE, l, u,
          0, 0, &TTNeutralGenesSH::getGlobalAlleleFreq, setter);
    }
  }
 
  setter = (AGE == ADULTS ? &TTNeutralGenesSH::setAdultHeterozygosity :
      &TTNeutralGenesSH::setOffspringHeterozygosity );
 
  for (unsigned int l = 0; l < nb_locus; ++l) {
    add("", prefix + "ntrl.l" + tstring::int2str(l+1) + ".Het", AGE, l, 0, 0,
        &TTNeutralGenesSH::getHeterozygosity, 0, setter);
    //    add("", prefix + "ntrl.l" + tstring::int2str(l) + ".Hom", AGE, l, 0, 0,
    //        &TTNeutralGenesSH::getHomozygosity, 0, 0);
  }
 
}

References TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, StatHandler< SH >::add(), ADULTS, TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), getGlobalAlleleFreq(), getHeterozygosity(), tstring::int2str(), OFFSPRG, setAdultAlleleFreq(), setAdultHeterozygosity(), setOffspringAlleleFreq(), and setOffspringHeterozygosity().

Referenced by setStatRecorders().

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setFreqRecordersPerPatch()

void TTNeutralGenesSH::setFreqRecordersPerPatch

(

age_t

AGE

)

setFst_li()

void TTNeutralGenesSH::setFst_li	(	unsigned int	N,
		unsigned int	L,
		double **	array
	)

Computes the per-locus per-patch Fst values using Weir&Hill 2002 approach.

{
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
  
  assert(N == patchNbr);
  assert(L == nb_locus);
  
  setAlleleTables(ADULTS);
  
  double *pop_weights = new double[patchNbr];
  double *pop_sizes = new double[patchNbr];
  double *denominator = new double[nb_locus];
  double sum_weights = 0;
  
  double tot_size = _pop->size(ADULTS) * 2; //diploids!
  
  for(unsigned int i = 0; i < patchNbr; ++i) {
    pop_sizes[i] = _pop->size(ADULTS, i) * 2; 
    pop_weights[i] = pop_sizes[i] - (pop_sizes[i] * pop_sizes[i] / tot_size); //n_ic in Weir & Hill 2002
    sum_weights += pop_weights[i];
    for(unsigned int j = 0; j < nb_locus; ++j)
      array[i][j] = nanf("NULL");
  }
  
  for(unsigned int l = 0; l < nb_locus; ++l)
    denominator[l] = 0;
  
  double p, pq, var;
  
  for (unsigned int i = 0; i < patchNbr; ++i) {
    
    if( !pop_sizes[i] ) continue;
    
    for (unsigned int l = 0; l < nb_locus; ++l) {
      
      array[i][l] = 0;
      
      for (unsigned int u = 0; u < nb_allele; ++u) {
        
        p = _alleleFreqTable.get(i, l, u); //p_liu
        
        pq = p * (1 - p);
        
        var = p - _globalAlleleFreq.get(l, u); //(p_liu - pbar_u)
        
        var *= var;
        
        array[i][l] += pq * pop_sizes[i] / (pop_sizes[i] -1);
        
        denominator[l] += pop_sizes[i] * var + pop_weights[i] * pq;
        
      } // end for allele
    }// end for locus
  }//end for pop
  
  
  for (unsigned int i = 0; i < patchNbr; ++i) {
    if( !pop_sizes[i] ) continue;
    for (unsigned int l = 0; l < nb_locus; ++l) 
      array[i][l] = 1 - ( array[i][l] * sum_weights / denominator[l]);
  }
 
  delete [] pop_weights;
  delete [] pop_sizes;
  delete [] denominator;
}

References _alleleFreqTable, _globalAlleleFreq, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, ADULTS, DataTable< T >::get(), TMatrix::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), setAlleleTables(), and Metapop::size().

Referenced by TTNeutralGenesFH::write_Fst_i().

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setFstat()

void TTNeutralGenesSH::setFstat

(

age_t

AGE

)

Computes the F-statistics following Nei & Chesser (1983).

{
  double harmonic = 0, nbpatch = 0, nbind;
  unsigned int patchNbr = _pop->getPatchNbr();
  age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
  
  //check if the population size has changed:
  if(_alleleCountTable.getNumGroups() != patchNbr)
    allocateTables(_SHLinkedTrait->get_locus_num(), _SHLinkedTrait->get_allele_num());
  
  setAlleleTables(AGE);
  
  setLociDivCounter(AGE);
 
  //harmonic mean of patch sizes:
  for (unsigned int i = 0; i < patchNbr; ++i){
    
    nbind = _pop->size(AGE, i);
    if(nbind != 0){
      nbpatch++;
      harmonic += 1.0/nbind;
    }
  }
  
  harmonic = nbpatch / harmonic;
  
  _ho = setHo(age_pos);
  _hs = setHs(age_pos);
  _ht = setHt(age_pos);
  //Nei's corrections:
  _hsnei = (nbpatch != 0 ? harmonic/(harmonic-1.0)*(_hs-(_ho/(2.0*harmonic))) : nanf("NULL") );
  _htnei = (nbpatch != 0 ? _ht + (_hsnei/(harmonic*nbpatch))
            -(_ho/(2.0*harmonic*nbpatch)) : nanf("NULL") );
  
  _fis = ( _hsnei ? 1.0-(_ho/_hsnei) : nanf("NULL") );
  _fit = ( _htnei ? 1.0-(_ho/_htnei) : nanf("NULL") );
  _fst = ( _htnei ? 1.0-(_hsnei/_htnei) : nanf("NULL") );
}

References _alleleCountTable, _fis, _fit, _fst, _ho, _hs, _hsnei, _ht, _htnei, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, ADLTx, ADULTS, allocateTables(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), DataTable< T >::getNumGroups(), Metapop::getPatchNbr(), OFFSx, setAlleleTables(), setHo(), setHs(), setHt(), setLociDivCounter(), and Metapop::size().

Referenced by setAdultsFstat(), and setOffsprgFstat().

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setFstat2()

void TTNeutralGenesSH::setFstat2

(

age_t

AGE

)

New version of Nei & Chesser.

{
  double harmonic = 0, nbpatch = 0, nbind;
  unsigned int patchNbr = _pop->getPatchNbr();
  age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
  unsigned int nloc = _SHLinkedTrait->get_locus_num();
  
  //check if the population size has changed:
  if(_alleleCountTable.getNumGroups() != patchNbr)
    allocateTables(_SHLinkedTrait->get_locus_num(), _SHLinkedTrait->get_allele_num());
  
  setAlleleTables(AGE);
  
  setLociDivCounter(AGE);
  
  //harmonic mean of patch sizes:
  for (unsigned int i = 0; i < patchNbr; ++i){
    
    nbind = _pop->size(AGE, i);
    if(nbind != 0){
      nbpatch++;
      harmonic += 1.0/nbind;
    }
  }
  
  harmonic = nbpatch / harmonic;
  
  deque<double> ho = setHo2(age_pos);
  deque<double> hs = setHs2(age_pos);
  deque<double> ht = setHt2(age_pos);
  
  _fis = _fit = _fst = 0;
  
  double hsnei, htnei;
  
  for (unsigned int l = 0; l < nloc; ++l) {
  
  //Nei's corrections:
  hsnei = (nbpatch != 0 ? harmonic/(harmonic-1.0)*(hs[l]-(ho[l]/(2.0*harmonic))) : nanf("NULL") );
  htnei = (nbpatch != 0 ? ht[l] + (hsnei/(harmonic*nbpatch))
            -(ho[l]/(2.0*harmonic*nbpatch)) : 0 );
  _hsnei += hsnei;
  _htnei += htnei;
//    _hsnei += hs[l];
//    _htnei += ht[l];
    _ho += ho[l];
//  _fis = ( _hsnei ? 1.0-(_ho/_hsnei) : nanf("NULL") );
//  _fit = ( _htnei ? 1.0-(_ho/_htnei) : nanf("NULL") );
    if(ht[l] == 0) nloc--; //would mean locus is fixed
    _fst += ( ht[l] != 0 ? 1.0-(hsnei/htnei) : 0);
 
//    if(ht[l] == 0) nloc--;
//    
//    _fst += (ht[l] != 0 ? 1 - (hs[l]/ht[l]) : 0);
  }
  _hsnei /= nloc;
  _htnei /= nloc;
  _ho /= nloc;
  _fst /= nloc;
}

References _alleleCountTable, _fis, _fit, _fst, _ho, _hsnei, _htnei, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, ADLTx, ADULTS, allocateTables(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), DataTable< T >::getNumGroups(), Metapop::getPatchNbr(), OFFSx, setAlleleTables(), setHo2(), setHs2(), setHt2(), setLociDivCounter(), and Metapop::size().

Referenced by setAdultsFstat2(), and setOffsprgFstat2().

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setFstat2Recorders()

void TTNeutralGenesSH::setFstat2Recorders

(

age_t

AGE

)

{
  if(AGE & OFFSPRG) {
    add("Ho     (offsprg)","off.ho2",OFFSPRG,0,0,&TTNeutralGenesSH::getHo,0,0,
        &TTNeutralGenesSH::setOffsprgFstat2);
    add("Hs-Nei (offsprg)","off.hsnei2",OFFSPRG,0,0,&TTNeutralGenesSH::getHsnei,0,0,0);
    add("Ht-Nei (offsprg)","off.htnei2",OFFSPRG,0,0,&TTNeutralGenesSH::getHtnei,0,0,0);
    add("Fst    (offsprg)","off.fst2",OFFSPRG,0,0,&TTNeutralGenesSH::getFst,0,0,0);
  }
 
  if(AGE & ADULTS) {
    add("Ho       (adult)","adlt.ho2",ADULTS,0,0,&TTNeutralGenesSH::getHo,0,0,
        &TTNeutralGenesSH::setAdultsFstat2);
    add("Hs-Nei   (adult)","adlt.hsnei2",ADULTS,0,0,&TTNeutralGenesSH::getHsnei,0,0,0);
    add("Ht-Nei   (adult)","adlt.htnei2",ADULTS,0,0,&TTNeutralGenesSH::getHtnei,0,0,0);
    add("Fst      (adult)","adlt.fst2",ADULTS,0,0,&TTNeutralGenesSH::getFst,0,0,0);
  }
}

References StatHandler< SH >::add(), ADULTS, getFst(), getHo(), getHsnei(), getHtnei(), OFFSPRG, setAdultsFstat2(), and setOffsprgFstat2().

Referenced by setStatRecorders().

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setFstatRecorders()

void TTNeutralGenesSH::setFstatRecorders

(

age_t

AGE

)

{
  if(AGE & OFFSPRG) {
    add("Nbr of Alleles per Locus - local  (offsprg)","off.allnbp",OFFSPRG,0,0,
        &TTNeutralGenesSH::getNbAllLocal,0,0,&TTNeutralGenesSH::setOffsprgFstat);
    add("Nbr of Alleles per Locus - global (offsprg)","off.allnb",OFFSPRG,0,0,&TTNeutralGenesSH::getNbAllGlobal,0,0,0);
    add("Nbr of Fixed Loci per Patch  (offsprg)","off.fixlocp",OFFSPRG,0,0,&TTNeutralGenesSH::getFixLocLocal,0,0,0);
    add("Nbr of Fixed Loci in the Pop (offsprg)","off.fixloc",OFFSPRG,0,0,&TTNeutralGenesSH::getFixLocGlobal,0,0,0);
    add("Ho     (offsprg)","off.ho",OFFSPRG,0,0,&TTNeutralGenesSH::getHo,0,0,0);
    add("Hs-Nei (offsprg)","off.hsnei",OFFSPRG,0,0,&TTNeutralGenesSH::getHsnei,0,0,0);
    add("Ht-Nei (offsprg)","off.htnei",OFFSPRG,0,0,&TTNeutralGenesSH::getHtnei,0,0,0);
    add("Fis    (offsprg)","off.fis",OFFSPRG,0,0,&TTNeutralGenesSH::getFis,0,0,0);
    add("Fst    (offsprg)","off.fst",OFFSPRG,0,0,&TTNeutralGenesSH::getFst,0,0,0);
    add("Fit    (offsprg)","off.fit",OFFSPRG,0,0,&TTNeutralGenesSH::getFit,0,0,0);
  }
 
  if(AGE & ADULTS) {
    add("Nbr of Alleles per Locus - local  (adult)","adlt.allnbp",ADULTS,0,0,
        &TTNeutralGenesSH::getNbAllLocal,0,0,&TTNeutralGenesSH::setAdultsFstat);
    add("Nbr of Alleles per Locus - global (adult)","adlt.allnb",ADULTS,0,0,&TTNeutralGenesSH::getNbAllGlobal,0,0,0);
    add("Nbr of Fixed Loci per Patch  (adult)","adlt.fixlocp",ADULTS,0,0,&TTNeutralGenesSH::getFixLocLocal,0,0,0);
    add("Nbr of Fixed Loci in the Pop (adult)","adlt.fixloc",ADULTS,0,0,&TTNeutralGenesSH::getFixLocGlobal,0,0,0);
    add("Ho       (adult)","adlt.ho",ADULTS,0,0,&TTNeutralGenesSH::getHo,0,0,0);
    add("Hs-Nei   (adult)","adlt.hsnei",ADULTS,0,0,&TTNeutralGenesSH::getHsnei,0,0,0);
    add("Ht-Nei   (adult)","adlt.htnei",ADULTS,0,0,&TTNeutralGenesSH::getHtnei,0,0,0);
    add("Fis      (adult)","adlt.fis",ADULTS,0,0,&TTNeutralGenesSH::getFis,0,0,0);
    add("Fst      (adult)","adlt.fst",ADULTS,0,0,&TTNeutralGenesSH::getFst,0,0,0);
    add("Fit      (adult)","adlt.fit",ADULTS,0,0,&TTNeutralGenesSH::getFit,0,0,0);
  }
}

References StatHandler< SH >::add(), ADULTS, getFis(), getFit(), getFixLocGlobal(), getFixLocLocal(), getFst(), getHo(), getHsnei(), getHtnei(), getNbAllGlobal(), getNbAllLocal(), OFFSPRG, setAdultsFstat(), and setOffsprgFstat().

Referenced by setStatRecorders().

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setFstatWCRecorders()

void TTNeutralGenesSH::setFstatWCRecorders

(

age_t

AGE

)

{
  if(AGE & OFFSPRG) {
 
    add("Fis Weir & Cockerham","off.fis.WC",OFFSPRG,0,0,&TTNeutralGenesSH::getFisWC,0,0,&TTNeutralGenesSH::setOffspringFstatWeirCockerham);
    add("Fst Weir & Cockerham","off.fst.WC",OFFSPRG,0,0,&TTNeutralGenesSH::getFstWC,0,0,0);
    add("Fit Weir & Cockerham","off.fit.WC",OFFSPRG,0,0,&TTNeutralGenesSH::getFitWC,0,0,0);
  }
 
  if(AGE & ADULTS) {
 
    add("Fis Weir & Cockerham","adlt.fis.WC",ADULTS,0,0,&TTNeutralGenesSH::getFisWC,0,0,&TTNeutralGenesSH::setAdultsFstatWeirCockerham);
    add("Fst Weir & Cockerham","adlt.fst.WC",ADULTS,0,0,&TTNeutralGenesSH::getFstWC,0,0,0);
    add("Fit Weir & Cockerham","adlt.fit.WC",ADULTS,0,0,&TTNeutralGenesSH::getFitWC,0,0,0);
 
  }
}

References StatHandler< SH >::add(), ADULTS, getFisWC(), getFitWC(), getFstWC(), OFFSPRG, setAdultsFstatWeirCockerham(), and setOffspringFstatWeirCockerham().

Referenced by setStatRecorders().

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setFstatWeirCockerham()

void TTNeutralGenesSH::setFstatWeirCockerham

(

age_t

AGE

)

Computes the Weir & Cockerham (1984) Fstat values (Theta, F, and f).

{
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
  //age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
  
  setAlleleTables(AGE);
  setHeteroTable(AGE);
  
  //init
  double *pop_sizes = new double [patchNbr];
  double tot_size, inv_ntot;
  double sum_weights = 0;
  double nbar, nc, inv_nbar;
  unsigned int extantPs = 0;
  
  tot_size = _pop->size(AGE);
  
  for(unsigned int i = 0; i < patchNbr; i++) {
    pop_sizes[i] = _pop->size(AGE, i); 
    if(pop_sizes[i]) {
      extantPs++;
      sum_weights += (pop_sizes[i] * pop_sizes[i] / tot_size);
    }
  }
  nbar = tot_size/extantPs;
  nc = (tot_size - sum_weights)/(extantPs-1);
  inv_nbar = 1/(nbar - 1);
  inv_ntot = 1/tot_size;
  
  double var;
  double s2, pbar, hbar;
  double s2_denom = 1.0/((extantPs-1)*nbar),
                  r = (double)(extantPs-1)/extantPs,
                  hbar_factor=(2*nbar-1)/(4*nbar);
  double a = 0, b = 0, c = 0, x;
  
  for (unsigned int l = 0; l < nb_locus; ++l) {
    
    for (unsigned int u = 0; u < nb_allele; ++u) {
      
      s2 = pbar = hbar = 0;
      
      for (unsigned int i = 0; i < patchNbr; ++i) {
        
        var = _alleleFreqTable.get(i, l, u) - _globalAlleleFreq.get(l, u); //(p_liu - pbar_u)^2 
        
        var *= var;
        
        s2 += var * pop_sizes[i];
        
        hbar += _heteroTable.get(i, l, u);
        
      }//end for pop
      
      s2 *= s2_denom;
      pbar = _globalAlleleFreq.get(l, u);
      hbar *= inv_ntot;
      
      x = pbar * (1 - pbar) - r * s2;
      a += s2 - inv_nbar*( x - 0.25 * hbar);
      b += x - hbar_factor * hbar;
      c += hbar;
      
      
    } // end for allele
    
  }// end for locus
    
  a *= nbar/nc;
  b *= nbar/(nbar - 1);
  c *= 0.5;
  
  _fst_WC = a / (a + b + c);
  _fit_WC = (a + b) / (a + b + c);
  _fis_WC = b / (b + c);
  
  delete [] pop_sizes;   
}

References _alleleFreqTable, _fis_WC, _fit_WC, _fst_WC, _globalAlleleFreq, _heteroTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, DataTable< T >::get(), TMatrix::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), setAlleleTables(), setHeteroTable(), and Metapop::size().

Referenced by setAdultsFstatWeirCockerham(), and setOffspringFstatWeirCockerham().

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setFstatWeirCockerham_MS()

void TTNeutralGenesSH::setFstatWeirCockerham_MS

(

age_t

AGE

)

Computes W&C F-stats using the Mean Squares approach, similar to the implementation in Hierfstat. This code gives the exact same results as the other version.

{ 
        unsigned int patchNbr = this->_pop->getPatchNbr();
        unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
        unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
        //age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
 
        setAlleleTables(AGE);
        setHeteroTable(AGE);
 
        //init
        double *pop_sizes = new double [patchNbr];
        double tot_size;
        double sum_weights = 0;
        double nc;
        unsigned int extantPs = 0;
 
        tot_size = _pop->size(AGE);
 
        for(unsigned int i = 0; i < patchNbr; i++) {
                pop_sizes[i] = _pop->size(AGE, i);
                if(pop_sizes[i]) {
                        extantPs++;
                        sum_weights += (pop_sizes[i] * pop_sizes[i] / tot_size);
                }
        }
 
        nc = (tot_size - sum_weights)/(extantPs-1);
 
//      unsigned int np = extantPs;
        unsigned int npl = extantPs; //all loci typed in all patches
 
        //p = _alleleFreqTable
        //pb = _globalAlleleFreq
 
        unsigned int *alploc = new unsigned int [nb_locus];
 
        unsigned int **alploc_table = new unsigned int* [nb_locus];
 
        for(unsigned int i = 0; i < nb_locus; ++i)
                alploc_table[i] = new unsigned int[nb_allele];
 
        unsigned int tot_num_allele = 0;
 
        for(unsigned int l = 0; l < nb_locus; ++l){
 
                alploc[l] = 0;
 
                for(unsigned int cnt,  a = 0; a < nb_allele; ++a) {
 
                        cnt=0;
 
                        for(unsigned int i = 0; i < patchNbr; i++) {
 
                                 cnt += _alleleCountTable.get(i,l,a);
 
                        }
                        alploc_table[l][a] = (cnt != 0);
                        alploc[l] += (cnt != 0);
                }
 
                tot_num_allele += alploc[l];
        }
 
        //n, and nal are given by pop_sizes, same num ind typed at all loci in each patch
        //nc is the same for each locus
        //nt is given by tot_size, same tot num of ind typed for all loci
 
        //SSG: het/2 for each allele
        double *SSG = new double[tot_num_allele];
        double *SSP = new double[tot_num_allele];
        double *SSi = new double[tot_num_allele];
 
        unsigned int all_cntr = 0;
 
        double het, freq, var;
 
        for(unsigned int l = 0; l < nb_locus; ++l) {
 
                for(unsigned int a = 0; a < nb_allele & all_cntr < tot_num_allele; ++a) {
 
                        if(alploc_table[l][a] == 0) continue; //do not consider alleles not present in the pop
 
                        SSG[all_cntr] = 0;
                        SSi[all_cntr] = 0;
                        SSP[all_cntr] = 0;
 
                        for(unsigned int p = 0; p < patchNbr; ++p){
 
                                if(!_pop->size(AGE, p)) continue; //skip empty patches
 
                                het = _heteroTable.get(p, l, a);
 
                                freq = _alleleFreqTable.get(p, l, a);
 
                                var = freq - _globalAlleleFreq.get(l, a); //(p_liu - pbar_u)^2
 
                                var *= var;
 
                                SSG[all_cntr] += het;
 
                                SSi[all_cntr] += 2*pop_sizes[p]*freq*(1-freq) - het/2;
 
                                SSP[all_cntr] += 2*pop_sizes[p]*var;
                        }
 
                        all_cntr++;
                }
 
        }
 
 
        assert(all_cntr == tot_num_allele);
 
        double *MSG = new double[tot_num_allele];
        double *MSP = new double[tot_num_allele];
        double *MSI = new double[tot_num_allele];
        double *sigw = new double[tot_num_allele];
        double *siga = new double[tot_num_allele];
        double *sigb = new double[tot_num_allele];
 
//      double *FST_pal = new double[tot_num_allele];
//      double *FIS_pal = new double[tot_num_allele];
 
        double SIGA = 0, SIGB = 0, SIGW = 0;
 
        for(unsigned int i = 0; i < tot_num_allele; ++i){
 
                MSG[i] = SSG[i] / (2 * tot_size);
                sigw[i] = MSG[i]; //wasted!
 
                MSP[i] = SSP[i] / (npl-1);
 
                MSI[i] = SSi[i]/ (tot_size - npl);
 
                sigb[i] = 0.5*(MSI[i] - MSG[i]);
 
                siga[i] = (MSP[i] - MSI[i])/(2*nc);
 
//              FST_pal[i] = siga[i]/(siga[i]+sigb[i]+sigw[i]);
//              FIS_pal[i] = sigb[i]/(sigb[i]+sigw[i]);
 
                SIGA += siga[i];
                SIGB += sigb[i];
                SIGW += sigw[i];
        }
 
        //per locus stats:
        if(_fst_WC_loc) delete [] _fst_WC_loc; _fst_WC_loc = new double [nb_locus];
        if(_fis_WC_loc) delete [] _fis_WC_loc; _fis_WC_loc = new double [nb_locus];
        if(_fit_WC_loc) delete [] _fit_WC_loc; _fit_WC_loc = new double [nb_locus];
 
        double lsiga, lsigb, lsigw;
 
//      cout<<"  computing sigma per locus\n";
 
        for(unsigned int allcntr = 0, i = 0; i < nb_locus; ++i) {
 
                lsiga = lsigb = lsigw = 0;
 
                for(unsigned int l = 0; l < alploc[i]; ++l) {
 
                        lsiga += siga[allcntr];
                        lsigb += sigb[allcntr];
                        lsigw += sigw[allcntr];
 
                        allcntr++;
 
                }
 
                _fst_WC_loc[i] = lsiga /(lsiga + lsigb + lsigw);
                _fis_WC_loc[i] = lsigb /(lsigb + lsigw);
                _fit_WC_loc[i] = (lsiga +lsigb) /(lsiga + lsigb + lsigw);
 
        }
 
 
        // Total F-stats
        _fst_WC = SIGA / (SIGA + SIGB + SIGW);
        _fit_WC = (SIGA + SIGB) / (SIGA + SIGB + SIGW);
        _fis_WC = SIGB / (SIGB + SIGW);
 
        delete[]pop_sizes;
        delete[]alploc;
        for(unsigned int i = 0; i < nb_locus; ++i)
                delete[]alploc_table[i];
        delete[]alploc_table;
        delete[]SSG;
        delete[]SSi;
        delete[]SSP;
        delete[]MSG;
        delete[]MSI;
        delete[]MSP;
        delete[]sigw;
        delete[]siga;
        delete[]sigb;
 
}

References _alleleCountTable, _alleleFreqTable, _fis_WC, _fis_WC_loc, _fit_WC, _fit_WC_loc, _fst_WC, _fst_WC_loc, _globalAlleleFreq, _heteroTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, DataTable< T >::get(), TMatrix::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), setAlleleTables(), setHeteroTable(), and Metapop::size().

setFstMatrix()

void TTNeutralGenesSH::setFstMatrix	(	age_t	AGE,
		unsigned char	dim
	)

Computes the weighted within and between patch Fst's as well as the overall Fst (Theta).

The method used here is that of Weir & Hill 2002, Ann. Rev. Genet. 36:721-750. The weighting is done for samples (patches) of unequal sizes.

Parameters

AGE	the age class
dim	the dimension of the matrix to fill: 1 = the diagonal (i.e. the wihtin patch Fst or theta_ii) 2 = the upper half (i.e. the between patch Fst or theta_ii') 3 = both

{
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
 
  setAlleleTables(AGE);
  
  if(_fst_matrix == NULL)
    
    _fst_matrix = new TMatrix(patchNbr, patchNbr);
  
  else if( _fst_matrix->length() != patchNbr * patchNbr)
    
    _fst_matrix->reset(patchNbr, patchNbr);
  
  _fst_matrix->assign(nanf("NULL"));
  
  //init
  double *pop_weights = new double[patchNbr];
  double *pop_sizes = new double[patchNbr];
  double **numerator = new double*[patchNbr];
  for(unsigned int i = 0; i < patchNbr; i++) numerator[i] = new double [patchNbr];
  double tot_size;
  double numerator_W = 0;
  double denominator = 0;
  double sum_weights = 0;
  
  tot_size = _pop->size(AGE) * 2; 
  
  for(unsigned int i = 0; i < patchNbr; ++i) {
    pop_sizes[i] = _pop->size(AGE, i) * 2; 
    pop_weights[i] = pop_sizes[i] - (pop_sizes[i] * pop_sizes[i] / tot_size); //n_ic in Weir & Hill 2002
    sum_weights += pop_weights[i];
    for(unsigned int j = 0; j < patchNbr; j++)
      numerator[i][j] = 0;
  }
  
   double p, pq, var, num;
 
   for (unsigned int i = 0; i < patchNbr; ++i) {
     
     if( !pop_sizes[i] ) continue;
     
     for (unsigned int l = 0; l < nb_locus; ++l) {
       
       for (unsigned int u = 0; u < nb_allele; ++u) {
         
         p = _alleleFreqTable.get(i, l, u); //p_liu
         
         pq = p * (1 - p);
         
         var = p - _globalAlleleFreq.get(l, u); //(p_liu - pbar_u)^2 
         
         var *= var;
         
         num = pq * pop_sizes[i] / (pop_sizes[i] -1);
 
         numerator[i][i] += num;
         
         numerator_W += num * pop_sizes[i]; //see equ. 9, Weir & Hill 2002
         
         denominator += pop_sizes[i] * var + pop_weights[i] * pq; //common denominator
         
       } // end for allele
     }// end for locus
   }//end for pop
 
  for (unsigned int i = 0; i < patchNbr; ++i) {
    if( !pop_sizes[i] ) continue;
    _fst_matrix->set(i, i, 1 - (numerator[i][i] * sum_weights / denominator) );
  }   
   _fst_WH = 1 - ((numerator_W * sum_weights) / (denominator * tot_size)); //equ. 9 Weir & Hill 2002
   
   //pairwise Fst:
   if(dim & 2) {
     double pi, pj;
     for (unsigned int l = 0; l < nb_locus; ++l)
       for (unsigned int u = 0; u < nb_allele; ++u)
         for (unsigned int i = 0; i < patchNbr - 1; ++i) {
           if( !pop_sizes[i] ) continue;
           for (unsigned int j = i + 1; j < patchNbr; ++j) {
             if( !pop_sizes[j] ) continue;
             pi = _alleleFreqTable.get(i, l, u);
             pj = _alleleFreqTable.get(j, l, u);
             numerator[i][j] += pi * (1 - pj) + pj * (1 - pi); //equ. 7 of Weir & Hill 2002
           }
         }
     for (unsigned int i = 0; i < patchNbr - 1; ++i){
       if( !pop_sizes[i] ) continue;
       for (unsigned int j = i + 1; j < patchNbr; ++j){
         if( !pop_sizes[j] ) continue;
         _fst_matrix->set(i, j, 1 - ( (numerator[i][j] * sum_weights) / (2 * denominator)) );
       }
     }
   }
 
  
  delete [] pop_weights;
  delete [] pop_sizes;
  for(unsigned int i = 0; i < patchNbr; i++) delete [] numerator[i];
  delete [] numerator;
}

References _alleleFreqTable, _fst_matrix, _fst_WH, _globalAlleleFreq, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TMatrix::assign(), DataTable< T >::get(), TMatrix::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), TMatrix::length(), TMatrix::reset(), TMatrix::set(), setAlleleTables(), and Metapop::size().

Referenced by setAdultsFstBetween(), setAdultsFstMatrix(), setAdultsFstWithin(), setOffsprgFstBetween(), setOffsprgFstMatrix(), and setOffsprgFstWithin().

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setFstMatrixRecorders()

void TTNeutralGenesSH::setFstMatrixRecorders	(	age_t	AGE,
		unsigned char	dim
	)

{
  std::ostringstream name, sub_name;
 
  void (TTNeutralGenesSH::* setter) () = (AGE == ADULTS ?
      ( dim & 3 ? &TTNeutralGenesSH::setAdultsFstMatrix :
          dim & 2 ? &TTNeutralGenesSH::setAdultsFstBetween :
              &TTNeutralGenesSH::setAdultsFstWithin ) :
              ( dim & 3 ? &TTNeutralGenesSH::setOffsprgFstMatrix :
                  dim & 2 ? &TTNeutralGenesSH::setOffsprgFstBetween :
                      &TTNeutralGenesSH::setOffsprgFstWithin) );
 
  const char *prefix = (AGE == ADULTS ? "adlt." : "off.");
 
  unsigned int nbpatch =  _pop->getPatchNbr();
  unsigned int scale = (unsigned int)pow(10.0, (int)log10((float)nbpatch) + 1);
 
  name<<"Weir&Hill weighted Fst ("<<prefix<<")";
  sub_name<< prefix << "fst.WH";
  add(name.str(), sub_name.str(),  AGE, 0, 0, &TTNeutralGenesSH::getWeightedFst, 0, 0, setter);
  name.str("");
  sub_name.str("");
 
  if(dim & 1) {
    for(unsigned int i = 0; i < nbpatch; ++i) {
      name<<"Weighted Fst "<<i+1<<"."<<i+1;
      sub_name<< prefix << "fst" << i+1 << "." << i+1;
      add(name.str(), sub_name.str(),  AGE, i*scale + i, 0, 0, &TTNeutralGenesSH::getFst_ij, 0,  0);
      name.str("");
      sub_name.str("");
    }
  }
  if(dim & 2){
    for(unsigned int i = 0; i < nbpatch; ++i) {
      for(unsigned int j = i+1; j < nbpatch; ++j) {
        name<<"Weighted Fst "<<i+1<< "." <<j+1;
        sub_name<< prefix << "fst" << i+1 << "." << j+1;
        add(name.str(), sub_name.str(),  AGE, i*scale + j, 0, 0, &TTNeutralGenesSH::getFst_ij, 0, 0);
        name.str("");
        sub_name.str("");
      }
    }
  }
 
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADULTS, getFst_ij(), Metapop::getPatchNbr(), getWeightedFst(), setAdultsFstBetween(), setAdultsFstMatrix(), setAdultsFstWithin(), setOffsprgFstBetween(), setOffsprgFstMatrix(), and setOffsprgFstWithin().

Referenced by setStatRecorders().

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setHeteroTable()

void TTNeutralGenesSH::setHeteroTable

(

age_t

AGE

)

{
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
  Patch* patch;
  unsigned int isHetero;
  unsigned char** genes;
  age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
    
  unsigned int **sizes;
  
  sizes = new unsigned int * [patchNbr];
  
  for(unsigned int i = 0; i < patchNbr; ++i) {
    sizes[i] = new unsigned int [nb_locus];
    for(unsigned int j = 0; j < nb_locus; ++j)
      sizes[i][j] = nb_allele;
  }
  
  _heteroTable.update(patchNbr, nb_locus, sizes);
  _heteroTable.init(0);
  
  
  for (unsigned int i = 0; i < patchNbr; ++i) {
    
    patch = _pop->getPatch(i);
    
    if(!patch->size(age_pos)) continue;
    
    for(unsigned int j = 0, size = patch->size(FEM, age_pos); j < size; ++j) {
      
      genes = (unsigned char**)patch->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < nb_locus; ++l) {
        isHetero = (genes[0][l] != genes[1][l]);
        _heteroTable.plus(i, l, genes[0][l], isHetero);
        _heteroTable.plus(i, l, genes[1][l], isHetero);
      }
    }
    
    for(unsigned int j = 0, size = patch->size(MAL, age_pos); j < size; ++j) {
      
      genes = (unsigned char**)patch->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int l = 0; l < nb_locus; ++l) {
        isHetero = (genes[0][l] != genes[1][l]);
        _heteroTable.plus(i, l, genes[0][l], isHetero);
        _heteroTable.plus(i, l, genes[1][l], isHetero);
      }
    }
  }  
  for(unsigned int i = 0; i < patchNbr; ++i) delete [] sizes[i];
  delete [] sizes;
 
}

References _heteroTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, ADLTx, ADULTS, FEM, Patch::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), DataTable< T >::init(), MAL, OFFSx, DataTable< T >::plus(), Patch::size(), and DataTable< T >::update().

Referenced by setFstatWeirCockerham(), setFstatWeirCockerham_MS(), setHeterozygosity(), and TTNeutralGenesFH::write_varcompWC().

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setHeterozygosity()

void TTNeutralGenesSH::setHeterozygosity

(

age_t

AGE

)

{
  unsigned int patchNbr  = this->_pop->getPatchNbr();
  unsigned int nb_locus  = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
  Patch* patch;
  age_idx age_pos = (AGE == ADULTS ? ADLTx : OFFSx);
 
  setHeteroTable(AGE);
  
  for (unsigned int i = 0, size; i < patchNbr; ++i) {
    
    patch = _pop->getPatch(i);
    size = patch->size(age_pos);
    
    if(!size) continue;
 
    for (unsigned int l = 0; l < nb_locus; ++l) {
      for (unsigned int u = 0; u < nb_allele; ++u) {
        _heteroTable.divide(i, l , u, size);
      }
    }
  }
  
  
}

References _heteroTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, ADLTx, ADULTS, DataTable< T >::divide(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatch(), Metapop::getPatchNbr(), OFFSx, setHeteroTable(), and Patch::size().

Referenced by setAdultHeterozygosity(), and setOffspringHeterozygosity().

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setHo()

double TTNeutralGenesSH::setHo

(

age_idx

age_pos

)

{
  unsigned int nloc = _SHLinkedTrait->get_locus_num(), nbpatch = _pop->getPatchNbr(), psize;
  double indloc = 0, hetero = 0;
  unsigned char** genes;
  Patch* current_patch;
  
  for (unsigned int i = 0; i < nbpatch; ++i) {
    
    current_patch = _pop->getPatch(i);
    
    psize = current_patch->size(FEM, age_pos);
    
    indloc += psize;
    
    for(unsigned int j = 0; j < psize; ++j) {
      
      genes = (unsigned char**)current_patch->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int k = 0; k < nloc; ++k)  hetero += (genes[0][k] != genes[1][k]);
    }
  }
  //doing some unrolling, loops for the males here:
  for (unsigned int i = 0; i < nbpatch; ++i) {
    
    current_patch = _pop->getPatch(i);
    
    psize = current_patch->size(MAL, age_pos);
    
    indloc += psize;
    
    for(unsigned int j = 0; j < psize; ++j) {
      
      genes = (unsigned char**)current_patch->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int k = 0; k < nloc; ++k)  hetero += (genes[0][k] != genes[1][k]);
    }
  }
  
  indloc *= nloc;
  
  return (indloc != 0 ? hetero/indloc : 0.0);
}

References StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, FEM, Patch::get(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), MAL, and Patch::size().

Referenced by setFstat().

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setHo2()

deque< double > TTNeutralGenesSH::setHo2

(

age_idx

age_pos

)

{
  unsigned int nloc = _SHLinkedTrait->get_locus_num(), nbpatch = _pop->getPatchNbr();
  unsigned int msize, fsize, psize;
  deque<double> hetero(nloc,0);
  unsigned char** genes;
  Patch* current_patch;
    
  for (unsigned int i = 0; i < nbpatch; ++i) {
    
    current_patch = _pop->getPatch(i);
    
    fsize = current_patch->size(FEM, age_pos);
    
    for(unsigned int j = 0; j < fsize; ++j) {
      
      genes = (unsigned char**)current_patch->get(FEM, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int k = 0; k < nloc; ++k)  hetero[k] += (genes[0][k] != genes[1][k]);
    }
        
    msize = current_patch->size(MAL, age_pos);
    
    for(unsigned int j = 0; j < msize; ++j) {
      
      genes = (unsigned char**)current_patch->get(MAL, age_pos, j)->getTrait(_SHLinkedTraitIndex)->get_sequence();
      
      for (unsigned int k = 0; k < nloc; ++k)  hetero[k] += (genes[0][k] != genes[1][k]);
    }
    
  }
 
  psize = _pop->size(age_pos);
  
  if(psize != 0) 
    for (unsigned int k = 0; k < nloc; ++k)  
      hetero[k] /= psize;
  
  return hetero;
}

References StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, FEM, Patch::get(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTrait(), MAL, Metapop::size(), and Patch::size().

Referenced by setFstat2(), and TTNeutralGenesFH::write_varcompWC().

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setHs()

double TTNeutralGenesSH::setHs

(

age_idx

age_pos

)

{
  unsigned int i, k, x, nb_patch=0;
  double hs = 0;
  unsigned int nbLoc = _SHLinkedTrait->get_locus_num(), nbAll = _SHLinkedTrait->get_allele_num();
  unsigned int patchNbr = _pop->getPatchNbr();
  deque<double>genehet(nbLoc,1);
  deque<double>hspop(patchNbr,0);
  double freq;
  Patch* current_patch;
  
  //compute the expected heterozygosity for each patch and return average:
  for (i = 0; i < patchNbr; ++i) {
    
    current_patch = _pop->getPatch(i);
                
    genehet.assign(nbLoc, 1);
    
    if(current_patch->size(age_pos) != 0) {
      
      nb_patch++;
      
      for (k = 0; k < nbLoc; ++k) {
        
        for (x = 0; x < nbAll; ++x) {
          
          freq = _alleleFreqTable.get(i, k, x);
          
          freq *= freq; //squared frequencies (expected _homozygosity)
          
          genehet[k] -= freq; //1 - sum of p2 = expected heterozygosity
        }
        //expected heterozygosity:
        hspop[i] += genehet[k];
      }
    }//end_if size!=0
    
    hs += hspop[i];
  }//end patch loop
  
  return (nb_patch !=0 ? hs/(nbLoc*nb_patch) : 0.0);
}

References _alleleFreqTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, Patch::assign(), DataTable< T >::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatch(), Metapop::getPatchNbr(), and Patch::size().

Referenced by setFstat().

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setHs2()

deque< double > TTNeutralGenesSH::setHs2

(

age_idx

age_pos

)

{
  unsigned int i, k, x, nb_patch = 0;
  unsigned int nbLoc = _SHLinkedTrait->get_locus_num(), nbAll = _SHLinkedTrait->get_allele_num();
  unsigned int patchNbr = _pop->getPatchNbr();
  deque<double>genehet(nbLoc,1);
  deque<double>hsloc(nbLoc,0);
  double freq;
  Patch* current_patch;
  
  for (i = 0; i < patchNbr; ++i) {
    if(_pop->size(age_pos, i) != 0)
      nb_patch++;
  }
  
  //compute the expected heterozygosity for each patch and return average:
  for (k = 0; k < nbLoc; ++k) {    
    
    for (i = 0; i < patchNbr; ++i) {
      
      current_patch = _pop->getPatch(i);
      
      genehet[k] = 1;
      
      if(current_patch->size(age_pos) != 0) {
        
        for (x = 0; x < nbAll; ++x) {
          
          freq = _alleleFreqTable.get(i, k, x);
          
          freq *= freq; //squared frequencies (expected _homozygosity)
          
          genehet[k] -= freq; //1 - sum of p2 = expected heterozygosity
        }
        
      }//end_if size!=0
      
      hsloc[k] += genehet[k];
      
    }//end patch loop
    
    if(nb_patch !=0) hsloc[k] /= nb_patch;
    
  }//end loci loop
  
  return  hsloc;
}

References _alleleFreqTable, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, DataTable< T >::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatch(), Metapop::getPatchNbr(), Metapop::size(), and Patch::size().

Referenced by setFstat2().

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setHt()

double TTNeutralGenesSH::setHt

(

age_idx

age_pos

)

{
  double ht = 0;
  unsigned int nbLoc = _SHLinkedTrait->get_locus_num(), nbAll = _SHLinkedTrait->get_allele_num();
  deque<double> genehet(nbLoc, 1);
  double freq;
  
  //get global allele frequencies per locus
  for (unsigned int l = 0; l < nbLoc; ++l) {
    for (unsigned int u = 0; u < nbAll; ++u) {
      
      freq = _globalAlleleFreq.get(l, u);
      
      freq *= freq; //squared frequencies
      
          genehet[l] -= freq;  //1 - sum of p2 = expected heterozygosity
    }
    
    ht += genehet[l];
  }
  
  return (ht/nbLoc);
}

References _globalAlleleFreq, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TMatrix::get(), TProtoNeutralGenes::get_allele_num(), and TProtoNeutralGenes::get_locus_num().

Referenced by setFstat().

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setHt2()

deque< double > TTNeutralGenesSH::setHt2

(

age_idx

age_pos

)

{
  unsigned int nbLoc = _SHLinkedTrait->get_locus_num(), nbAll = _SHLinkedTrait->get_allele_num();
  deque<double> genehet(nbLoc, 1);
  double freq;
  
  //get global allele frequencies per locus
  for (unsigned int l = 0; l < nbLoc; ++l) {
  
    for (unsigned int u = 0; u < nbAll; ++u) {
      
      freq = _globalAlleleFreq.get(l, u);
      
      freq *= freq; //squared frequencies
      
      genehet[l] -= freq;  //1 - sum of p2 = expected heterozygosity
    }
  }
  
  return genehet;
}

References _globalAlleleFreq, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TMatrix::get(), TProtoNeutralGenes::get_allele_num(), and TProtoNeutralGenes::get_locus_num().

Referenced by setFstat2().

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setLociDivCounter()

void TTNeutralGenesSH::setLociDivCounter

(

age_t

AGE

)

Sets the allelic diversity counters.

{
  unsigned int i, j, k;
  unsigned int nbLoc = _SHLinkedTrait->get_locus_num(), nbAll = _SHLinkedTrait->get_allele_num();
  unsigned int nbpatch = 0, patchNbr = _pop->getPatchNbr();
  double patch_mean, pop_mean = 0;
  bool **pop_div;
  
  //number of alleles per locus, Patch and pop counters:
  pop_div = new bool * [nbLoc];
  
  for(i = 0; i < nbLoc; ++i) {
    pop_div[i] = new bool [nbAll];
    for(j = 0; j < nbAll;++j)
      pop_div[i][j] = 0;
  }
  
  for(k = 0; k < patchNbr; ++k) 
    nbpatch += (_pop->size(AGE, k) != 0);
  
  for(k = 0; k < patchNbr; ++k) {
        
    patch_mean = 0;
        
    for(i = 0; i < nbLoc; ++i)    
          for(j = 0; j < nbAll;++j) {
                patch_mean += (_alleleCountTable.get(k,i,j) != 0);
        pop_div[i][j] |= (_alleleCountTable.get(k,i,j) != 0);
      }
        //add mean nb of alleles per locus for Patch k to the pop mean
        pop_mean += patch_mean/nbLoc;
  }
  
  _nb_all_local = (nbpatch ? pop_mean/nbpatch : nanf("NULL"));
 
  _nb_all_global = 0;
  
  for(i = 0; i < nbLoc; ++i)      
    for(j = 0; j < nbAll;++j)
      _nb_all_global += pop_div[i][j];
  
  _nb_all_global /= nbLoc;
  
  for(i = 0; i < nbLoc; ++i)
    delete [] pop_div[i];
  delete [] pop_div;
      
  //number of fixed loci, local and global counters:
  _fix_loc_local = 0;
  
  for (k = 0; k < patchNbr; ++k)
    for (i = 0; i < nbLoc; ++i)
      for (j = 0; j < nbAll; ++j)        
        _fix_loc_local += ( _alleleFreqTable.get(k, i, j) == 1 );
  
  _fix_loc_local /= nbpatch;
  
  _fix_loc_global = 0;
      
  //globally:  
  for (i = 0; i < nbLoc; ++i)
    for (j = 0; j < nbAll; ++j)  
      _fix_loc_global += ( _globalAlleleFreq.get(i, j) == 1 );
 
}

References _alleleCountTable, _alleleFreqTable, _fix_loc_global, _fix_loc_local, _globalAlleleFreq, _nb_all_global, _nb_all_local, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, DataTable< T >::get(), TMatrix::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), and Metapop::size().

Referenced by setFstat(), and setFstat2().

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setNeiGeneticDistance()

void TTNeutralGenesSH::setNeiGeneticDistance

(

age_t

AGE

)

{
  //see: Nei, M. 1978. Genetics 89:583-590
  unsigned int patchNbr = this->_pop->getPatchNbr();
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  unsigned int nb_allele = this->_SHLinkedTrait->get_allele_num();
  
  setAlleleTables(AGE);
  
  if(_D == NULL) 
    
    _D = new TMatrix(patchNbr, patchNbr);
  
  else if( _D->length() != patchNbr*patchNbr )
    
    _D->reset(patchNbr, patchNbr);
  
  _D->assign(nanf("NULL"));
  
  double num, denom, p1, p2, sum;
  double *sum_square = new double [patchNbr];
  double *sample_size = new double [patchNbr];
  
  for(unsigned int i = 0; i < patchNbr; ++i) {
    
    sample_size[i] = 2 * _pop->size(AGE, i);
    
    sum_square[i] = 0;
    
    if( !sample_size[i] ) continue;
    
    for(unsigned int l = 0; l < nb_locus; ++l) {
      
      sum = 0;
      
      for(unsigned int u = 0; u < nb_allele ; ++u) {
        p1 = _alleleFreqTable.get(i, l, u);
        sum += p1*p1;
      }
      
      sum_square[i] += (sample_size[i] * sum -1) / (sample_size[i] -1); //unbiased estimate, equ. 6 in Nei 1978 (Genetics)
    }
  }
  
  unsigned int pairs = 0;
  double Dpair;
  _meanD = 0;
  
  for(unsigned int i = 0; i < patchNbr-1; ++i) {
    
    if( !sample_size[i] ) continue;
    
    for(unsigned int j = i + 1; j < patchNbr; ++j) {
 
      if( !sample_size[j] ) continue;
      
      num = 0;
      pairs++;
      
      for(unsigned int l = 0; l < nb_locus; ++l) {
        for(unsigned int u = 0; u < nb_allele ; ++u) {
          p1 = _alleleFreqTable.get(i, l, u);
          p2 = _alleleFreqTable.get(j, l, u);
          num += p1*p2;
        }
      }      
      
      denom = sqrt(sum_square[i] * sum_square[j]);
      Dpair = -log(num/denom);
      _meanD += Dpair;
      _D->set(i, j, Dpair);
    }
  }
  _meanD /= pairs;
  
  delete [] sum_square;
  delete [] sample_size;
}

References _alleleFreqTable, _D, _meanD, StatHandlerBase::_pop, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TMatrix::assign(), DataTable< T >::get(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), Metapop::getPatchNbr(), TMatrix::length(), TMatrix::reset(), TMatrix::set(), setAlleleTables(), and Metapop::size().

Referenced by setAdltNeiGeneticDistance(), and setOffsprgNeiGeneticDistance().

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setNeiGeneticDistanceRecorders()

void TTNeutralGenesSH::setNeiGeneticDistanceRecorders	(	age_t	AGE,
		bool	pairwise
	)

{
  string name, sub_name;
  unsigned int nbpatch =  _pop->getPatchNbr();
  string prefix = (AGE == ADULTS ? "adlt." : "off.");
  unsigned int scale = (unsigned int)pow(10.0, (int)log10((float)nbpatch) + 1);
 
  void (TTNeutralGenesSH::* setter) () = (AGE == ADULTS ?
      &TTNeutralGenesSH::setAdltNeiGeneticDistance
      : &TTNeutralGenesSH::setOffsprgNeiGeneticDistance );
 
  sub_name = prefix + "D";
  add("Average between pop Nei's D", sub_name,  AGE, 0, 0,
      &TTNeutralGenesSH::getMeanNeiGeneticDistance, 0, 0, setter);
 
  if(pairwise) {
 
    for(unsigned int i = 0; i < nbpatch -1; i++){
      for(unsigned int j = i+1; j < nbpatch; j++) {
        name = "Nei's D between pop" + tstring::int2str(i+1) + " and pop" + tstring::int2str(j+1);
        sub_name = prefix + "D.p" + tstring::int2str(i+1) + "p" + tstring::int2str(j+1);
        add(name, sub_name,  AGE, i*scale + j, 0, 0, &TTNeutralGenesSH::getNeiGeneticDistance, 0, 0);
      }
    }
  }
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADULTS, getMeanNeiGeneticDistance(), getNeiGeneticDistance(), Metapop::getPatchNbr(), tstring::int2str(), setAdltNeiGeneticDistance(), and setOffsprgNeiGeneticDistance().

Referenced by setStatRecorders().

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setOffsprgCoaBetween()

void TTNeutralGenesSH::setOffsprgCoaBetween ( )

inline

{setCoaMatrix(OFFSx, 2);}

References OFFSx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setOffsprgCoaMatrix()

void TTNeutralGenesSH::setOffsprgCoaMatrix ( )

inline

{setCoaMatrix(OFFSx, 3);}

References OFFSx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setOffsprgCoaWithin()

void TTNeutralGenesSH::setOffsprgCoaWithin ( )

inline

{setCoaMatrix(OFFSx, 1);}

References OFFSx, and setCoaMatrix().

Referenced by setCoaMatrixRecorders(), and setStatRecorders().

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setOffsprgFstat()

void TTNeutralGenesSH::setOffsprgFstat ( )

inline

{setFstat(OFFSPRG);}

References OFFSPRG, and setFstat().

Referenced by setFstatRecorders().

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setOffsprgFstat2()

void TTNeutralGenesSH::setOffsprgFstat2 ( )

inline

{setFstat2(OFFSPRG);}

References OFFSPRG, and setFstat2().

Referenced by setFstat2Recorders().

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setOffsprgFstBetween()

void TTNeutralGenesSH::setOffsprgFstBetween ( )

inline

{setFstMatrix(OFFSPRG, 2);}

References OFFSPRG, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setOffsprgFstMatrix()

void TTNeutralGenesSH::setOffsprgFstMatrix ( )

inline

{setFstMatrix(OFFSPRG, 3);}

References OFFSPRG, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setOffsprgFstWithin()

void TTNeutralGenesSH::setOffsprgFstWithin ( )

inline

{setFstMatrix(OFFSPRG, 1);}

References OFFSPRG, and setFstMatrix().

Referenced by setFstMatrixRecorders().

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setOffsprgNeiGeneticDistance()

void TTNeutralGenesSH::setOffsprgNeiGeneticDistance ( )

inline

{setNeiGeneticDistance(OFFSPRG);}

References OFFSPRG, and setNeiGeneticDistance().

Referenced by setNeiGeneticDistanceRecorders().

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setOffspringAlleleFreq()

void TTNeutralGenesSH::setOffspringAlleleFreq ( )

inline

{setAlleleTables(OFFSPRG);}\

References OFFSPRG, and setAlleleTables().

Referenced by setFreqRecorders().

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setOffspringFstatWeirCockerham()

void TTNeutralGenesSH::setOffspringFstatWeirCockerham ( )

inline

{setFstatWeirCockerham(OFFSPRG);}

References OFFSPRG, and setFstatWeirCockerham().

Referenced by setFstatWCRecorders().

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setOffspringHeterozygosity()

void TTNeutralGenesSH::setOffspringHeterozygosity ( )

inline

{setHeterozygosity(OFFSPRG);}

References OFFSPRG, and setHeterozygosity().

Referenced by setFreqRecorders().

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setSibCoa()

void TTNeutralGenesSH::setSibCoa	(	Individual *	I1,
		Individual *	I2
	)

{
  unsigned int nb_locus = this->_SHLinkedTrait->get_locus_num();
  //non sibs [3]
  if((I1->getMotherID() != I2->getMotherID()) && (I1->getFatherID() != I2->getFatherID())) {
    _sib_prop[3]++;
    _sib_coa[3] += Coancestry(I1->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              I2->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              nb_locus);
  }
  //maternal half sibs [2]
  else if((I1->getMotherID() == I2->getMotherID()) && (I1->getFatherID() != I2->getFatherID())) {
    _sib_prop[2]++;
    _sib_coa[2] += Coancestry(I1->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              I2->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              nb_locus);
  }
  //paternal half sibs [1]
  else if((I1->getMotherID() != I2->getMotherID()) && (I1->getFatherID() == I2->getFatherID())) {
    _sib_prop[1]++;
    _sib_coa[1] += Coancestry(I1->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              I2->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              nb_locus);
  }
  //full sibs [0]
  else if((I1->getMotherID() == I2->getMotherID()) && (I1->getFatherID() == I2->getFatherID())) {
    _sib_prop[0]++;
    _sib_coa[0] += Coancestry(I1->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              I2->getTrait(_SHLinkedTraitIndex)->get_sequence(),
                              nb_locus);
  }
}  

References TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTrait, TraitStatHandler< TProtoNeutralGenes, TTNeutralGenesSH >::_SHLinkedTraitIndex, _sib_coa, _sib_prop, Coancestry(), TProtoNeutralGenes::get_locus_num(), TTrait::get_sequence(), Individual::getFatherID(), Individual::getMotherID(), and Individual::getTrait().

Referenced by setSibStats().

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setSibStats()

void TTNeutralGenesSH::setSibStats

(

)

{
  unsigned int i,j,k;
  unsigned int patchNbr = this->_pop->getPatchNbr(), Fsize, Msize;
  Patch* current_patch;
  Individual *I1, *I2;
  
  for(i = 0;i < 4; ++i) {
    _sib_prop[i] = 0.0;
    _sib_coa[i] = 0.0;
  }
  
  for( i = 0; i < patchNbr; ++i) {
    
    current_patch = _pop->getPatch(i);
    
    if ( (Fsize = current_patch->size(FEM, OFFSx)) != 0) {
      
      for(j = 0; j < Fsize -1; ++j) {
        
        I1 = current_patch->get(FEM, OFFSx, j);
        
        for(k = j+1; k < Fsize; ++k) {
          
          I2 = current_patch->get(FEM, OFFSx, k);
          
          setSibCoa(I1, I2);
        }
      }
    }
    
    if ( (Msize = current_patch->size(MAL, OFFSx)) != 0) {
      
      for(j = 0; j < Msize -1; ++j) {
        
        I1 = current_patch->get(MAL, OFFSx, j);
        
        for(k = j+1; k < Msize; ++k) {
          
          I2 = current_patch->get(MAL, OFFSx, k);
          
          setSibCoa(I1, I2);
        }
      }
    }
    
    //male-female
    for(j = 0; j < Msize; ++j) {
      
      I1 = current_patch->get(MAL, OFFSx, j);
      
      for(k = 0; k < Fsize; ++k) {
        
        I2 = current_patch->get(FEM, OFFSx, k);
        
        setSibCoa(I1, I2);
      }
    }
    
  }
  
  double tot = _sib_prop[0] + _sib_prop[1] + _sib_prop[2] + _sib_prop[3];
  
  for(i = 0 ; i < 4; ++i) {
    _sib_coa[i] = ( (_sib_prop[i] != 0) ? _sib_coa[i]/_sib_prop[i] : nanf("NULL"));
    _sib_prop[i] /= tot;
  }
}

References StatHandlerBase::_pop, _sib_coa, _sib_prop, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, OFFSx, setSibCoa(), and Patch::size().

Referenced by setStatRecorders().

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setStatRecorders()

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

virtual

Implements StatHandlerBase.

{
#ifdef _DEBUG_
  message("-TTNeutralGenesSH::setStatRecorders ");
#endif
  if(token.compare("coa") == 0) {
 
    add("Wtn Patch Coancestry (offsprg)","off.theta",OFFSPRG,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setOffsprgCoaMatrix);
    add("Btn Patch Coancestry (offsprg)","off.alpha",OFFSPRG,0,0,&TTNeutralGenesSH::getMeanAlpha,0,0,0);
 
    add("Wtn Patch Coancestry   (adult)","adlt.theta",ADULTS,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setAdultsCoaMatrix);
    add("Btn Patch Coancestry   (adult)","adlt.alpha",ADULTS,0,0,&TTNeutralGenesSH::getMeanAlpha,0,0,0);
 
  } else if(token.compare("adlt.coa") == 0) {
 
    add("Wtn Patch Coancestry   (adult)","adlt.theta",ADULTS,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setAdultsCoaMatrix);
    add("Btn Patch Coancestry   (adult)","adlt.alpha",ADULTS,0,0,&TTNeutralGenesSH::getMeanAlpha,0,0,0);
 
  } else if(token.compare("off.coa") == 0) {
 
    add("Wtn Patch Coancestry (offsprg)","off.theta",OFFSPRG,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setOffsprgCoaMatrix);
    add("Btn Patch Coancestry (offsprg)","off.alpha",OFFSPRG,0,0,&TTNeutralGenesSH::getMeanAlpha,0,0,0);
 
  } else if(token.compare("adlt.coa.persex") == 0) {
 
    add("Female Theta      (adult)","adlt.theta",ADULTS,0,0,
        &TTNeutralGenesSH::getMeanTheta, 0, 0, &TTNeutralGenesSH::setAdults_Theta);
    add("Female Theta      (adult)","adlt.thetaFF",ADULTS,0,0,&TTNeutralGenesSH::getTheta_FF,0,0,0);
    add("Male Theta        (adult)","adlt.thetaMM",ADULTS,0,0,&TTNeutralGenesSH::getTheta_MM,0,0,0);
    add("Female-Male Theta (adult)","adlt.thetaFM",ADULTS,0,0,&TTNeutralGenesSH::getTheta_FM,0,0,0);
 
  } else if(token.compare("adlt.coa.within") == 0) {
 
    add("Wtn Patch Coancestry   (adult)","adlt.theta",ADULTS,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setAdultsCoaWithin);
 
  } else if(token.compare("off.coa.within") == 0) {
 
    add("Wtn Patch Coancestry (offsprg)","off.theta",OFFSPRG,0,0,
        &TTNeutralGenesSH::getMeanTheta,0,0,&TTNeutralGenesSH::setOffsprgCoaWithin);
 
  } else if(token.compare("adlt.coa.between") == 0) {
 
    add("Btn Patch Coancestry   (adult)","adlt.alpha",ADULTS,0,0,
        &TTNeutralGenesSH::getMeanAlpha,0,0,&TTNeutralGenesSH::setAdultsCoaBetween);
 
  } else if(token.compare("off.coa.between") == 0) {
 
    add("Btn Patch Coancestry (offsprg)","off.alpha",OFFSPRG,0,0,
        &TTNeutralGenesSH::getMeanAlpha,0,0,&TTNeutralGenesSH::setOffsprgCoaBetween);
 
  } else if(token.compare("coa.matrix") == 0) {
 
    setCoaMatrixRecorders(OFFSPRG, 3);
    setCoaMatrixRecorders(ADULTS, 3);
 
  } else if(token.compare("off.coa.matrix") == 0) {
 
    setCoaMatrixRecorders(OFFSPRG, 3);
 
  } else if(token.compare("adlt.coa.matrix") == 0) {
 
    setCoaMatrixRecorders(ADULTS, 3);
 
  } else if(token.compare("coa.matrix.within") == 0) {
 
    setCoaMatrixRecorders(OFFSPRG, 1);
    setCoaMatrixRecorders(ADULTS, 1);
 
  } else if(token.compare("off.coa.matrix.within") == 0) {
 
    setCoaMatrixRecorders(OFFSPRG, 1);
 
  } else if(token.compare("adlt.coa.matrix.within") == 0) {
 
    setCoaMatrixRecorders(ADULTS, 1);
 
  } else if(token.compare("sibcoa") == 0) {
 
    add("Proportion of full-sib offspring","prop.fsib",OFFSPRG,0,0,
        0,&TTNeutralGenesSH::getSibProportions,0,&TTNeutralGenesSH::setSibStats);
    add("Proportion of paternal half-sib ","prop.phsib",OFFSPRG,1,0,0,&TTNeutralGenesSH::getSibProportions,0,0);
    add("Proportion of maternal half-sib ","prop.mhsib",OFFSPRG,2,0,0, &TTNeutralGenesSH::getSibProportions,0,0);
    add("Proportion of non-sib offspring ","prop.nsib",OFFSPRG,3,0,0,&TTNeutralGenesSH::getSibProportions,0,0);
    add("Coancestry of full-sib offspring","coa.fsib",OFFSPRG,0,0,0,&TTNeutralGenesSH::getSibCoaMeans,0,0);
    add("Coancestry of paternal half-sib ","coa.phsib",OFFSPRG,1,0,0,&TTNeutralGenesSH::getSibCoaMeans,0,0);
    add("Coancestry of maternal half-sib ","coa.mhsib",OFFSPRG,2,0,0,&TTNeutralGenesSH::getSibCoaMeans,0,0);
    add("Coancestry of non-sib offspring ","coa.nsib",OFFSPRG,3,0,0,&TTNeutralGenesSH::getSibCoaMeans,0,0);
 
  } else if (token == "ntrl.freq") {
 
    setFreqRecorders(OFFSPRG);
    setFreqRecorders(ADULTS);
 
  } else if (token == "off.ntrl.freq") {
 
    setFreqRecorders(OFFSPRG);
 
  } else if (token == "adlt.ntrl.freq") {
 
    setFreqRecorders(ADULTS);
 
    //  } else if (token == "ntrl.freq.patch") {
    //
    //    setFreqRecordersPerPatch(ALL);
    //
    //  } else if (token == "off.ntrl.freq.patch") {
    //
    //    setFreqRecordersPerPatch(OFFSPRG);
    //
    //  } else if (token == "adlt.ntrl.freq.patch") {
    //
    //    setFreqRecordersPerPatch(ADULTS);
 
  } else if(token.compare("offsprgfstat") == 0 || token.compare("off.fstat") == 0) {
 
    setFstatRecorders(OFFSPRG);
 
  } else if(token.compare("adultfstat") == 0 || token.compare("adlt.fstat") == 0) {
 
    setFstatRecorders(ADULTS);
 
  } else if(token.compare("fstat") == 0) {
 
    setFstatRecorders(ALL);
 
  } else if(token == "off.fstat2") {
 
    setFstat2Recorders(OFFSPRG);
 
  } else if(token == "adlt.fstat2") {
 
    setFstat2Recorders(ADULTS);
 
  } else if(token == "fstat2") {
 
    setFstat2Recorders(ALL);
 
  } else if(token.compare("fstWC") == 0 || token.compare("fstatWC") == 0) {
 
    setFstatWCRecorders(ALL);
 
  } else if(token.compare("off.fstWC") == 0 || token.compare("off.fstatWC") == 0) {
 
    setFstatWCRecorders(OFFSPRG);
 
  } else if(token.compare("adlt.fstWC") == 0 || token.compare("adlt.fstatWC") == 0) {
 
    setFstatWCRecorders(ADULTS);
 
  } else if(token.compare("weighted.fst") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 0);
    setFstMatrixRecorders(ADULTS, 0);
 
  } else if(token.compare("off.weighted.fst") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 0);
 
  } else if(token.compare("adlt.weighted.fst") == 0) {
 
    setFstMatrixRecorders(ADULTS, 0);
 
  } else if(token.compare("weighted.fst.matrix") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 3);
    setFstMatrixRecorders(ADULTS, 3);
 
  } else if(token.compare("off.weighted.fst.matrix") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 3);
 
  } else if(token.compare("adlt.weighted.fst.matrix") == 0) {
 
    setFstMatrixRecorders(ADULTS, 3);
 
  } else if(token.compare("weighted.fst.within") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 1);
    setFstMatrixRecorders(ADULTS, 1);
 
  } else if(token.compare("off.weighted.fst.within") == 0) {
 
    setFstMatrixRecorders(OFFSPRG, 1);
 
  } else if(token.compare("adlt.weighted.fst.within") == 0) {
 
    setFstMatrixRecorders(ADULTS, 1);
 
  } else if(token.compare("adlt.NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(ADULTS, true);
 
  } else if(token.compare("off.NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(OFFSPRG, true);
 
  } else if(token.compare("NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(ADULTS, true);
    setNeiGeneticDistanceRecorders(OFFSPRG, true);
 
  } else if(token.compare("mean.NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(ADULTS, false);
    setNeiGeneticDistanceRecorders(OFFSPRG, false);
 
  } else if(token.compare("adlt.mean.NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(ADULTS, false);
 
  } else if(token.compare("off.mean.NeiDistance") == 0) {
 
    setNeiGeneticDistanceRecorders(OFFSPRG, false);
 
  } else if(token.compare("Dxy") == 0) {
 
    setDxyRecorders(ADULTS, false);
    setDxyRecorders(OFFSPRG, false);
 
  } else if(token.compare("off.Dxy") == 0) {
 
    setDxyRecorders(OFFSPRG, false);
 
  } else if(token.compare("adlt.Dxy") == 0) {
 
    setDxyRecorders(ADULTS, false);
 
  } else if(token.compare("Dxy.patch") == 0) {
 
    setDxyRecorders(ADULTS, true);
    setDxyRecorders(OFFSPRG, true);
 
  } else if(token.compare("off.Dxy.patch") == 0) {
 
    setDxyRecorders(OFFSPRG, true);
 
  } else if(token.compare("adlt.Dxy.patch") == 0) {
 
    setDxyRecorders(ADULTS, true);
 
  } else
    return false;
 
  return true;
}

References StatHandler< SH >::add(), ADULTS, ALL, getMeanAlpha(), getMeanTheta(), getSibCoaMeans(), getSibProportions(), getTheta_FF(), getTheta_FM(), getTheta_MM(), message(), OFFSPRG, setAdults_Theta(), setAdultsCoaBetween(), setAdultsCoaMatrix(), setAdultsCoaWithin(), setCoaMatrixRecorders(), setDxyRecorders(), setFreqRecorders(), setFstat2Recorders(), setFstatRecorders(), setFstatWCRecorders(), setFstMatrixRecorders(), setNeiGeneticDistanceRecorders(), setOffsprgCoaBetween(), setOffsprgCoaMatrix(), setOffsprgCoaWithin(), and setSibStats().

Member Data Documentation

_alleleCountTable

DataTable< unsigned int > TTNeutralGenesSH::_alleleCountTable

private

Referenced by allocateTables(), getAlleleCountTable(), setAlleleTables(), setFstat(), setFstat2(), setFstatWeirCockerham_MS(), and setLociDivCounter().

_alleleFreqTable

DataTable< double > TTNeutralGenesSH::_alleleFreqTable

private

Referenced by allocateTables(), getAlleleFreqTable(), setAlleleTables(), setFst_li(), setFstatWeirCockerham(), setFstatWeirCockerham_MS(), setFstMatrix(), setHs(), setHs2(), setLociDivCounter(), and setNeiGeneticDistance().

_coa_matrix

TMatrix* TTNeutralGenesSH::_coa_matrix

private

Referenced by getCoa(), setCoaMatrix(), and ~TTNeutralGenesSH().

_D

TMatrix* TTNeutralGenesSH::_D

private

Referenced by getNeiGeneticDistance(), setNeiGeneticDistance(), and ~TTNeutralGenesSH().

_fis

double TTNeutralGenesSH::_fis

private

Referenced by getFis(), setFstat(), and setFstat2().

_fis_WC

double TTNeutralGenesSH::_fis_WC

private

Referenced by getFisWC(), setFstatWeirCockerham(), and setFstatWeirCockerham_MS().

_fis_WC_loc

double * TTNeutralGenesSH::_fis_WC_loc

private

Referenced by setFstatWeirCockerham_MS(), and ~TTNeutralGenesSH().

_fit

double TTNeutralGenesSH::_fit

private

Referenced by getFit(), setFstat(), and setFstat2().

_fit_WC

double TTNeutralGenesSH::_fit_WC

private

Referenced by getFitWC(), setFstatWeirCockerham(), and setFstatWeirCockerham_MS().

_fit_WC_loc

double * TTNeutralGenesSH::_fit_WC_loc

private

Referenced by setFstatWeirCockerham_MS(), and ~TTNeutralGenesSH().

_fix_loc_global

double TTNeutralGenesSH::_fix_loc_global

private

Referenced by getFixLocGlobal(), and setLociDivCounter().

_fix_loc_local

double TTNeutralGenesSH::_fix_loc_local

private

Referenced by getFixLocLocal(), and setLociDivCounter().

_fst

double TTNeutralGenesSH::_fst

private

Referenced by getFst(), setFstat(), and setFstat2().

_fst_matrix

TMatrix* TTNeutralGenesSH::_fst_matrix

private

Pairwise Fst matrix.

Referenced by getFst_ij(), setFstMatrix(), and ~TTNeutralGenesSH().

_fst_W1

double TTNeutralGenesSH::_fst_W1

private

_fst_W2

double TTNeutralGenesSH::_fst_W2

private

_fst_WC

double TTNeutralGenesSH::_fst_WC

private

Weir & Cockerham (1984) F-stat estimates.

Referenced by getFstWC(), setFstatWeirCockerham(), and setFstatWeirCockerham_MS().

_fst_WC_loc

double* TTNeutralGenesSH::_fst_WC_loc

private

Per-locus F-stats (Weir&Cockerham).

Referenced by setFstatWeirCockerham_MS(), and ~TTNeutralGenesSH().

_fst_WH

double TTNeutralGenesSH::_fst_WH

private

Weir & Hill (2002) F-stat estimates.

Referenced by getWeightedFst(), and setFstMatrix().

_globalAlleleFreq

TMatrix TTNeutralGenesSH::_globalAlleleFreq

private

Referenced by allocateTables(), getGlobalAlleleFreq(), getGlobalFreqs(), setAlleleTables(), setFst_li(), setFstatWeirCockerham(), setFstatWeirCockerham_MS(), setFstMatrix(), setHt(), setHt2(), and setLociDivCounter().

_heteroTable

DataTable< double > TTNeutralGenesSH::_heteroTable

private

Referenced by getHeteroTable(), getHeterozygosity(), setFstatWeirCockerham(), setFstatWeirCockerham_MS(), setHeteroTable(), and setHeterozygosity().

_ho

double TTNeutralGenesSH::_ho

private

F-statistics.

Referenced by getHo(), setFstat(), and setFstat2().

_hs

double TTNeutralGenesSH::_hs

private

Referenced by getHs(), and setFstat().

_hsnei

double TTNeutralGenesSH::_hsnei

private

Referenced by getHsnei(), setFstat(), and setFstat2().

_ht

double TTNeutralGenesSH::_ht

private

Referenced by getHt(), and setFstat().

_htnei

double TTNeutralGenesSH::_htnei

private

Referenced by getHtnei(), setFstat(), and setFstat2().

_mean_alpha

double TTNeutralGenesSH::_mean_alpha

private

Referenced by getMeanAlpha(), and setCoaMatrix().

_mean_theta

double TTNeutralGenesSH::_mean_theta

private

Referenced by getMeanTheta(), setAdults_Theta(), and setCoaMatrix().

_meanD

double TTNeutralGenesSH::_meanD

private

Referenced by getMeanNeiGeneticDistance(), and setNeiGeneticDistance().

_nb_all_global

double TTNeutralGenesSH::_nb_all_global

private

Referenced by getNbAllGlobal(), and setLociDivCounter().

_nb_all_local

double TTNeutralGenesSH::_nb_all_local

private

Referenced by getNbAllLocal(), and setLociDivCounter().

_sib_coa

double TTNeutralGenesSH::_sib_coa[4]

private

Referenced by getSibCoaMeans(), setSibCoa(), and setSibStats().

_sib_prop

double TTNeutralGenesSH::_sib_prop[4]

private

Kinship classes proportions.

Referenced by getSibProportions(), setSibCoa(), and setSibStats().

_table_set_age

unsigned int TTNeutralGenesSH::_table_set_age

private

Referenced by allocateTables(), and setAlleleTables().

_table_set_gen

unsigned int TTNeutralGenesSH::_table_set_gen

private

Referenced by allocateTables(), and setAlleleTables().

_table_set_repl

unsigned int TTNeutralGenesSH::_table_set_repl

private

Referenced by allocateTables(), and setAlleleTables().

Theta_FF

double TTNeutralGenesSH::Theta_FF

private

Referenced by getTheta_FF(), and setAdults_Theta().

Theta_FM

double TTNeutralGenesSH::Theta_FM

private

Referenced by getTheta_FM(), and setAdults_Theta().

Theta_MM

double TTNeutralGenesSH::Theta_MM

private

Referenced by getTheta_MM(), and setAdults_Theta().

---

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

• ttneutralgenes.h
• stats_coa.cc
• stats_fstat.cc
• ttneutralgenes.cc