PesticideToxicity Class Reference

#include <PesticideToxicity.h>

Inheritance diagram for PesticideToxicity:

Public Member Functions
	PesticideToxicity ()
void	doToxicity (double a_mass, double a_para_index)
	The default function to calculate the toxicity effect. More...
void	setToxicityFuncPointer (void(PesticideToxicity::*a_toxicity_func)(double, double))
	The function to set the toxicity function pointer. More...
void	setDecayFuncPointer (void(PesticideToxicity::*a_decay_func)(void))
	The function to set the decay function pointer. More...
void	doOverspray (void)
	The function for the animal to be oversprayed when the pesticide application is happening where the animal is. More...
void	doContact (void)
	The function to calculate the pesticide contamination through contact. More...
virtual void	tick (int a_step_counter_in_a_day, double a_mass=1, double a_para_index=0)
	The function to update pesticide contamination every time step. More...
std::vector< double >	supplyPesticideVector (void)
	The function to return the pesticide amount array. More...
void	SetPesticideVector (std::vector< double > a_pest_amount_vec)
double	supplyPesticide (PlantProtectionProducts a_type=ppp_1)
	The function to supply the pesticide residue for the given pesticide type, the default type is 0, i.e., single product. More...
double	supplyPestMortality (void)
	The function to supply the host's mortality rate caused by pest. More...
void	setHostAnimalPointer (TAnimal *animal)
	The function to set the host animal pointer. More...
virtual void	reset (void)
	Reset PesticideToxicity class, this should be called when the host animal is dead. More...
void	eatingFromStorePest (PesticideStore *a_store, double a_eating_amount, double a_total_amount)
	The function for eating from a store to add pesticide. More...
double	GetTotalPest (void)
	Return the total pesticide. More...
Public Member Functions inherited from PesticideStore
	PesticideStore ()
void	addPesticide (double eating_amount, double amount_per_square, double(Landscape::*a_supply_pest_func_pointer)(int, int, PlantProtectionProducts), int loc_x, int loc_y)
	The function to add pesticide based on the eating amount and the amount of food per square meter. More...
void	addPesticide (double a_mount, PlantProtectionProducts a_type)
	The function to add pesticide based on the given amount and the given type. More...
std::vector< double > *	supplyPesticide (void)
	The function to return the pesticide amount array. More...
double	supplyPesticide (PlantProtectionProducts a_type)
	The function to return the pesticide amount. More...
double	supplyTotalPesticide (void)
	The function to return the total pesticide amount. More...
void	doDecay (void)
	The default fuction to decay the pesticide body burden. More...
virtual void	tick (int a_step_counter_in_a_day)
	The function to update pesticide contamination every time step. More...

Private Attributes
TAnimal *	m_my_animal_host
	The pointer to the host animal. More...
double	m_total_pest_sum
	The summation of the total pesticide body burden. More...
double	m_pest_hazard
	The hazard of the pesticide. More...
void(PesticideToxicity::*	m_toxicity_func_pointer )(double, double)
	The function pointer to point the function for toxicity effect calculation. More...
void(PesticideToxicity::*	m_decay_func_pointer )(void)
	The function pointer to point the function for decay calculation. More...
double	m_my_animal_mortality
	The mortality rate of the host animal caused by pesticide body burden. More...
int	m_location_previous_x
	The x-coordinate is used to remember the location from the previous time-step. More...
int	m_location_previous_y
	The y-coordinate is used to remember the location from the previous time-step. More...

Additional Inherited Members
Static Public Member Functions inherited from PesticideStore
static void	setLandscapePointer (Landscape *a_landscape)
	The function to set the static landscape pointer. More...
Protected Attributes inherited from PesticideStore
std::vector< double >	m_pest_amount_vec
	The vector to store the pesticide amount for each pesticide. More...
Static Protected Attributes inherited from PesticideStore
static Landscape *	m_ALandscape = nullptr
	The static landscape pointer. More...

Constructor & Destructor Documentation

PesticideToxicity()

PesticideToxicity::PesticideToxicity

(

)

                                       {
    if(!l_pest_enable_pesticide_engine.value()) return;
    //default settings
    reset();
    
    m_toxicity_func_pointer = &PesticideToxicity::doToxicity;
    m_decay_func_pointer = &PesticideToxicity::doDecay;
}

References PesticideStore::doDecay(), doToxicity(), l_pest_enable_pesticide_engine, m_decay_func_pointer, m_toxicity_func_pointer, reset(), and CfgBool::value().

Member Function Documentation

doContact()

void PesticideToxicity::doContact

(

void

)

The function to calculate the pesticide contamination through contact.

                                        {
    //get the host animal's current location
    int temp_current_x = m_my_animal_host->Supply_m_Location_x();
    int temp_current_y = m_my_animal_host->Supply_m_Location_y();
 
    //check whether the host animal moved to another location, if yes, apply contact
    if(temp_current_x != m_location_previous_x || temp_current_y != m_location_previous_y){
        double current_pest = 0;
 
        for (int i=0; i<l_pest_NoPPPs.value(); i++){
 
            //use the plant surface for contact
            current_pest = m_ALandscape->SupplyPesticidePlantSurface(temp_current_x, temp_current_y, PlantProtectionProducts(i));
            //Please note that the unit of current_pest is mg/m2
            m_pest_amount_vec[i] += pest_contact_animal_ratio.value()*current_pest;
        } 
 
    }
 
    //record the current location as the previous location for next time step
    m_location_previous_x = temp_current_x;
    m_location_previous_y = temp_current_y;
}

References l_pest_NoPPPs, PesticideStore::m_ALandscape, m_location_previous_x, m_location_previous_y, m_my_animal_host, PesticideStore::m_pest_amount_vec, pest_contact_animal_ratio, TAnimal::Supply_m_Location_x(), TAnimal::Supply_m_Location_y(), Landscape::SupplyPesticidePlantSurface(), CfgInt::value(), and CfgFloat::value().

Referenced by tick().

doOverspray()

void PesticideToxicity::doOverspray

(

void

)

The function for the animal to be oversprayed when the pesticide application is happening where the animal is.

                                          {
    //test against the chance
    if(g_rand_uni_fnc()>= pest_animal_overspray_chance.value()) {return;}
    //get the host animal's current location
    int temp_current_x = m_my_animal_host->Supply_m_Location_x();
    int temp_current_y = m_my_animal_host->Supply_m_Location_y();
    //get the sprayed pesticide type
    PlantProtectionProducts current_ppp_type = m_ALandscape->SupplySprayPesticideType(temp_current_x, temp_current_y);
    //get the sprayed pesticide application rate
    double current_ppp_rate = m_ALandscape->SupplySprayPesticideRate(temp_current_x, temp_current_y);
    //add the overspray pesticide
    m_pest_amount_vec[current_ppp_type] += pest_overspray_animal_surface.value()*pest_overspray_animal_rate.value()*current_ppp_rate;
}

References g_rand_uni_fnc(), PesticideStore::m_ALandscape, m_my_animal_host, PesticideStore::m_pest_amount_vec, pest_animal_overspray_chance, pest_overspray_animal_rate, pest_overspray_animal_surface, TAnimal::Supply_m_Location_x(), TAnimal::Supply_m_Location_y(), Landscape::SupplySprayPesticideRate(), Landscape::SupplySprayPesticideType(), and CfgFloat::value().

Referenced by Osmia_Female::OnFarmEvent().

doToxicity()

void PesticideToxicity::doToxicity	(	double	a_mass,
		double	a_para_index
	)

The default function to calculate the toxicity effect.

                                                                        {
    //sum all the pesticide
    m_total_pest_sum = 0.0;
    for (int i=0; i<l_pest_NoPPPs.value(); i++){
        m_total_pest_sum += m_pest_amount_vec[i];
    }
 
    //GUTS-SD model (Death Dilemma and Organism Recovery in Ecotoxicology, Roman Ashauer, 2015)
    //calculation of the hazard rate, the background hazard rate is excluded since this will be included in the animal mortality calculation
    double pest_diff = m_total_pest_sum/a_mass - pest_animal_effect_amount.value()[a_para_index];
    if (pest_diff > 0){
        double temp_hazard_rate = pest_animal_killing_rate.value()[a_para_index]*pest_diff;
        m_pest_hazard += temp_hazard_rate;
        m_my_animal_mortality = 1 - exp(-m_pest_hazard);
    }
 
}

References l_pest_NoPPPs, m_my_animal_mortality, PesticideStore::m_pest_amount_vec, m_pest_hazard, m_total_pest_sum, pest_animal_effect_amount, pest_animal_killing_rate, CfgInt::value(), and CfgArray_Double::value().

Referenced by PesticideToxicity().

eatingFromStorePest()

void PesticideToxicity::eatingFromStorePest	(	PesticideStore *	a_store,
		double	a_eating_amount,
		double	a_total_amount
	)

The function for eating from a store to add pesticide.

                                                                                                                   {
    double temp_pest = 0.0;
    double temp_frac = a_eating_amount/a_total_amount;
    for (int i = 0; i<l_pest_NoPPPs.value(); i++){
        temp_pest = a_store->supplyPesticide(PlantProtectionProducts(i))*temp_frac;
        m_pest_amount_vec[i] += temp_pest;
        //deduce the pesticide from the store
        a_store->addPesticide(-temp_pest, PlantProtectionProducts(i));
    }
}

References PesticideStore::addPesticide(), l_pest_NoPPPs, PesticideStore::m_pest_amount_vec, PesticideStore::supplyPesticide(), and CfgInt::value().

GetTotalPest()

double PesticideToxicity::GetTotalPest ( void  )

inline

Return the total pesticide.

{return m_total_pest_sum;}

References m_total_pest_sum.

reset()

void PesticideToxicity::reset ( void  )

virtual

Reset PesticideToxicity class, this should be called when the host animal is dead.

Reimplemented from PesticideStore.

                                    {
    m_location_previous_x = -1;
    m_location_previous_y = -1;
    m_total_pest_sum = 0;
    m_pest_hazard = 0;
    m_my_animal_mortality = 0;
    for (int i = 0; i<l_pest_NoPPPs.value(); i++){
        m_pest_amount_vec[i] = 0.0;
    } 
}

References l_pest_NoPPPs, m_location_previous_x, m_location_previous_y, m_my_animal_mortality, PesticideStore::m_pest_amount_vec, m_pest_hazard, m_total_pest_sum, and CfgInt::value().

Referenced by TAnimal::KillThis(), and PesticideToxicity().

setDecayFuncPointer()

void PesticideToxicity::setDecayFuncPointer ( void(PesticideToxicity::*)(void)  a_decay_func )

inline

The function to set the decay function pointer.

{m_decay_func_pointer = a_decay_func;}

References m_decay_func_pointer.

setHostAnimalPointer()

void PesticideToxicity::setHostAnimalPointer ( TAnimal *  animal )

inline

The function to set the host animal pointer.

{m_my_animal_host = animal;}

References m_my_animal_host.

Referenced by TAnimal::TAnimal().

SetPesticideVector()

void PesticideToxicity::SetPesticideVector ( std::vector< double >  a_pest_amount_vec )

inline

{ m_pest_amount_vec = a_pest_amount_vec;}

References PesticideStore::m_pest_amount_vec.

setToxicityFuncPointer()

void PesticideToxicity::setToxicityFuncPointer ( void(PesticideToxicity::*)(double, double)  a_toxicity_func )

inline

The function to set the toxicity function pointer.

{m_toxicity_func_pointer = a_toxicity_func;}

References m_toxicity_func_pointer.

supplyPesticide()

double PesticideToxicity::supplyPesticide ( PlantProtectionProducts  a_type = ppp_1 )

inline

The function to supply the pesticide residue for the given pesticide type, the default type is 0, i.e., single product.

{return m_pest_amount_vec[a_type];}

References PesticideStore::m_pest_amount_vec.

supplyPesticideVector()

std::vector<double> PesticideToxicity::supplyPesticideVector ( void  )

inline

The function to return the pesticide amount array.

{ return m_pest_amount_vec; }

References PesticideStore::m_pest_amount_vec.

supplyPestMortality()

double PesticideToxicity::supplyPestMortality ( void  )

inline

The function to supply the host's mortality rate caused by pest.

{return m_my_animal_mortality;}

References m_my_animal_mortality.

Referenced by Osmia_Female::BeginStep(), and Osmia_Female::st_Develop().

tick()

void PesticideToxicity::tick ( int  a_step_counter_in_a_day, double  a_mass = 1, double  a_para_index = 0  )

virtual

The function to update pesticide contamination every time step.

                                                                                              {
    if(!l_pest_enable_pesticide_engine.value()) return;
    //These only be done once per day even for the species with finer time step, e.g., 1 hr
    if(a_step_counter_in_a_day == 0){
        //first, do decay
        (this->*m_decay_func_pointer)();
        //second, do toxicity
        (this->*m_toxicity_func_pointer)(a_mass,  a_para_index);
    }
    
    //third, check whether contact happens, contact can happen when the animal moves to a new place
    if(cfg_pest_animal_contact_on.value()){
        doContact();
    }
}

References cfg_pest_animal_contact_on, doContact(), l_pest_enable_pesticide_engine, m_decay_func_pointer, m_toxicity_func_pointer, and CfgBool::value().

Referenced by Osmia_Female::BeginStep().

Member Data Documentation

m_decay_func_pointer

void(PesticideToxicity::* PesticideToxicity::m_decay_func_pointer) (void)

private

The function pointer to point the function for decay calculation.

Referenced by PesticideToxicity(), setDecayFuncPointer(), and tick().

m_location_previous_x

int PesticideToxicity::m_location_previous_x

private

The x-coordinate is used to remember the location from the previous time-step.

Referenced by doContact(), and reset().

m_location_previous_y

int PesticideToxicity::m_location_previous_y

private

The y-coordinate is used to remember the location from the previous time-step.

Referenced by doContact(), and reset().

m_my_animal_host

TAnimal* PesticideToxicity::m_my_animal_host

private

The pointer to the host animal.

Referenced by doContact(), doOverspray(), and setHostAnimalPointer().

m_my_animal_mortality

double PesticideToxicity::m_my_animal_mortality

private

The mortality rate of the host animal caused by pesticide body burden.

Referenced by doToxicity(), reset(), and supplyPestMortality().

m_pest_hazard

double PesticideToxicity::m_pest_hazard

private

The hazard of the pesticide.

Referenced by doToxicity(), and reset().

m_total_pest_sum

double PesticideToxicity::m_total_pest_sum

private

The summation of the total pesticide body burden.

Referenced by doToxicity(), GetTotalPest(), and reset().

m_toxicity_func_pointer

void(PesticideToxicity::* PesticideToxicity::m_toxicity_func_pointer) (double, double)

private

The function pointer to point the function for toxicity effect calculation.

Referenced by PesticideToxicity(), setToxicityFuncPointer(), and tick().

---

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

• /builds/ALMaSS/ALMaSS_MIDox/Landscape/PesticideToxicity.h
• /builds/ALMaSS/ALMaSS_MIDox/Landscape/PesticideToxicity.cpp