Species< Model > Class Template Reference

#include <species.h>

Inheritance diagram for Species< Model >:

Collaboration diagram for Species< Model >:

Public Member Functions
	Species (std::vector< double > breaks=std::vector< double >())
	Species (Model M)
void	resize (int _J)
double	get_maxSize ()
void	print ()
void	set_xb (double _xb)
void	set_ub (double _ub)
void	set_birthTime (int i, double t0)
void	setX (int i, double _x)
void	setU (int i, double _u)
double	getX (int i)
double	getU (int i)
double	init_density (int i, double x, void *env)
void	initAndCopyExtraState (double t, void *env, std::vector< double >::iterator &it)
void	initBoundaryCohort (double t, void *env)
void	copyExtraStateToCohorts (std::vector< double >::iterator &it)
void	copyCohortsExtraToState (std::vector< double >::iterator &it)
double	establishmentProbability (double t, void *env)
double	calc_boundary_u (double gb, double pe)
double	get_boundary_u ()
void	triggerPreCompute ()
double	growthRate (int i, double x, double t, void *env)
double	growthRateOffset (int i, double x, double t, void *env)
std::vector< double >	growthRateGradient (int i, double x, double t, void *env, double grad_dx)
std::vector< double >	growthRateGradientCentered (int i, double xplus, double xminus, double t, void *env)
double	mortalityRate (int i, double x, double t, void *env)
std::vector< double >	mortalityRateGradient (int i, double x, double t, void *env, double grad_dx)
double	birthRate (int i, double x, double t, void *env)
void	getExtraRates (std::vector< double >::iterator &it)
void	addCohort ()
void	addCohort (Cohort< Model > bc)
void	removeDensestCohort ()
void	removeDenseCohorts (double dxcut)
void	removeDeadCohorts (double ucut)
Cohort< Model > &	getCohort (int i)
Public Member Functions inherited from Species_Base
virtual	~Species_Base ()=0
int	xsize ()
int	size ()
void	set_inputBirthFlux (double b)
void	set_bfin_is_u0in (bool flag)
template<class T >
void	addCohort (T bc)

Protected Attributes
std::vector< Cohort< Model > >	cohorts
Cohort< Model >	boundaryCohort
Cohort< Model >	savedCohort
Protected Attributes inherited from Species_Base
int	J
int	n_extra_statevars = 0
std::list< double >	birth_flux_out_history
std::vector< double >	X
std::vector< double >	x
std::vector< double >	h
std::vector< double >	schedule

Additional Inherited Members
Public Attributes inherited from Species_Base
double	birth_flux_in
bool	bfin_is_u0in = false
double	xb
bool	is_resident

Detailed Description

template<class Model>
class Species< Model >

Definition at line 107 of file species.h.

Constructor & Destructor Documentation

Species() [1/2]

template<class Model >

Species< Model >::Species

(

std::vector< double >

breaks = std::vector<double>()

)

Definition at line 36 of file species.tpp.

                                               {
    J = breaks.size(); // changes with 
    cohorts.resize(J, boundaryCohort);
    for (int i=0; i<J; ++i) cohorts[i].x = breaks[i];   
}

Species() [2/2]

template<class Model >

Species< Model >::Species

(

Model

M

)

Definition at line 44 of file species.tpp.

                              {
    boundaryCohort = savedCohort = Cohort<Model>(M); 
}

Member Function Documentation

addCohort() [1/2]

template<class Model >

void Species< Model >::addCohort ( )

virtual

Implements Species_Base.

Definition at line 305 of file species.tpp.

                              {
    cohorts.push_back(boundaryCohort);
    ++J;
}

addCohort() [2/2]

template<class Model >

void Species< Model >::addCohort

(

Cohort< Model >

bc

)

Definition at line 315 of file species.tpp.

                                              {
    cohorts.push_back(bc);
    ++J;
    // FIXME: add option to sort cohorts here.
}

birthRate()

template<class Model >

double Species< Model >::birthRate ( int  i, double  x, double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 292 of file species.tpp.

                                                                     {
    Cohort<Model> &c = (i<0)? boundaryCohort : cohorts[i];
    return c.birthRate(c.x,t,env);
}

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calc_boundary_u()

template<class Model >

double Species< Model >::calc_boundary_u ( double  gb, double  pe  )

virtual

Implements Species_Base.

Definition at line 205 of file species.tpp.

                                                          {
    std::cout << "calc_boundary_u\n";
    if (bfin_is_u0in){
        boundaryCohort.u = birth_flux_in;
    }
    else {
        boundaryCohort.u = (gb>0)? birth_flux_in * pe/gb  :  0; 
    }
    return boundaryCohort.u;
}

copyCohortsExtraToState()

template<class Model >

void Species< Model >::copyCohortsExtraToState ( std::vector< double >::iterator &  it )

virtual

Implements Species_Base.

Definition at line 185 of file species.tpp.

                                                                         {
    for (auto& c : cohorts) c.get_state(it);
}

copyExtraStateToCohorts()

template<class Model >

void Species< Model >::copyExtraStateToCohorts ( std::vector< double >::iterator &  it )

virtual

Implements Species_Base.

Definition at line 179 of file species.tpp.

                                                                         {
    for (auto& c : cohorts) c.set_state(it);
}

establishmentProbability()

template<class Model >

double Species< Model >::establishmentProbability ( double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 198 of file species.tpp.

                                                                   {
    return boundaryCohort.establishmentProbability(t, env);
}

get_boundary_u()

template<class Model >

double Species< Model >::get_boundary_u ( )

virtual

Implements Species_Base.

Definition at line 113 of file species.tpp.

                                     {
    return boundaryCohort.u;
}

get_maxSize()

template<class Model >

double Species< Model >::get_maxSize ( )

virtual

Implements Species_Base.

Definition at line 25 of file species.tpp.

                                  { // TODO ALERT: make sure this sees the latest state
    if (!X.empty()) return *x.rbegin(); // for FMU, get this from X
    else if (cohorts.empty()) return 0;
    else {                              // else get from state vector
        return cohorts[0].x;            // cohorts are sorted descending
    }
}

getCohort()

template<class Model >

Cohort< Model > & Species< Model >::getCohort

(

int

i

)

Definition at line 94 of file species.tpp.

                                             {
    if (i == -1) return boundaryCohort;
    else return cohorts[i];
}

getExtraRates()

template<class Model >

void Species< Model >::getExtraRates ( std::vector< double >::iterator &  it )

virtual

Implements Species_Base.

Definition at line 299 of file species.tpp.

                                                               {
    for (auto& c : cohorts) c.get_rates(it);
}

getU()

template<class Model >

double Species< Model >::getU ( int  i )

virtual

Implements Species_Base.

Definition at line 107 of file species.tpp.

                                {
    return cohorts[i].u;
}

getX()

template<class Model >

double Species< Model >::getX ( int  i )

virtual

Implements Species_Base.

Definition at line 100 of file species.tpp.

                                {
    if (i == -1) return boundaryCohort.x;
    else return cohorts[i].x;
}

growthRate()

template<class Model >

double Species< Model >::growthRate ( int  i, double  x, double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 218 of file species.tpp.

                                                                      {
    Cohort<Model> &c = (i<0)? boundaryCohort : cohorts[i];
    return c.growthRate(c.x,t,env);
}

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growthRateGradient()

template<class Model >

std::vector< double > Species< Model >::growthRateGradient ( int  i, double  x, double  t, void *  env, double  grad_dx  )

virtual

Implements Species_Base.

Definition at line 235 of file species.tpp.

                                                                                                         {
    Cohort<Model> &c = (i<0)? boundaryCohort : cohorts[i];

    Cohort<Model> cplus = c;
    cplus.set_size(c.x + grad_dx);
    //cplus.preCompute(cplus.x,t,env);
    
    double g = c.growthRate(c.x,t,env);
    double gplus = cplus.growthRate(cplus.x, t, env);

    return {g, (gplus-g)/grad_dx};
}

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growthRateGradientCentered()

template<class Model >

std::vector< double > Species< Model >::growthRateGradientCentered ( int  i, double  xplus, double  xminus, double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 250 of file species.tpp.

                                                                                                                    {
    assert(i>=0);

    Cohort<Model> cplus = cohorts[i];
    cplus.set_size(xplus);
    //cplus.preCompute(cplus.x,t,env);

    Cohort<Model> cminus = cohorts[i];
    cminus.set_size(xminus);
    //cminus.preCompute(cminus.x,t,env);
    
    double gplus  = cplus.growthRate(cplus.x, t, env);
    double gminus = cminus.growthRate(cminus.x, t, env);
    
    return {gplus, gminus};
}

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growthRateOffset()

template<class Model >

double Species< Model >::growthRateOffset ( int  i, double  x, double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 225 of file species.tpp.

                                                                            {
    Cohort<Model> coff = (i<0)? boundaryCohort : cohorts[i];
    coff.set_size(x);
    //coff.preCompute(coff.x,t,env);

    return coff.growthRate(coff.x,t,env);
}

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init_density()

template<class Model >

double Species< Model >::init_density ( int  i, double  x, void *  env  )

virtual

Implements Species_Base.

Definition at line 173 of file species.tpp.

                                                                {
    return cohorts[i].init_density(_x, _env, birth_flux_in);
}

initAndCopyExtraState()

template<class Model >

void Species< Model >::initAndCopyExtraState ( double  t, void *  env, std::vector< double >::iterator &  it  )

virtual

Implements Species_Base.

Definition at line 152 of file species.tpp.

                                                                                             {
    // init boundary cohort (no copy required)
    boundaryCohort.init_state(t, env); 
    // init internal cohorts and copy to state vector
    for (auto& c : cohorts){
        c.init_state(t, env);   // init state
        auto it_prev = it;      
        it = c.get_state(it);   // copy the initialized state into state vector
        assert(distance(it_prev, it) == n_extra_statevars);
    }
}

initBoundaryCohort()

template<class Model >

void Species< Model >::initBoundaryCohort ( double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 166 of file species.tpp.

                                                           {
    boundaryCohort.birth_time = t;
    boundaryCohort.init_state(t, env);
}

mortalityRate()

template<class Model >

double Species< Model >::mortalityRate ( int  i, double  x, double  t, void *  env  )

virtual

Implements Species_Base.

Definition at line 269 of file species.tpp.

                                                                         {
    assert(i>=0);
    Cohort<Model> &c = cohorts[i];
    return c.mortalityRate(c.x,t,env);
}

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mortalityRateGradient()

template<class Model >

std::vector< double > Species< Model >::mortalityRateGradient ( int  i, double  x, double  t, void *  env, double  grad_dx  )

virtual

Implements Species_Base.

Definition at line 277 of file species.tpp.

                                                                                                            {
    Cohort<Model> &c = (i<0)? boundaryCohort : cohorts[i];

    Cohort<Model> cplus = c;
    cplus.set_size(x + grad_dx);
    //cplus.preCompute(cplus.x,t,env);
    
    double g = c.mortalityRate(c.x,t,env);
    double gplus = cplus.mortalityRate(cplus.x, t, env);
    
    return {g, (gplus-g)/grad_dx};
}

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print()

template<class Model >

void Species< Model >::print ( )

virtual

Implements Species_Base.

Definition at line 50 of file species.tpp.

                          {
    std::cout << "~~~~~ Species ~~~~~\n";
    //auto iset = get_iterators(sv);
    //std::cout << "start index = " << start_index <<"\n";
    //std::cout << "Model = " << mod << "\n";
    std::cout << "xb = " << boundaryCohort.x << " / " << xb << "\n";
    std::cout << "xsize = " << J << "\n";
    std::cout << "Extra state variables: " << n_extra_statevars << "\n";
    std::cout << "Input birth flux = " << birth_flux_in << "\n";
    //if (!X.empty()){
    //    iset.push_back("_X", X.begin(),1);
    //    iset.push_back("_h", h.begin(),1);
    std::cout << "x (" << x.size() << "): "; 
    for (auto xx : x) std::cout << xx << " ";
    std::cout << "\n";
    //}

    std::cout << "Cohorts: (" << cohorts.size() << ")\n";
    std::cout << "t0" << "\tx" << "\t" << "u" << "\t";
    if (!cohorts.empty()){
        for (auto s : cohorts[0].varnames) std::cout << s << "\t";
    }
    std::cout << "\n";
    for (auto& c : cohorts) {
        //c.print_xu(); //std::cout << c.x << "\t" << c.u << "\t";
        c.print();
        std::cout << "\n";
    }
    std::cout << "- - - - - - - - - - - - - - - - - - - - - - - \n";
    //boundaryCohort.print_xu(); //std::cout << c.x << "\t" << c.u << "\t";
    boundaryCohort.print();
    std::cout << "\n";
    std::cout << "Max size = " << get_maxSize() << "\n";
    //std::cout << "State (" << size() << "):\n";
    //iset.print();
    
    //std::cout << "Rates (" << size() << "):\n";
    //auto irates = get_iterators(rv);
    //irates.print();
    std::cout << "-------\n\n"; std::cout.flush();

}

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removeDeadCohorts()

template<class Model >

void Species< Model >::removeDeadCohorts ( double  ucut )

virtual

Implements Species_Base.

Definition at line 360 of file species.tpp.

                                                 {
    // mark cohorts to remove; skip pi0-cohort (index J-1)
    for (int i=0; i<J-1; ++i){
        if (cohorts[i].u < ucut) cohorts[i].remove = true;
    }

    // remove marked cohorts
    auto it_end = std::remove_if(cohorts.begin(), cohorts.end(), [](Cohort<Model> &c){return c.remove;});
    cohorts.erase(it_end, cohorts.end());

    // reset size
    J = cohorts.size();
}

removeDenseCohorts()

template<class Model >

void Species< Model >::removeDenseCohorts ( double  dxcut )

virtual

Implements Species_Base.

Definition at line 341 of file species.tpp.

                                                   {
    // mark cohorts to remove; skip 1st and last cohort
    for (int i=1; i<J-1; i+=2){
        double dx_lo = cohorts[i-1].x-cohorts[i].x;
        double dx_hi = cohorts[i].x-cohorts[i+1].x;

        if (dx_lo < dxcut || dx_hi < dxcut) cohorts[i].remove = true;
    }

    // remove marked cohorts
    auto it_end = std::remove_if(cohorts.begin(), cohorts.end(), [](Cohort<Model> &c){return c.remove;});
    cohorts.erase(it_end, cohorts.end());

    // reset size
    J = cohorts.size();
}

removeDensestCohort()

template<class Model >

void Species< Model >::removeDensestCohort ( )

virtual

Implements Species_Base.

Definition at line 323 of file species.tpp.

                                        {
    if (cohorts.size() < 3) return; // do nothing if there are 2 or fewer cohorts
    int i_min = 1;
    double dx_min = cohorts[0].x - cohorts[2].x;  
    for (int i=1; i<J-1; ++i){ // skip first and last cohorts
        double dx = cohorts[i-1].x - cohorts[i+1].x;
        if (dx < dx_min){
            dx_min = dx;
            i_min = i;
        }
    }

    cohorts.erase(cohorts.begin()+i_min);
    --J;
}

resize()

template<class Model >

void Species< Model >::resize ( int  _J )

virtual

Implements Species_Base.

Definition at line 18 of file species.tpp.

                                 {
    J = _J;
    cohorts.resize(J, boundaryCohort);  // when resizing, always insert copies of boundary cohort
}

set_birthTime()

template<class Model >

void Species< Model >::set_birthTime ( int  i, double  t0  )

virtual

Implements Species_Base.

Definition at line 133 of file species.tpp.

                                                  {
    cohorts[i].birth_time = t0;
}

set_ub()

template<class Model >

void Species< Model >::set_ub ( double  _ub )

virtual

Implements Species_Base.

Definition at line 127 of file species.tpp.

                                     {
    boundaryCohort.u = _ub;
}

set_xb()

template<class Model >

void Species< Model >::set_xb ( double  _xb )

virtual

Implements Species_Base.

Definition at line 119 of file species.tpp.

                                     {
    xb = _xb;
    boundaryCohort.x = _xb;
    boundaryCohort.set_size(_xb);
}

setU()

template<class Model >

void Species< Model >::setU ( int  i, double  _u  )

virtual

Implements Species_Base.

Definition at line 146 of file species.tpp.

                                         {
    cohorts[i].u = _u;
}

setX()

template<class Model >

void Species< Model >::setX ( int  i, double  _x  )

virtual

Implements Species_Base.

Definition at line 139 of file species.tpp.

                                         {
    cohorts[i].x = _x;
    cohorts[i].set_size(_x);
}

triggerPreCompute()

template<class Model >

void Species< Model >::triggerPreCompute ( )

virtual

Implements Species_Base.

Definition at line 191 of file species.tpp.

                                      {
    for (auto& c : cohorts) c.need_precompute = true;
    boundaryCohort.need_precompute = true;
}

Member Data Documentation

boundaryCohort

template<class Model >

Cohort<Model> Species< Model >::boundaryCohort

protected

Definition at line 110 of file species.h.

cohorts

template<class Model >

std::vector<Cohort<Model> > Species< Model >::cohorts

protected

Definition at line 109 of file species.h.

savedCohort

template<class Model >

Cohort<Model> Species< Model >::savedCohort

protected

Definition at line 112 of file species.h.

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

• include/species.h
• src/species.tpp