ALMaSS: Aphid_Population_Manager Class Reference

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The class to handle all Aphid population related matters in the whole landscape. More...

#include <Aphid_Population_Manager.h>

Inheritance diagram for Aphid_Population_Manager:

Public Member Functions
	Aphid_Population_Manager (Landscape *L, string a_aphid_specie_name="English grain aphid")

virtual	~Aphid_Population_Manager ()

Aphid *	CreateObjects (TAnimal pvo, struct_Aphid data, int number)

virtual int	calNextStage (int current_stage, double density=1)
	Return the next life stage for the given life stage. More...

virtual void	updateDevelopmentSeason ()
	The function to update the development season. More...

virtual unsigned	supplyDevelopmentSeason ()
	The function to supply the development season. More...

virtual void	initialisePopulation ()
	The function to initialise the population when starting aphid simulation, this function is called in the subpopulation_mananger constructor. More...

int	calNextStageShared (int current_stage)
	The function to calculate the next life stage for all aphids. More...

void	initialiseSimWithEggs (void)
	The function to initilise the simulation with eggs. More...

virtual void	updateMortalityArray (void)
	The fucntion to update the base mortality rate, it will call the corresponding function pointer. More...

void	updateMortalityArrayShared (void)
	The function to calculate the base mortality rate for all aphids. More...

virtual int	calOffspringStage (int current_stage, double offspring_num=NULL, double a_age=1, double a_density=-1, double a_growth_stage=0, double a_propotion=NULL, bool winter_host_flag=false)
	The function to calculate the offspring stage. More...

int	calOffspringStageEGandPEA (int current_stage, double offspring_num=NULL, double a_age=1, double a_density=-1, double a_growth_stage=0, double a_propotion=NULL, bool winter_host_flag=false)
	The function to calculate the offspring stage for English grain and pea aphids. More...

int	calOffspringStageBBandPP (int current_stage, double offspring_num=NULL, double a_age=1, double a_density=-1, double a_growth_stage=0, double a_propotion=NULL, bool winter_host_flag=false)
	The function to calcto calculate the offspring stage for black bean and peach potato aphids. More...

virtual bool	isEnoughNextLifeStage (int a_life_stage)

bool	isEnoughNextLifeStageShared (int a_life_stage)

double	supplyNymphNumWeight (void)
	The function to return the daily nymph number weight. More...

virtual void	doSpeciesLastThing ()
	The function to return the species. More...

virtual void	writeCalibrationFiles (void)
	Write probe files for calibration. More...

virtual double	calHatchChance ()
	The function to calculate the hatch chance for eggs, this function must be override in the derived class. More...

double	SupplyAphidDensity (int a_x, int a_y)
	Function to supply the aphid density in the given location. More...

void	KillAphid (int a_x, int a_y, double a_num)
	Function to kill the given number of aphids in the given location. More...

Public Member Functions inherited from SubPopulation_Population_Manager
	SubPopulation_Population_Manager (Landscape *L, string DevReproFile="", int a_sub_w=10, int a_sub_h=10, int a_num_life_stage=5, int a_max_long_dist=1000, int a_peak_long_dist=100, float a_scale_wind_speed=1.1, float a_max_wind_speed=16, int a_wind_direc_num=8, int a_wind_speed_step_size=2, int a_max_alive_day=300)

virtual	~SubPopulation_Population_Manager (void)
	SubPopulation_Manager Destructor. More...

double	supplyAllPopulationGivenStage (int index)
	Supply the population size at the given life stage for the who landscape. More...

double	supplyTotalPopulationInCell (int x_indx, int y_indx)
	Supply whole population size at the given cell. More...

int	supplyCellNumX ()
	Supply number of subpopulation in x coordinate. More...

int	supplyCellNumY ()
	Supply number of subpopulation in y coordinate. More...

double	supplyCellWidth ()
	Supply the width of a subpopulation cell. More...

double	supplyCellHeight ()
	Supply the height of a subpopulation cell. More...

double	supplySizeSubpopulationCell ()
	Supply the size of aphid subpopulation cell. More...

bool	openSubpopulationBaseProbeFile ()
	Open the storing file. More...

virtual void	subpopuBaseOutputProbe ()
	Below are the functions for saving result. More...

double	getTotalSubpopulationInCell (int x_indx, int y_indx)
	Supply the total subpopulation size in the given cell. More...

double	getSubpopulationInCellLifeStage (int x_indx, int y_indx, int a_life_stage)
	Supply the subpopulation size at the given life stage in the given cell. More...

double	getSuitabilityInCell (int x_indx, int y_indx)
	Supply the suitability in the given cell. More...

SubPopulation *	supplySubPopulationPointer (int indx, int indy)
	Supply the pointer of the subpopulation object in the given cell. More...

int	supplyLifeStageNum ()
	Supply the number of life stage. More...

int	supplyMaxColNum ()
	Supply the maximum number of column in the development array. More...

int	supplyNextLifeStage (int life_circle_index, int life_stage_index)
	Supply the next life stage index for a given life stage and a given life path. More...

std::vector< int >	supplyOldEnoughIndex (int life_stage_index)

int	supplyNewestIndex (int life_stage_index)

virtual unsigned	GetLiveArraySize (int a_listindex)
	Must be re-implemented in descendent classes. Gets the number of 'live' objects. More...

void	readDevReproFile (string inputfile)
	Function to read the development time and lifestage. More...

void	relocatePopulation (void)
	Relocate the population in each cell based on the suitability and movement ability. More...

virtual void	DoLast ()

virtual void	DoFirst ()

virtual void	calLongMovementMask (void)
	Function to calculate the movement mask. More...

void	doDevelopment ()
	Function to make the development for all the subpopulation object. More...

void	addNewDay ()
	Add new day to the newest and oldest array. More...

void	updateWholePopulationArray (int a_listindex, double number)
	The function to update the whole population array in the whole landscape. More...

void	updateWholePopulationArray (blitz::Array< double, 1 > a_array)

void	setFirstFlagLifeStage (int life_stage, bool pvalue)
	The function to set the flag indicating whether a given lifestage is the first time of existing. More...

bool	supplyFirstFlagLifeStage (int life_stage)
	The function to supply the flag of first for the given life stage. More...

void	setOldIndex (int life_stage, int p_value)
	The function to set the oldest index for the given life stage. More...

void	doFlying (int ind, int index_x, int index_y)
	The function to fly the winged adults. More...

void	doLocalMovement (int index_x, int index_y, double proportion)
	The function for local movement. More...

bool	isWinterHostTole (TTypesOfLandscapeElement a_ele)
	Test whether it is a winter host tole. More...

bool	isSummerHostTole (TTypesOfLandscapeElement a_ele)
	Test whether it is a summer host tole. More...

bool	isWinterHostTov (TTypesOfVegetation a_ele)
	Test whether it is a winter host tov. More...

bool	isSummerHostTov (TTypesOfVegetation a_ele)
	Test whether it is a summer host tov. More...

double	supplyMortality (int a_life_stage, int a_age)
	The function to supply the mortality rate for the given life stage and the age. More...

blitz::Array< double, 2 >	supplyMortalityWholeArray (void)
	The function to supply the whole base mortality rate array. More...

blitz::Array< double, 1 >	supplyMortalityStageArray (int a_life_stage)
	The function to supply the 1D base morality rate array for the given life stage. More...

double	calLandingCurve (double a_dis, double a_peak, double a_furthest)
	The function to calculate the landing curve along the wind direction. More...

SubPopulation *	CreateObjects (TAnimal pvo, struct_SubPopulation data, int number)

int	supplyAgeInDay (int lifestage_index, int column_index)
	The function to return the age in days given an element in the subpopulation table. More...

double	supplyAgeInDayDegree (int lifestage_index, int column_index)

virtual void	SupplyLocXY (unsigned index_x, unsigned index_y, int &x, int &y)
	A stub for identifying an individual at a location. More...

std::vector< int >	supplyVecFlyingLifeStages ()
	Supply the vector of life stages for flying. More...

int	supplyNumFlyingLifeStages ()
	Supply the number of life stages that can fly. More...

std::vector< int >	supplyVecLocMoveLifeStages ()
	Supply the vector of life stages that can do local movement. More...

int	supplyNumLocMovLifeStages ()
	Supply the number of life stages thah can do local movement. More...

virtual unsigned	GetPopulationSize (int a_listindex)
	Must be re-implemented in descendent classes. More...

std::vector< int >	supplyWinterTolePeriod (TTypesOfLandscapeElement a_tole)
	The function to supply the available period vector for the given winter tole host. More...

std::vector< int >	supplySummerTolePeriod (TTypesOfLandscapeElement a_tole)
	The function to supply the available period vector for the given summer tole host. More...

virtual void	doParasitoidDevelopment ()
	The function for parasitoid calculation, it does nothing in this base class. More...

virtual void	doSpecicesLastThing ()
	The special last thing for the drived species. More...

void	updateWholePopulation ()
	Update whole population info. More...

virtual void	SetNoProbesAndSpeciesSpecificFunctions (int a_pn)
	Sets up probe and species specifics. More...

virtual void	readHosts (string a_file_name)
	The fuction to read the host lists for aphid. More...

bool	supplySummerHostOn (void)

bool	supplyWinterHostOn (void)

Public Member Functions inherited from Population_Manager_Base
	Population_Manager_Base (Landscape *L)
	The Population_Manager_Base constructor. More...

virtual void	Catastrophe (int)
	Must be re-implemented in descendent classes. More...

int	SupplySimW () const
	Returns landscape width in m. More...

int	SupplySimH () const
	Returns landscape height in m. More...

int	SupplySimWH () const
	Returns half the landscape width in m. More...

int	SupplySimHH () const
	Returns half the landscape height in m. More...

virtual int	ProbeFileInput (char *p_Filename, int p_ProbeNo)
	A stub to build specfic probes and functions. More...

virtual char *	SpeciesSpecificReporting (int, int)
	A stub to build specfic reporting. More...

int	SupplyListNameLength () const

const char *	SupplyListName (int a_i) const
	Get a list name from the list. More...

virtual TAnimal *	FindClosest (int, int, unsigned)
	A stub for identifying an individual at a location. More...

std::string	SupplySimulationName ()

virtual void	OpenTheAOROutputProbe (const string &a_string)
	An empty method that needs to be here because the population manager lists might contain sub-population models which will skip Population_Manager functionality. More...

void	SetStepCounterInADay (int a_counter)
	Set step counter in a day. More...

int	GetStepCounterInADay (void)
	Return the sep counter in a day. More...

virtual double	GetAphidDensity (int, int)
	Return the aphid density, it is only used when aphid simulations are running. More...

virtual TAnimal *	SupplyAnimalPtr (unsigned int a_index, unsigned int a_animal)
	Return the animal pointer for the give life stage and number. More...

Private Attributes
string	m_aphid_specie_name
	This is to store the aphid species name. More...

double	m_aphid_egg_mortality
	The variable to store the aphid egg mortality. More...

double	m_aphid_egg_mortality_sd
	The variable to store the standard deviation of the gee mortality. More...

double	m_aphid_nymph_mortality_para_a
	The variable to store the nymph temperature based mortality parameter A. More...

double	m_aphid_nymph_mortality_para_b
	The variable to store the nymph temperature based mortality parameter B. More...

double	m_aphid_nymph_mortality_para_c
	The variable to store the nymph temperature based mortality parameter C. More...

double	m_aphid_adult_mortality_para_a
	The variable to store the adult mortality parameter A. More...

double	m_aphid_adult_mortality_para_b
	The variable to store the adult mortality parameter B. More...

double	m_aphid_adult_mortality_para_c
	The variable to store the adult mortality parameter C. More...

double	m_aphid_adult_longevity_para_a
	The variable to store the adult longevity parameter A. More...

double	m_aphid_adult_longevity_para_b
	The variable to store the adult longevity parameter B. More...

double	m_aphid_egg_starting_degree_days
	The variable to store the egg's starting degree days when the simulation starts. More...

double	m_aphid_egg_hatch_chance_para_a
	The variable to store the egg hatch chance parameter A. More...

double	m_aphid_egg_hatch_chance_para_b
	The variable to store the egg hatch chance parameter B. More...

double	m_aphid_egg_hatch_chance_threshold
	The threshold of hatch value to start the delay of egg hatch, this is to avoid the eggs hatching from the same day. More...

double	m_aphid_egg_hatch_delay_degree_days
	The number of degree days to delay the egg's hatch. More...

double	m_aphid_egg_hatch_chance_para_a_after_threshold
	The variable to store the egg hatch chance parameter A after threshold. More...

double	m_aphid_egg_hatch_chance_para_b_after_threshold
	The variable to store the egg hatch chance parameter B after threshold. More...

double	m_aphid_egg_hatch_chance_turing_degree_days
	The variable to store the turning degree day for egg hatch chance. More...

double	m_aphid_egg_hatch_chance_max_degree_days
	The variable to store the largest degree days for egg hatch chance being one. More...

double	m_aphid_nymph_with_wings_development_day_degrees
	The variable to store the nymph with wings development day degrees. More...

double	m_aphid_nymph_with_wings_development_day_degrees_sd
	The variable to store the nymph with wings development day degrees's standard deviation. More...

double	m_aphid_nymph_without_wings_development_day_degrees
	The variable to store the nymph without wings development day degrees. More...

double	m_aphid_nymph_without_wings_development_day_degrees_sd
	The variable to store the nymph without wings development day degrees's standard deviation. More...

double	m_aphid_egg_production_para_a
	The variable to store the egg production parameter A. More...

double	m_aphid_egg_production_para_b
	The variable to store the egg production parameter B. More...

double	m_aphid_egg_production_para_c
	The variable to store the egg production parameter C. More...

double	m_aphid_egg_production_para_sd
	The variable to store the egg production parameter's standard deviation. More...

double	m_aphid_nymph_production_para_a1
	The variable to store the nymph production parameter A1. More...

double	m_aphid_nymph_production_para_b1
	The variable to store the nymph production parameter B1. More...

double	m_aphid_nymph_production_para_a2
	The variable to store the nymph production parameter A2. More...

double	m_aphid_nymph_production_para_b2
	The variable to store the nymph production parameter B2. More...

double	m_aphid_nymph_production_changing_add
	The variable to store the nymph production changing accumulated degree days. More...

double	m_aphid_nymph_production_temp_weight_para_a
	The variable to store the temperature weighted nymph production parameter A. More...

double	m_aphid_nymph_production_temp_weight_para_b
	The variable to store the temperature weighted nymph production parameter B. More...

double	m_aphid_nymph_production_temp_weight_para_c
	The variable to store the temperature weighted nymph production parameter C. More...

double	m_aphid_alate_proportion_para_a
	The variable to store alate proportion calculation parameter A. More...

double	m_aphid_alate_proportion_para_b
	The variable to store alate proportion calculation parameter B. More...

double	m_aphid_alate_proportion_para_c
	The variable to store alate proportion calculation parameter C. More...

double	m_aphid_male_reproduction_day_length
	The day length in minutes for male reproduction. This is used for EG and PEA. More...

double	m_aphid_female_reproduction_day_length
	The day length in minutes for female reproduction. This is used for EG and PEA. More...

double	m_aphid_winter_host_day_length
	THe day length in minutes to turn on winter host. This is used for BB and PP. More...

double	m_aphid_summer_host_day_length
	The day length in minutes to turn on summer host. This is used for BB and PP. More...

vector< double >	m_aphid_adult_mortality_inflection_point_dd
	The vector to store inflection point of accumulated day degrees for adult mortality. More...

vector< double >	m_aphid_adult_mortality_vec
	The vector to store the adult mortality for the inflection point. More...

double	m_aphid_sexual_reproduction_average_add
	The average required accumulated degree days to enable sexual reproduction after the first egg hatches. More...

double	m_aphid_sexual_reproduction_add_sd
	The standard deviation of the required accumulated degree days to enable sexual reproduction after the first egg hatches. More...

TTypesOfAphidDevelopmentSeason	m_current_developtype
	The variable to show the development season. More...

int(Aphid_Population_Manager::*	m_next_life_func_pointer )(int current_stage)
	The function pointer for calculation of next life stage. More...

void(Aphid_Population_Manager::*	m_update_mortality_array_pointer )()
	The function pointer for calculation of the shared base mortality rate for the whole landscape. More...

int(Aphid_Population_Manager::*	m_offspring_func_pointer )(int current_stage, double offspring_num, double a_age, double a_density, double a_growth_stage, double a_propotion, bool winter_host_flag)
	The function pointer for calculation of the offsrping stage number. More...

bool(Aphid_Population_Manager::*	m_is_ready_next_liff_func_pointer )(int a_life_stage)
	THe function pointer for testing whether the given life stage is ready for the next one. More...

int	m_max_adult_dd
	THe variable to store the maximum number of degree days for aphid. More...

vector< double >	m_nymph_per_day
	The vector to store the age (in degree days) related reproduction offsping nymph. More...

vector< double >	m_egg_per_day
	The vector to store the age (in degree days) related reproduction offspring egg. More...

double	m_nymph_produced_num_weight
	The weight to regulate the number of nymph produced per day based on temperature. More...

bool	m_egg_reproduction_flag
	The flag to enable sexual development. More...

double	m_accu_ddeg_egg_reproduction
	The accumulated day degrees to enable sexual development. More...

bool	m_first_egg_hatch_flag
	The flag to show the first hatch of egg. More...

double	m_max_day_degree_adult
	The longest day degrees that a adult can have. More...

Additional Inherited Members
Public Attributes inherited from Population_Manager_Base
Probe_Data *	TheProbe [100] = {nullptr}
	Holds a list of pointers to standard output probes. More...

Protected Member Functions inherited from SubPopulation_Population_Manager
virtual void	Run (int NoTSteps)

Protected Member Functions inherited from Population_Manager_Base
	~Population_Manager_Base ()=default

Protected Attributes inherited from SubPopulation_Population_Manager
blitz::Array< double, 2 >	m_development_degree_day
	The array to store the average max and std development time for each life stage, max and std time for reproducing. More...

int	m_num_x_range
	The number of subpopulation in x range. More...

int	m_num_y_range
	The number of subpopulation in y range. More...

int	m_num_life_stage
	The number of life stages for the animal. More...

bool	m_mul_hosts_flag
	Flag to show whether it has both winter and summer host. More...

int	m_sub_w
	Variable to record the width of the subpopulation cell. More...

int	m_sub_h
	Variable to record the height of the subpopulation cell. More...

blitz::Array< double, 2 >	m_cell_popu_density
	Array for weighted population density in each subpopulation cell. More...

blitz::Array< double, 2 >	m_cell_suitability
	Array for suitable value in each subpopulation cell. More...

blitz::Array< SubPopulation *, 2 >	m_the_subpopulation_array
	Vector to store the all the pointers for the subpopulation object. More...

blitz::Array< double, 4 >	m_short_move_mask
	Short distance movement mask. More...

blitz::Array< double, 4 >	m_long_move_mask
	Long distance movement mask. More...

int	m_max_long_distance
	The longest distance that the specieces can fly for long distance dispersal. More...

int	m_peak_long_distance
	The distance for the peak amount of landing. More...

float	m_scale_wind_speed
	The scale for wind. More...

float	m_max_flying_wind_speed
	The larget wind speed for winged adults to fly. More...

int	m_wind_speed_step_size
	The sampling step size for wind speed. More...

int	m_wind_direction_num
	The number of wind directions. More...

int	m_wind_speed_num
	The number of wind speed samples. More...

blitz::Array< int, 1 >	m_wind_speed_lookup_table
	The look up table for wind speed index in the flying mask. More...

double	m_max_short_distance
	The longest distance that the specieces can move for short distance dispersal. More...

int	m_long_move_mask_x_num
	Variable to record the dimension of the long distance movement mask. - x. More...

int	m_long_move_mask_y_num
	Variable to record the dimension of the long distance movement mask. - y. More...

int	m_long_move_mask_x_num_half
	Variable to record the dimension of the short distance movement mask. - x. More...

int	m_long_move_mask_y_num_half

blitz::Array< int, 1 >	m_long_move_mask_x_num_half_array
	Array to store the number of cells for longest flying at different windspeed. More...

blitz::Array< int, 1 >	m_long_move_mask_y_num_half_array

int	m_short_move_mask_x_num

int	m_short_move_mask_y_num
	Variable to record the dimension of the short distance movement mask. - y. More...

blitz::Array< double, 2 >	m_accumu_degree_days
	Array for accumulated degree days for each life circle. More...

blitz::Array< int, 2 >	m_index_new_old
	Array for index of the newest and oldest life stages. More...

int	m_max_alive_days
	The longest alive day among all the life stages. More...

blitz::Array< double, 1 >	m_lowest_temp_dev
	Lowest development temperatures for each life stage. This is the last step in each day. More...

blitz::Array< double, 2 >	m_life_circle_path
	The life circle array. It could have more than one life circle paths. More...

bool	m_hibernated_hatch_flag
	Flag variable to indicate hibernated eggs are ready to hatch. More...

blitz::Array< bool, 1 >	m_first_flag_life_stage
	Array to track whether it is the first existence for a life stage. More...

blitz::Array< double, 1 >	m_current_flying_array
	Temporal array for the flying subpopulation. More...

blitz::Array< double, 1 >	m_current_landing_array
	Temporal array for the landing subpopulation. More...

std::vector< TTypesOfLandscapeElement >	m_winter_hosts_tole
	The vector to hold winter host landscape type. More...

std::vector< std::vector< int > >	m_winter_hosts_tole_period
	The vector to store the exsiting period for winter host tole. More...

std::map< int, int >	m_winter_hosts_tole_period_map
	The map to store the index for the winter host period. More...

std::vector< TTypesOfVegetation >	m_winter_hosts_tov
	The vector to hold winter host vegetation type. More...

std::vector< TTypesOfLandscapeElement >	m_summer_hosts_tole
	The vector to hold summer host landscape type. More...

std::vector< std::vector< int > >	m_summer_hosts_tole_period
	The vector to store the exsiting period for summer host tole. More...

std::map< int, int >	m_summer_hosts_tole_period_map
	The map to store the index for the summer host period. More...

std::vector< TTypesOfVegetation >	m_summer_hosts_tov
	The vector to hold sumber host vegetation type. More...

blitz::Array< double, 2 >	m_current_mortality_array
	This a lookup table for the age and temperature dependent mortality rate. This is the same for the whole landscape for each day. Further cell specific related calculate should be done in the SubPopulation class. More...

blitz::Array< double, 2 >	m_wind_direction_array
	The array to hold the wind directions. More...

blitz::Array< blitz::Array< double, 2 >, 2 >	m_landing_masks
	The array to store the landing masks. The vector is indexed by the wind speed index first and the second index is the wind direction. Each element is a 2-D dimensional blitz array. More...

std::vector< int >	m_flying_life_stage_array
	The vector to store the life stages that can fly. More...

std::vector< int >	m_landing_life_stage_array
	The vector to store the life stage when a flying one lands, it could be different from the flying one, e.g., they drop theri wings. More...

std::vector< int >	m_local_moving_life_stage_array
	The vector to store the life stags that can move locally. More...

std::ofstream	m_subpopulation_base_prb_file
	The file for the storing the data. More...

std::vector< std::vector< SubPopulation * > >	m_vec_subpopulation_pointers_polygon
	The vector used to store the pointers of all the subpopulation objects in each polygon. More...

bool	m_summer_host_on
	The flag to enable summer host. More...

bool	m_winter_host_on
	The flag to enalble winter host. More...

Protected Attributes inherited from Population_Manager_Base
int	SimH
	stores the simulation height More...

int	SimW
	stores the simulation width More...

int	SimHH
	stores the simulation height halved More...

int	SimWH
	stores the simulation width halved More...

string	m_SimulationName
	stores the simulation name More...

Landscape *	m_TheLandscape
	holds an internal pointer to the landscape More...

int	m_ListNameLength {}
	the number of life-stages simulated in the population manager More...

const char *	m_ListNames [32] {}
	A list of life-stage names. More...

std::string	m_AORProbeFileName {"AOR_Probe.txt"}
	name of the AOR Probe file More...

std::string	m_ProbeFileName {"Probe.res"}
	name of the Probe file More...

int	m_step_counter_in_a_day
	Step counter in a day, this is used for the animals with finer step size other than one day. More...

Detailed Description

The class to handle all Aphid population related matters in the whole landscape.

Constructor & Destructor Documentation

◆ Aphid_Population_Manager()

Aphid_Population_Manager::Aphid_Population_Manager	(	Landscape *	L,
		string	a_aphid_specie_name = `"English grain aphid"`
	)

Construct a new Aphid_Population_Manger object

                                                                                            : SubPopulation_Population_Manager(L, "-1", cfg_AphidCellWidth.value(), cfg_AphidCellHeight.value(), cfg_AphidLifeStageNum.value(), cfg_AphidMaxLongDistance.value(), cfg_AphidPeakLongDistance.value(), cfg_AphidScaleWindSpeed.value(), cfg_AphidMaxWindSpeed.value(), cfg_AphidMovMaskWindDirectionNum.value(), cfg_AphidMovMaskWindSpeedStepSize.value(), cfg_AphidMaxAliveDay.value(), false)
 {
     m_accu_ddeg_egg_reproduction = 0;
     m_aphid_specie_name = a_aphid_specie_name;
  
     initialisePopulation(); 
     #ifdef __APHID_CALIBRATION
         openAphidCalibFiles();
     #endif
  
     m_egg_reproduction_flag = false;
     m_first_egg_hatch_flag = false;
  
     if(cfg_Subpopu_Base_Output_Used.value()){
         //open the new one using 
         string temp_file_name = "";
         if (m_aphid_specie_name == "English grain aphid") {
             temp_file_name = "EnglishGrainAphid";
         }
         else if (m_aphid_specie_name == "Pea aphid") {
             temp_file_name = "PeaAphid";
         }
         else if (m_aphid_specie_name == "Aphis fabae") {
             temp_file_name = "BlackBeanAphid";
         }
         else if (m_aphid_specie_name == "Peach potato aphid") {
             temp_file_name = "PeachPotatoAphid";
         }
         else {
             temp_file_name = a_aphid_specie_name;
             remove(temp_file_name.begin(), temp_file_name.end(), ' ');
         }
         openSubpopulationBaseProbeFile(cfg_AphidResultPath.value()+temp_file_name+cfg_AphidResultFileSuffix.value()+".txt");
     }
  
  
     //calculate the egg hatch chances
     //the turning for new slop degree days
     m_aphid_egg_hatch_chance_turing_degree_days = (m_aphid_egg_hatch_chance_threshold-m_aphid_egg_hatch_chance_para_b)/m_aphid_egg_hatch_chance_para_a;
  
     int temp_full_dd = (1-m_aphid_egg_hatch_chance_para_b)/m_aphid_egg_hatch_chance_para_a + m_aphid_egg_hatch_delay_degree_days;
     m_aphid_egg_hatch_chance_para_a_after_threshold = (1- m_aphid_egg_hatch_chance_threshold)/(temp_full_dd-m_aphid_egg_hatch_chance_turing_degree_days);
     m_aphid_egg_hatch_chance_para_b_after_threshold = 1-temp_full_dd*m_aphid_egg_hatch_chance_para_a_after_threshold;
  
     //calculate the egg production based on the adult's accumulated degree days
     m_egg_per_day.resize(m_max_adult_dd+1);
     m_nymph_per_day.resize(m_max_adult_dd+1);
         
     //initialise the look up vectors for offpring
     for (int i=0; i<=m_max_adult_dd; i++){
         if (i<=m_aphid_nymph_production_changing_add){
             m_nymph_per_day[i] = m_aphid_nymph_production_para_a1*i + m_aphid_nymph_production_para_b1;
             
         }
         else {
             m_nymph_per_day[i]= m_aphid_nymph_production_para_a2*i + m_aphid_nymph_production_para_b2;
         }
         if (m_nymph_per_day[i]<0) m_nymph_per_day[i] = 0;
         m_egg_per_day[i] = m_aphid_egg_production_para_a*exp(m_aphid_egg_production_para_b*i)*(m_aphid_egg_production_para_c + (g_rand_uni_fnc()-0.5)*2*m_aphid_egg_production_para_sd);
         if (m_egg_per_day[i]<0) m_egg_per_day[i] =0;
     }
  
     //set the landing survival rate
     m_landing_survival_rate = cfg_AphidLandingSurvivalRateVec.value()[m_running_species_number];
 }

References cfg_AphidLandingSurvivalRateVec, cfg_AphidResultFileSuffix, cfg_AphidResultPath, cfg_Subpopu_Base_Output_Used, g_rand_uni_fnc(), initialisePopulation(), m_accu_ddeg_egg_reproduction, m_aphid_egg_hatch_chance_para_a, m_aphid_egg_hatch_chance_para_a_after_threshold, m_aphid_egg_hatch_chance_para_b, m_aphid_egg_hatch_chance_para_b_after_threshold, m_aphid_egg_hatch_chance_threshold, m_aphid_egg_hatch_chance_turing_degree_days, m_aphid_egg_hatch_delay_degree_days, m_aphid_egg_production_para_a, m_aphid_egg_production_para_b, m_aphid_egg_production_para_c, m_aphid_egg_production_para_sd, m_aphid_nymph_production_changing_add, m_aphid_nymph_production_para_a1, m_aphid_nymph_production_para_a2, m_aphid_nymph_production_para_b1, m_aphid_nymph_production_para_b2, m_aphid_specie_name, m_egg_per_day, m_egg_reproduction_flag, m_first_egg_hatch_flag, m_max_adult_dd, m_nymph_per_day, SubPopulation_Population_Manager::openSubpopulationBaseProbeFile(), CfgBool::value(), CfgStr::value(), and CfgArray_Double::value().

◆ ~Aphid_Population_Manager()

Aphid_Population_Manager::~Aphid_Population_Manager ( )

virtual

                                                    {
     #ifdef __APHID_CALIBRATION
         closeAphidCalibFiles();
     #endif
 }

Member Function Documentation

◆ calHatchChance()

double Aphid_Population_Manager::calHatchChance ( )

virtual

The function to calculate the hatch chance for eggs, this function must be override in the derived class.

                                                  {
     double temp_hatch_chance = 0;
     if(m_accumu_degree_days(0,0)>1){
         if(m_accumu_degree_days(0,0)<m_aphid_egg_hatch_chance_turing_degree_days){
             temp_hatch_chance = m_aphid_egg_hatch_chance_para_a*m_accumu_degree_days(0,0)+m_aphid_egg_hatch_chance_para_b;
         }
         else if(m_accumu_degree_days(0,0)<m_aphid_egg_hatch_chance_max_degree_days){
             temp_hatch_chance = m_aphid_egg_hatch_chance_para_a_after_threshold*(m_accumu_degree_days(0,0) - m_aphid_egg_hatch_chance_turing_degree_days)+m_aphid_egg_hatch_chance_para_b_after_threshold;
         }
         else{
             temp_hatch_chance = 1;
         }
     }
     return temp_hatch_chance;
 }

References SubPopulation_Population_Manager::m_accumu_degree_days, m_aphid_egg_hatch_chance_max_degree_days, m_aphid_egg_hatch_chance_para_a, m_aphid_egg_hatch_chance_para_a_after_threshold, m_aphid_egg_hatch_chance_para_b, m_aphid_egg_hatch_chance_para_b_after_threshold, and m_aphid_egg_hatch_chance_turing_degree_days.

◆ calNextStage()

int Aphid_Population_Manager::calNextStage	(	int	current_stage,
		double	density = `1`
	)

virtual

Return the next life stage for the given life stage.

Return the next life stage based on the density

Reimplemented from SubPopulation_Population_Manager.

                                                                            {
     return (this->*m_next_life_func_pointer)(current_stage);
 }

References m_next_life_func_pointer.

◆ calNextStageShared()

int Aphid_Population_Manager::calNextStageShared ( int current_stage )

The function to calculate the next life stage for all aphids.

This function is used both for pean and english grain aphid.

Parameters

current_stage

Returns: int

                                                                  {
     //Spring
     
     if (current_stage == toa_Egg){
         //set the first hatch flag to be true
         if(!m_first_egg_hatch_flag) {
             m_first_egg_hatch_flag = true;
             m_egg_reproduction_flag = false;
         }
         return toa_Aptera;
     }
  
     if(current_stage == toa_Aptera || current_stage == toa_Alate || current_stage == toa_Female || current_stage == toa_Male){
         return -1; // let them die
     }
  
     if(current_stage == toa_Nymph){
         return toa_Aptera;
     }
  
     if(current_stage == toa_Nymph_W){
         return toa_Alate;
     }
  
     if(current_stage == toa_Nymph_F){
         return toa_Female;
     }
  
     if(current_stage == toa_Nymph_M){
         return toa_Male;
     }
 }

References m_egg_reproduction_flag, m_first_egg_hatch_flag, toa_Alate, toa_Aptera, toa_Egg, toa_Female, toa_Male, toa_Nymph, toa_Nymph_F, toa_Nymph_M, and toa_Nymph_W.

Referenced by initialisePopulation().

◆ calOffspringStage()

int Aphid_Population_Manager::calOffspringStage	(	int	current_stage,
		double *	offspring_num = `NULL`,
		double	a_age = `1`,
		double	a_density = `-1`,
		double	a_growth_stage = `0`,
		double *	a_propotion = `NULL`,
		bool	winter_host_flag = `false`
	)

virtual

The function to calculate the offspring stage.

Reimplemented from SubPopulation_Population_Manager.

                                                                                                                                                                                           {
     return (this->*m_offspring_func_pointer)(current_stage, offspring_num, a_age, a_density, a_growth_stage, a_propotion, winter_host_flag);
 }

References m_offspring_func_pointer.

◆ calOffspringStageBBandPP()

int Aphid_Population_Manager::calOffspringStageBBandPP	(	int	current_stage,
		double *	offspring_num = `NULL`,
		double	a_age = `1`,
		double	a_density = `-1`,
		double	a_growth_stage = `0`,
		double *	a_propotion = `NULL`,
		bool	winter_host_flag = `false`
	)

The function to calcto calculate the offspring stage for black bean and peach potato aphids.

This function is used both for black bean and peach potato Aphid.

Parameters

current_stage
offspring_num
a_age
a_density
a_growth_stage
a_propotion

Returns: int

                                                                                                                                                                                                  {
     if(current_stage == toa_Female){
         if (m_egg_reproduction_flag){
             *offspring_num = m_egg_per_day[int(ceil(a_age))];
         }
         else{
             *offspring_num = 0;
         }
         
         return toa_Egg;
     }
     if(current_stage == toa_Aptera || current_stage == toa_Alate){
         //nothing to produce
         if(a_density<0){
             *offspring_num = 0;
             return toa_Nymph;
         }
         double alate_prop = (m_aphid_alate_proportion_para_a*a_density+m_aphid_alate_proportion_para_c*a_growth_stage+m_aphid_alate_proportion_para_b)/100;
         if (alate_prop<0.001) alate_prop = 0;
         if (alate_prop>=1) alate_prop = 1;
         *offspring_num = m_nymph_per_day[int(ceil(a_age))]*m_nymph_produced_num_weight; // multiply with the temperature realted weight.
         
  
         //first check if it is on winter host and it is in the last half year, if yes, produce females
         if(m_winter_host_on && winter_host_flag && m_TheLandscape->SupplyMonth()>=8){
         //if (m_winter_host_on  && m_TheLandscape->SupplyMonth() >= 8) {
             return toa_Nymph_F;
         }
         else{
             if(a_propotion){                
                 *a_propotion = alate_prop;
                 return toa_Nymph_W;
             }
             else{
                 return toa_Nymph;
             }
         }
     }
 }

References m_aphid_alate_proportion_para_a, m_aphid_alate_proportion_para_b, m_aphid_alate_proportion_para_c, m_egg_per_day, m_egg_reproduction_flag, m_nymph_per_day, m_nymph_produced_num_weight, Population_Manager_Base::m_TheLandscape, SubPopulation_Population_Manager::m_winter_host_on, Landscape::SupplyMonth(), toa_Alate, toa_Aptera, toa_Egg, toa_Female, toa_Nymph, toa_Nymph_F, and toa_Nymph_W.

Referenced by initialisePopulation().

◆ calOffspringStageEGandPEA()

int Aphid_Population_Manager::calOffspringStageEGandPEA	(	int	current_stage,
		double *	offspring_num = `NULL`,
		double	a_age = `1`,
		double	a_density = `-1`,
		double	a_growth_stage = `0`,
		double *	a_propotion = `NULL`,
		bool	winter_host_flag = `false`
	)

The function to calculate the offspring stage for English grain and pea aphids.

This function is used both for Pea and English Grain Aphid.

Parameters

current_stage
offspring_num
a_age
a_density
a_growth_stage
a_propotion

Returns: int

                                                                                                                                                                                                   {
     if(current_stage == toa_Female){
         if (m_egg_reproduction_flag){
             *offspring_num = m_egg_per_day[int(ceil(a_age))];
         }
         else{
             *offspring_num = 0;
         }
  
         return toa_Egg;
     }
     if(current_stage == toa_Aptera || current_stage == toa_Alate){
         //nothing to produce
         if(a_density<0){
             *offspring_num = 0;
             return toa_Nymph;
         }
         double alate_prop = (m_aphid_alate_proportion_para_a*a_density+m_aphid_alate_proportion_para_c*a_growth_stage+m_aphid_alate_proportion_para_b)/100;
         if (alate_prop<0.001) alate_prop = 0;
         if (alate_prop>=1) alate_prop = 1;
         *offspring_num = m_nymph_per_day[int(ceil(a_age))]*m_nymph_produced_num_weight; // multiply with the temperature related weight.
         //if (alate_prop>0.5) *offspring_num *= (1-alate_prop+0.1);
         //cout<<*offspring_num<<"How many!!!!"<<endl;
         double current_day_length = g_landscape_ptr->SupplyDaylength();
         if(m_egg_reproduction_flag && current_day_length <m_aphid_male_reproduction_day_length && current_day_length > m_aphid_female_reproduction_day_length){
             return toa_Nymph_M;
         }
         else if(m_egg_reproduction_flag && current_day_length <= m_aphid_female_reproduction_day_length){
             return toa_Nymph_F;
         }
         else{
             if(a_propotion){                
                 *a_propotion = alate_prop;
                 return toa_Nymph_W;
             }
             else{
                 return toa_Nymph;
             }
         }
     }
 }

References g_landscape_ptr, m_aphid_alate_proportion_para_a, m_aphid_alate_proportion_para_b, m_aphid_alate_proportion_para_c, m_aphid_female_reproduction_day_length, m_egg_per_day, m_egg_reproduction_flag, m_nymph_per_day, m_nymph_produced_num_weight, Landscape::SupplyDaylength(), toa_Alate, toa_Aptera, toa_Egg, toa_Female, toa_Nymph, toa_Nymph_F, toa_Nymph_M, and toa_Nymph_W.

Referenced by initialisePopulation().

◆ CreateObjects()

Aphid * Aphid_Population_Manager::CreateObjects	(	TAnimal *	pvo,
		struct_Aphid *	data,
		int	number
	)

                                                                                           {
    Aphid*  new_Aphid;
    new_Aphid = new Aphid(data->x, data->y, data->w, data->h, data->L, data->NPM, data->empty_flag, data->starting_suitability, data->starting_popu_density, number, data->index_x, data->index_y, data->species, data->winter_landscape_host, data->summer_landscape_host, data->farm_flag);
    // always 0 since it is a subpopulation model
  
    //the simulation starts from Jan, we only have some eggs from the beginning.
    if(number > 0){
     //updateWholePopulationArray(toa_Egg, number);
     new_Aphid -> addAnimalNumGivenStageColumn(toa_Egg, 0, number);
     }
  
    new_Aphid->setWeightBiomass(data->random_biomass_weight);
    return new_Aphid;
 }

References struct_Aphid::empty_flag, struct_Aphid::farm_flag, struct_Aphid::h, struct_Aphid::index_x, struct_Aphid::index_y, struct_Aphid::L, struct_Aphid::NPM, struct_Aphid::random_biomass_weight, struct_Aphid::species, struct_Aphid::starting_popu_density, struct_Aphid::starting_suitability, struct_Aphid::summer_landscape_host, toa_Egg, struct_Aphid::w, struct_Aphid::winter_landscape_host, struct_Aphid::x, and struct_Aphid::y.

Referenced by initialiseSimWithEggs().

◆ doSpeciesLastThing()

void Aphid_Population_Manager::doSpeciesLastThing ( )

virtual

The function to return the species.

                                                    {
     
     for (int i = toa_Aptera; i<= toa_Male; i++){
         while(m_accumu_degree_days(i, m_index_new_old(i,1)) >= m_max_day_degree_adult){
             m_accumu_degree_days(i, m_index_new_old(i, 1)) = 0.0;
             m_index_new_old(i, 1) += 1;
             //when it reaches the end, set it to zero
             if (m_index_new_old(i,1) >= m_max_alive_days){
                 m_index_new_old(i,1) = 0;
             }
         }
     }
     
 }

References SubPopulation_Population_Manager::m_accumu_degree_days, SubPopulation_Population_Manager::m_index_new_old, SubPopulation_Population_Manager::m_max_alive_days, m_max_day_degree_adult, toa_Aptera, and toa_Male.

◆ initialisePopulation()

void Aphid_Population_Manager::initialisePopulation ( )

virtual

The function to initialise the population when starting aphid simulation, this function is called in the subpopulation_mananger constructor.

Reimplemented from SubPopulation_Population_Manager.

                                                    {
     //common code for all the aphid species
     //Pea aphid
     cout<<m_aphid_specie_name<<endl;
     if (m_aphid_specie_name == "Pea aphid"){
         m_ListNames[0]="Egg";
         m_ListNames[1]="Nymph";
         m_ListNames[2]="NymphW";
         m_ListNames[3]="NymphF";
         m_ListNames[4]="NymphM";
         m_ListNames[5]="Aptera";
         m_ListNames[6]="Alate";
         m_ListNames[7]="Female";
         m_ListNames[8]="Male";
         m_ListNameLength = 9;
         m_SimulationName = "Pea aphid simulation";
         m_running_species_number = toas_PEA;
         //read the host file
         readHosts(cfg_PEAAphidHostFile.value());
  
         //set the parameters
         m_aphid_egg_mortality = cfg_PEAAphidEggMortalityRate.value();
         m_aphid_egg_mortality_sd = cfg_PEAAphidEggMortalityRateStd.value();
         m_aphid_nymph_mortality_para_a = cfg_PEAAphidNymphMortalityParaA.value();
         m_aphid_nymph_mortality_para_b = cfg_PEAAphidNymphMortalityParaB.value();
         m_aphid_nymph_mortality_para_c = cfg_PEAAphidNymphMortalityParaC.value();
         m_aphid_adult_mortality_para_a = cfg_PEAAphidAdultMortalityParaA.value();
         m_aphid_adult_mortality_para_b = cfg_PEAAphidAdultMortalityParaB.value();
         m_aphid_adult_mortality_para_c = cfg_PEAAphidAdultMortalityParaC.value();
         m_aphid_adult_longevity_para_a = cfg_PEAAphidLongevityParaA.value();
         m_aphid_adult_longevity_para_b = cfg_PEAAphidLongevityParaB.value();
         for (int i=0; i<cfg_PEAAphidDevelopmentBaseTempArray.value().size(); i++){
             m_lowest_temp_dev(i) = cfg_PEAAphidDevelopmentBaseTempArray.value()[i];
             m_turning_temp_dev(i) = cfg_PEAAphidDevelopmentTurningTempArray.value()[i];
             m_weight_dd_lower_turning_temp_dev(i) = (m_turning_temp_dev(i)-m_lowest_temp_dev(i))/m_turning_temp_dev(i);
         }
         m_turning_temp_dev_used_flag = cfg_PEAAphidDualLinearModelFlagDD.value();
         m_aphid_egg_starting_degree_days = cfg_PEAAphidEggStartingADD.value();
         m_aphid_egg_hatch_chance_para_a = cfg_PEAAphidEggHatchChanceParaA.value();
         m_aphid_egg_hatch_chance_para_b = cfg_PEAAphidEggHatchChanceParaB.value();
         m_aphid_egg_hatch_chance_threshold = cfg_PEAAphidEggHatchDelayThreshold.value();
         m_aphid_egg_hatch_delay_degree_days = cfg_PEAAphidEggHatchDelayDD.value();
         m_aphid_nymph_with_wings_development_day_degrees = cfg_PEAAphidNymphDevDayDegWing.value();
         m_aphid_nymph_with_wings_development_day_degrees_sd = cfg_PEAAphidNymphDevDayDegWingStd.value();
         m_aphid_nymph_without_wings_development_day_degrees = cfg_PEAAphidNymphDevDayDegNoWing.value();
         m_aphid_nymph_without_wings_development_day_degrees_sd = cfg_PEAAphidNymphDevDayDegNoWingStd.value();
         m_aphid_egg_production_para_a = cfg_PEAAphidEggReproductionParaA.value();
         m_aphid_egg_production_para_b = cfg_PEAAphidEggReproductionParaB.value();
         m_aphid_egg_production_para_c = cfg_PEAAphidEggReproductionParaC.value();
         m_aphid_egg_production_para_sd = cfg_PEAAphidEggReproductionParaSTD.value();
         m_aphid_nymph_production_para_a1 = cfg_PEAAphidNymphReproductionParaA1.value();
         m_aphid_nymph_production_para_b1 = cfg_PEAAphidNymphReproductionParaB1.value();
         m_aphid_nymph_production_para_a2 = cfg_PEAAphidNymphReproductionParaA2.value();
         m_aphid_nymph_production_para_b2 = cfg_PEAAphidNymphReproductionParaB2.value();
         m_aphid_nymph_production_changing_add = cfg_PEAAphidNymphReproductionChangeADD.value();
         m_aphid_nymph_production_temp_weight_para_a = cfg_PEAAphidNymphReproductionTempWeightParaA.value();
         m_aphid_nymph_production_temp_weight_para_b = cfg_PEAAphidNymphReproductionTempWeightParaB.value();
         m_aphid_nymph_production_temp_weight_para_c = cfg_PEAAphidNymphReproductionTempWeightParaC.value();
         m_aphid_alate_proportion_para_a = cfg_PEAAphidAlatePropParaA.value();
         m_aphid_alate_proportion_para_b = cfg_PEAAphidAlatePropParaB.value();
         m_aphid_alate_proportion_para_c = cfg_PEAAphidAlatePropParaC.value();
         m_aphid_male_reproduction_day_length = cfg_PEAAphidDayLengthMale.value();
         m_aphid_female_reproduction_day_length = cfg_PEAAphidDayLengthFemale.value();
         int temp_length = cfg_PEAAphidAdultMortalityDdeg.value().size();
         m_aphid_adult_mortality_inflection_point_dd.resize(temp_length);
         m_aphid_adult_mortality_vec.resize(temp_length);
         for (int i =0; i<temp_length; i++){
             m_aphid_adult_mortality_inflection_point_dd[i] = cfg_PEAAphidAdultMortalityDdeg.value()[i];
             m_aphid_adult_mortality_vec[i] = cfg_PEAAphidAdultMortality.value()[i];
         }
         m_aphid_sexual_reproduction_average_add = cfg_PEAphidSexualDevelopmentRequiredDdeg.value();
         m_aphid_sexual_reproduction_add_sd = cfg_PEAphidSexualDevelopmentRequiredDdegStd.value();
  
  
         //set the function pointers
         m_next_life_func_pointer = &Aphid_Population_Manager::calNextStageShared;
         m_update_mortality_array_pointer = &Aphid_Population_Manager::updateMortalityArrayShared;
         m_offspring_func_pointer = &Aphid_Population_Manager::calOffspringStageEGandPEA;
         m_is_ready_next_liff_func_pointer = &Aphid_Population_Manager::isEnoughNextLifeStageShared;
  
         //Life stages that can fly
         m_flying_life_stage_array.clear();
         m_flying_life_stage_array.push_back(toa_Alate);
         m_landing_life_stage_array.clear();
         m_landing_life_stage_array.push_back(toa_Aptera);
         m_local_moving_life_stage_array.clear();
         m_local_moving_life_stage_array.push_back(toa_Aptera);
         //m_local_moving_life_stage_array.push_back(toa_Alate);
         //m_local_moving_life_stage_array.push_back(toa_Female);
         m_max_day_degree_adult = cfg_PEAAphidAdultMortalityDdeg.value()[cfg_PEAAphidAdultMortalityDdeg.value().size()-1];       
     }
  
     //English grain aphid
     if (m_aphid_specie_name == "English grain aphid"){
         m_ListNames[0]="Egg";
         m_ListNames[1]="Nymph";
         m_ListNames[2]="NymphW";
         m_ListNames[3]="NymphF";
         m_ListNames[4]="NymphM";
         m_ListNames[5]="Aptera";
         m_ListNames[6]="Alate";
         m_ListNames[7]="Female";
         m_ListNames[8]="Male";
         m_ListNameLength = 9;
         m_running_species_number = toas_EG;
         m_SimulationName = "English grain aphid simulation";
         //read the host file
         readHosts(cfg_EGAphidHostFile.value());
  
         //set the parameters
         m_aphid_egg_mortality = cfg_EGAphidEggMortalityRate.value();
         m_aphid_egg_mortality_sd = cfg_EGAphidEggMortalityRateStd.value();
         m_aphid_nymph_mortality_para_a = cfg_EGAphidNymphMortalityParaA.value();
         m_aphid_nymph_mortality_para_b = cfg_EGAphidNymphMortalityParaB.value();
         m_aphid_nymph_mortality_para_c = cfg_EGAphidNymphMortalityParaC.value();
         m_aphid_adult_mortality_para_a = cfg_EGAphidAdultMortalityParaA.value();
         m_aphid_adult_mortality_para_b = cfg_EGAphidAdultMortalityParaB.value();
         m_aphid_adult_mortality_para_c = cfg_EGAphidAdultMortalityParaC.value();
         m_aphid_adult_longevity_para_a = cfg_EGAphidLongevityParaA.value();
         m_aphid_adult_longevity_para_b = cfg_EGAphidLongevityParaB.value();
         for (int i=0; i<cfg_EGAphidDevelopmentBaseTempArray.value().size(); i++){
             m_lowest_temp_dev(i) = cfg_EGAphidDevelopmentBaseTempArray.value()[i];
             m_turning_temp_dev(i) = cfg_EGAphidDevelopmentTurningTempArray.value()[i];
             m_weight_dd_lower_turning_temp_dev(i) = (m_turning_temp_dev(i)-m_lowest_temp_dev(i))/m_turning_temp_dev(i);
         }
         m_turning_temp_dev_used_flag = cfg_EGAphidDualLinearModelFlagDD.value();
         m_aphid_egg_starting_degree_days = cfg_EGAphidEggStartingADD.value();
         m_aphid_egg_hatch_chance_para_a = cfg_EGAphidEggHatchChanceParaA.value();
         m_aphid_egg_hatch_chance_para_b = cfg_EGAphidEggHatchChanceParaB.value();
         m_aphid_egg_hatch_chance_threshold = cfg_EGAphidEggHatchDelayThreshold.value();
         m_aphid_egg_hatch_delay_degree_days = cfg_EGAphidEggHatchDelayDD.value();
         m_aphid_nymph_with_wings_development_day_degrees = cfg_EGAphidNymphDevDayDegWing.value();
         m_aphid_nymph_with_wings_development_day_degrees_sd = cfg_EGAphidNymphDevDayDegWingStd.value();
         m_aphid_nymph_without_wings_development_day_degrees = cfg_EGAphidNymphDevDayDegNoWing.value();
         m_aphid_nymph_without_wings_development_day_degrees_sd = cfg_EGAphidNymphDevDayDegNoWingStd.value();
         m_aphid_egg_production_para_a = cfg_EGAphidEggReproductionParaA.value();
         m_aphid_egg_production_para_b = cfg_EGAphidEggReproductionParaB.value();
         m_aphid_egg_production_para_c = cfg_EGAphidEggReproductionParaC.value();
         m_aphid_egg_production_para_sd = cfg_EGAphidEggReproductionParaSTD.value();
         m_aphid_nymph_production_para_a1 = cfg_EGAphidNymphReproductionParaA1.value();
         m_aphid_nymph_production_para_b1 = cfg_EGAphidNymphReproductionParaB1.value();
         m_aphid_nymph_production_para_a2 = cfg_EGAphidNymphReproductionParaA2.value();
         m_aphid_nymph_production_para_b2 = cfg_EGAphidNymphReproductionParaB2.value();
         m_aphid_nymph_production_changing_add = cfg_EGAphidNymphReproductionChangeADD.value();
         m_aphid_nymph_production_temp_weight_para_a = cfg_EGAphidNymphReproductionTempWeightParaA.value();
         m_aphid_nymph_production_temp_weight_para_b = cfg_EGAphidNymphReproductionTempWeightParaB.value();
         m_aphid_nymph_production_temp_weight_para_c = cfg_EGAphidNymphReproductionTempWeightParaC.value();
         m_aphid_alate_proportion_para_a = cfg_EGAphidAlatePropParaA.value();
         m_aphid_alate_proportion_para_b = cfg_EGAphidAlatePropParaB.value();
         m_aphid_alate_proportion_para_c = cfg_EGAphidAlatePropParaC.value();
         m_aphid_male_reproduction_day_length = cfg_EGAphidDayLengthMale.value();
         m_aphid_female_reproduction_day_length = cfg_EGAphidDayLengthFemale.value();
         int temp_length = cfg_EGAphidAdultMortalityDdeg.value().size();
         m_aphid_adult_mortality_inflection_point_dd.resize(temp_length);
         m_aphid_adult_mortality_vec.resize(temp_length);
         for (int i =0; i<temp_length; i++){
             m_aphid_adult_mortality_inflection_point_dd[i] = cfg_EGAphidAdultMortalityDdeg.value()[i];
             m_aphid_adult_mortality_vec[i] = cfg_EGAphidAdultMortality.value()[i];
         }
         m_aphid_sexual_reproduction_average_add = cfg_EGAphidSexualDevelopmentRequiredDdeg.value();
         m_aphid_sexual_reproduction_add_sd = cfg_EGAphidSexualDevelopmentRequiredDdegStd.value();
  
  
         //set the function pointers
         m_next_life_func_pointer = &Aphid_Population_Manager::calNextStageShared;
         m_update_mortality_array_pointer = &Aphid_Population_Manager::updateMortalityArrayShared;
         //same as pea aphid
         m_offspring_func_pointer = &Aphid_Population_Manager::calOffspringStageEGandPEA;
         m_is_ready_next_liff_func_pointer = &Aphid_Population_Manager::isEnoughNextLifeStageShared;
  
         //Life stages that can fly
         m_flying_life_stage_array.clear();
         m_flying_life_stage_array.push_back(toa_Alate);
         m_landing_life_stage_array.clear();
         m_landing_life_stage_array.push_back(toa_Aptera);
         m_local_moving_life_stage_array.clear();
         m_local_moving_life_stage_array.push_back(toa_Aptera);
         //m_local_moving_life_stage_array.push_back(toa_Alate);
         m_local_moving_life_stage_array.push_back(toa_Female);
         m_max_day_degree_adult = cfg_EGAphidAdultMortalityDdeg.value()[cfg_EGAphidAdultMortalityDdeg.value().size()-1];
     }
  
     //Aphis fabae
     if (m_aphid_specie_name == "Aphis fabae"){
         m_ListNames[0]="Egg";
         m_ListNames[1]="Nymph";
         m_ListNames[2]="NymphW";
         m_ListNames[3]="NymphF";
         m_ListNames[4]="NymphM";
         m_ListNames[5]="Aptera";
         m_ListNames[6]="Alate";
         m_ListNames[7]="Female";
         m_ListNames[8]="Male";
         m_ListNameLength = 9;
         m_SimulationName = "Aphis fabae Simulation";
         m_running_species_number = toas_BB;
         readHosts(cfg_BBAphidHostFile.value());
         
  
         //set the parameters
         m_aphid_egg_mortality = cfg_BBAphidEggMortalityRate.value();
         m_aphid_egg_mortality_sd = cfg_BBAphidEggMortalityRateStd.value();
         m_aphid_nymph_mortality_para_a = cfg_BBAphidNymphMortalityParaA.value();
         m_aphid_nymph_mortality_para_b = cfg_BBAphidNymphMortalityParaB.value();
         m_aphid_nymph_mortality_para_c = cfg_BBAphidNymphMortalityParaC.value();
         m_aphid_adult_mortality_para_a = cfg_BBAphidAdultMortalityParaA.value();
         m_aphid_adult_mortality_para_b = cfg_BBAphidAdultMortalityParaB.value();
         m_aphid_adult_mortality_para_c = cfg_BBAphidAdultMortalityParaC.value();
         m_aphid_adult_longevity_para_a = cfg_BBAphidLongevityParaA.value();
         m_aphid_adult_longevity_para_b = cfg_BBAphidLongevityParaB.value();
         for (int i=0; i<cfg_BBAphidDevelopmentBaseTempArray.value().size(); i++){
             m_lowest_temp_dev(i) = cfg_BBAphidDevelopmentBaseTempArray.value()[i];
             m_turning_temp_dev(i) = cfg_BBAphidDevelopmentTurningTempArray.value()[i];
             m_weight_dd_lower_turning_temp_dev(i) = (m_turning_temp_dev(i)-m_lowest_temp_dev(i))/m_turning_temp_dev(i);
         }
         m_turning_temp_dev_used_flag = cfg_BBAphidDualLinearModelFlagDD.value();
         m_aphid_egg_starting_degree_days = cfg_BBAphidEggStartingADD.value();
         m_aphid_egg_hatch_chance_para_a = cfg_BBAphidEggHatchChanceParaA.value();
         m_aphid_egg_hatch_chance_para_b = cfg_BBAphidEggHatchChanceParaB.value();
         m_aphid_egg_hatch_chance_threshold = cfg_BBAphidEggHatchDelayThreshold.value();
         m_aphid_egg_hatch_delay_degree_days = cfg_BBAphidEggHatchDelayDD.value();
         m_aphid_nymph_with_wings_development_day_degrees = cfg_BBAphidNymphDevDayDegWing.value();
         m_aphid_nymph_with_wings_development_day_degrees_sd = cfg_BBAphidNymphDevDayDegWingStd.value();
         m_aphid_nymph_without_wings_development_day_degrees = cfg_BBAphidNymphDevDayDegNoWing.value();
         m_aphid_nymph_without_wings_development_day_degrees_sd = cfg_BBAphidNymphDevDayDegNoWingStd.value();
         m_aphid_egg_production_para_a = cfg_BBAphidEggReproductionParaA.value();
         m_aphid_egg_production_para_b = cfg_BBAphidEggReproductionParaB.value();
         m_aphid_egg_production_para_c = cfg_BBAphidEggReproductionParaC.value();
         m_aphid_egg_production_para_sd = cfg_BBAphidEggReproductionParaSTD.value();
         m_aphid_nymph_production_para_a1 = cfg_BBAphidNymphReproductionParaA1.value();
         m_aphid_nymph_production_para_b1 = cfg_BBAphidNymphReproductionParaB1.value();
         m_aphid_nymph_production_para_a2 = cfg_BBAphidNymphReproductionParaA2.value();
         m_aphid_nymph_production_para_b2 = cfg_BBAphidNymphReproductionParaB2.value();
         m_aphid_nymph_production_changing_add = cfg_BBAphidNymphReproductionChangeADD.value();
         m_aphid_nymph_production_temp_weight_para_a = cfg_BBAphidNymphReproductionTempWeightParaA.value();
         m_aphid_nymph_production_temp_weight_para_b = cfg_BBAphidNymphReproductionTempWeightParaB.value();
         m_aphid_nymph_production_temp_weight_para_c = cfg_BBAphidNymphReproductionTempWeightParaC.value();
         m_aphid_alate_proportion_para_a = cfg_BBAphidAlatePropParaA.value();
         m_aphid_alate_proportion_para_b = cfg_BBAphidAlatePropParaB.value();
         m_aphid_alate_proportion_para_c = cfg_BBAphidAlatePropParaC.value();
         m_aphid_winter_host_day_length = cfg_BBAphidWinterHostDayLength.value();
         m_aphid_summer_host_day_length = cfg_BBAphidSummerHostDayLength.value();
         int temp_length = cfg_BBAphidAdultMortalityDdeg.value().size();
         m_aphid_adult_mortality_inflection_point_dd.resize(temp_length);
         m_aphid_adult_mortality_vec.resize(temp_length);
         for (int i =0; i<temp_length; i++){
             m_aphid_adult_mortality_inflection_point_dd[i] = cfg_BBAphidAdultMortalityDdeg.value()[i];
             m_aphid_adult_mortality_vec[i] = cfg_BBAphidAdultMortality.value()[i];
         }
         m_aphid_sexual_reproduction_average_add = cfg_BBAphidSexualDevelopmentRequiredDdeg.value();
         m_aphid_sexual_reproduction_add_sd = cfg_BBAphidSexualDevelopmentRequiredDdegStd.value();
         
  
         //set the function pointers
         m_next_life_func_pointer = &Aphid_Population_Manager::calNextStageShared;
         m_update_mortality_array_pointer = &Aphid_Population_Manager::updateMortalityArrayShared;
         m_offspring_func_pointer = &Aphid_Population_Manager::calOffspringStageBBandPP;
         m_is_ready_next_liff_func_pointer = &Aphid_Population_Manager::isEnoughNextLifeStageShared;
  
         //Life stages that can fly
         m_flying_life_stage_array.clear();
         m_flying_life_stage_array.push_back(toa_Alate);
         m_landing_life_stage_array.clear();
         m_landing_life_stage_array.push_back(toa_Aptera);
         m_local_moving_life_stage_array.clear();
         m_local_moving_life_stage_array.push_back(toa_Aptera);
         //m_local_moving_life_stage_array.push_back(toa_Alate);
         //m_local_moving_life_stage_array.push_back(toa_Female);
         m_max_day_degree_adult = cfg_BBAphidAdultMortalityDdeg.value()[cfg_BBAphidAdultMortalityDdeg.value().size()-1];
     }
  
     //Peach potato aphid
     if (m_aphid_specie_name == "Peach potato aphid"){
         m_ListNames[0]="Egg";
         m_ListNames[1]="Nymph";
         m_ListNames[2]="NymphW";
         m_ListNames[3]="NymphF";
         m_ListNames[4]="NymphM";
         m_ListNames[5]="Aptera";
         m_ListNames[6]="Alate";
         m_ListNames[7]="Female";
         m_ListNames[8]="Male";
         m_ListNameLength = 9;
         m_SimulationName = "Peach potato aphid Simulation";
         m_running_species_number = toas_PP;
         readHosts(cfg_PPAphidHostFile.value());
         
  
         //set the parameters
         m_aphid_egg_mortality = cfg_PPAphidEggMortalityRate.value();
         m_aphid_egg_mortality_sd = cfg_PPAphidEggMortalityRateStd.value();
         m_aphid_nymph_mortality_para_a = cfg_PPAphidNymphMortalityParaA.value();
         m_aphid_nymph_mortality_para_b = cfg_PPAphidNymphMortalityParaB.value();
         m_aphid_nymph_mortality_para_c = cfg_PPAphidNymphMortalityParaC.value();
         m_aphid_adult_mortality_para_a = cfg_PPAphidAdultMortalityParaA.value();
         m_aphid_adult_mortality_para_b = cfg_PPAphidAdultMortalityParaB.value();
         m_aphid_adult_mortality_para_c = cfg_PPAphidAdultMortalityParaC.value();
         m_aphid_adult_longevity_para_a = cfg_PPAphidLongevityParaA.value();
         m_aphid_adult_longevity_para_b = cfg_PPAphidLongevityParaB.value();
         for (int i=0; i<cfg_PPAphidDevelopmentBaseTempArray.value().size(); i++){
             m_lowest_temp_dev(i) = cfg_PPAphidDevelopmentBaseTempArray.value()[i];
             m_turning_temp_dev(i) = cfg_PPAphidDevelopmentTurningTempArray.value()[i];
             m_weight_dd_lower_turning_temp_dev(i) = (m_turning_temp_dev(i)-m_lowest_temp_dev(i))/m_turning_temp_dev(i);
         }
         m_turning_temp_dev_used_flag = cfg_PPAphidDualLinearModelFlagDD.value();
         m_aphid_egg_starting_degree_days = cfg_PPAphidEggStartingADD.value();
         m_aphid_egg_hatch_chance_para_a = cfg_PPAphidEggHatchChanceParaA.value();
         m_aphid_egg_hatch_chance_para_b = cfg_PPAphidEggHatchChanceParaB.value();
         m_aphid_egg_hatch_chance_threshold = cfg_PPAphidEggHatchDelayThreshold.value();
         m_aphid_egg_hatch_delay_degree_days = cfg_PPAphidEggHatchDelayDD.value();
         m_aphid_nymph_with_wings_development_day_degrees = cfg_PPAphidNymphDevDayDegWing.value();
         m_aphid_nymph_with_wings_development_day_degrees_sd = cfg_PPAphidNymphDevDayDegWingStd.value();
         m_aphid_nymph_without_wings_development_day_degrees = cfg_PPAphidNymphDevDayDegNoWing.value();
         m_aphid_nymph_without_wings_development_day_degrees_sd = cfg_PPAphidNymphDevDayDegNoWingStd.value();
         m_aphid_egg_production_para_a = cfg_PPAphidEggReproductionParaA.value();
         m_aphid_egg_production_para_b = cfg_PPAphidEggReproductionParaB.value();
         m_aphid_egg_production_para_c = cfg_PPAphidEggReproductionParaC.value();
         m_aphid_egg_production_para_sd = cfg_PPAphidEggReproductionParaSTD.value();
         m_aphid_nymph_production_para_a1 = cfg_PPAphidNymphReproductionParaA1.value();
         m_aphid_nymph_production_para_b1 = cfg_PPAphidNymphReproductionParaB1.value();
         m_aphid_nymph_production_para_a2 = cfg_PPAphidNymphReproductionParaA2.value();
         m_aphid_nymph_production_para_b2 = cfg_PPAphidNymphReproductionParaB2.value();
         m_aphid_nymph_production_changing_add = cfg_PPAphidNymphReproductionChangeADD.value();
         m_aphid_nymph_production_temp_weight_para_a = cfg_PPAphidNymphReproductionTempWeightParaA.value();
         m_aphid_nymph_production_temp_weight_para_b = cfg_PPAphidNymphReproductionTempWeightParaB.value();
         m_aphid_nymph_production_temp_weight_para_c = cfg_PPAphidNymphReproductionTempWeightParaC.value();
         m_aphid_alate_proportion_para_a = cfg_PPAphidAlatePropParaA.value();
         m_aphid_alate_proportion_para_b = cfg_PPAphidAlatePropParaB.value();
         m_aphid_alate_proportion_para_c = cfg_PPAphidAlatePropParaC.value();
         m_aphid_winter_host_day_length = cfg_PPAphidWinterHostDayLength.value();
         m_aphid_summer_host_day_length = cfg_PPAphidSummerHostDayLength.value();
         int temp_length = cfg_PPAphidAdultMortalityDdeg.value().size();
         m_aphid_adult_mortality_inflection_point_dd.resize(temp_length);
         m_aphid_adult_mortality_vec.resize(temp_length);
         for (int i =0; i<temp_length; i++){
             m_aphid_adult_mortality_inflection_point_dd[i] = cfg_PPAphidAdultMortalityDdeg.value()[i];
             m_aphid_adult_mortality_vec[i] = cfg_PPAphidAdultMortality.value()[i];
         }
         m_aphid_sexual_reproduction_average_add = cfg_PPAphidSexualDevelopmentRequiredDdeg.value();
         m_aphid_sexual_reproduction_add_sd = cfg_PPAphidSexualDevelopmentRequiredDdegStd.value();
  
         //set the function pointers
         m_next_life_func_pointer = &Aphid_Population_Manager::calNextStageShared;
         m_update_mortality_array_pointer = &Aphid_Population_Manager::updateMortalityArrayShared;
         //same as pea aphid
         m_offspring_func_pointer = &Aphid_Population_Manager::calOffspringStageBBandPP;
         m_is_ready_next_liff_func_pointer = &Aphid_Population_Manager::isEnoughNextLifeStageShared;
  
         //Life stages that can fly
         m_flying_life_stage_array.clear();
         m_flying_life_stage_array.push_back(toa_Alate);
         m_landing_life_stage_array.clear();
         m_landing_life_stage_array.push_back(toa_Aptera);
         m_local_moving_life_stage_array.clear();
         m_local_moving_life_stage_array.push_back(toa_Aptera);
         //m_local_moving_life_stage_array.push_back(toa_Alate);
         //m_local_moving_life_stage_array.push_back(toa_Female);
         m_max_day_degree_adult = cfg_PPAphidAdultMortalityDdeg.value()[cfg_PPAphidAdultMortalityDdeg.value().size()-1];
     }
  
     //m_max_day_degree_adult = -1*m_aphid_adult_longevity_para_b/m_aphid_adult_longevity_para_a;
     m_max_adult_dd = ceil(m_max_day_degree_adult);
  
     //initialise the simulation
     initialiseSimWithEggs();        
 }

Referenced by Aphid_Population_Manager().

◆ initialiseSimWithEggs()

void Aphid_Population_Manager::initialiseSimWithEggs ( void )

The function to initilise the simulation with eggs.

                                                           {
     int index_cell_i = 0;
     int index_cell_j = 0;
     struct_Aphid* sp;
     sp = new struct_Aphid;
     sp->NPM = this;
     sp->L = m_TheLandscape;
     //creat the aphid in each cell
     double different_count[4] = {0, 0, 0, 0};
     for (int i=0; i<SimW; i=i+m_sub_w)
     {
         index_cell_j = 0;
         for(int j=0; j<SimH; j=j+m_sub_h)
         {
             /*
             vector<int> poly_id_vec;
             bool not_found = true;
             int temp_poly_id;
             for(int check_x=i+m_sub_w/4; check_x<i+m_sub_w; check_x+=m_sub_w/2){
                 for(int check_y=j+m_sub_h/4; check_y<j+m_sub_h; check_y+=m_sub_h/2){
                     temp_poly_id = m_TheLandscape->SupplyPolyRef(check_x, check_y);
                     if (std::find(poly_id_vec.begin(), poly_id_vec.end(), temp_poly_id) == poly_id_vec.end())
                     poly_id_vec.push_back(temp_poly_id);
                     //cout<<check_x<<";"<<check_y<<";"<<endl;
                 }
             }
             //cout<<poly_id_vec[0]<<";"<<poly_id_vec[1]<<";"<<poly_id_vec[2]<<";"<<poly_id_vec[3]<<";"<<endl;
             different_count[poly_id_vec.size()-1] += 1;
             poly_id_vec.clear();
             */
             sp->x = i+m_sub_w/2.0; //use the center of the cell as the location
             sp->y = j+m_sub_h/2.0;
             sp->w = m_sub_w;
             sp->h = m_sub_h;
             sp->NPM = this;
             sp->empty_flag = true;
             sp->index_x = index_cell_i;
             sp->index_y = index_cell_j;
             TTypesOfLandscapeElement current_landtype = m_TheLandscape->SupplyElementType(sp->x, sp->y);
             sp->starting_popu_density = &(m_cell_popu_density(index_cell_j, index_cell_i));
             sp->starting_suitability = &(m_cell_suitability(index_cell_j, index_cell_i));
             sp->winter_landscape_host = tole_Foobar;
             sp->summer_landscape_host = tole_Foobar;
             //set the farm flag
             if(current_landtype == tole_Field){
                 sp->farm_flag = true;
                 sp->empty_flag = false;
                 sp->random_biomass_weight=1.0;
             }
             else {
                 sp->farm_flag = false;
                 sp->random_biomass_weight=g_rand_uni_fnc();
             }
             
             //double current_biomass = m_TheLandscape->SupplyGreenBiomassTotal(sp->x, sp->y);
             double current_biomass = m_TheLandscape->SupplyInterestedGreenBiomassTotal(sp->x, sp->y);
             //check whether there are multi-seaon host, if yes, use winter host to initialise, othervise using the summer host list. 
             
             bool suitable_flag = false;
             if(m_mul_hosts_flag){
                 suitable_flag = isWinterHostTole(current_landtype);
                 if (suitable_flag){
                     sp->winter_landscape_host = current_landtype;
                 }
                 
                 if(isSummerHostTole(current_landtype)){
                     sp->summer_landscape_host = current_landtype;
                 }
  
 /*              //if it is farm, check the vegetation
                 if(!suitable_flag){
                     suitable_flag = isWinterHostTov(m_TheLandscape->SupplyVegType(sp->x, sp->y));
                 }
                 */
             }
             else{
                 suitable_flag = isSummerHostTole(current_landtype);
                 if(suitable_flag){
                     sp->summer_landscape_host = current_landtype;
                     sp->empty_flag = false;
                 }
                 if (sp->farm_flag) suitable_flag = false;
                 /*
                  *if it is farm, check the vegetation
                 if(suitable_flag && sp->farm_flag){
                     suitable_flag = false;
                     if(isSummerHostTov(m_TheLandscape->SupplyVegType(sp->x, sp->y))){
                         if (m_TheLandscape->SupplyGreenBiomass(sp->x, sp->y) > 0) {
                             suitable_flag = true;
                         }
                     }
                 } */
             }
  
             if(suitable_flag){
                 //sp->starting_suitability = 1;
                 m_the_subpopulation_array[index_cell_j][index_cell_i] = CreateObjects(NULL, sp, cfg_AphidEggStartingNumVec.value()[m_running_species_number]);
                 m_accumu_degree_days(0,0) = m_aphid_egg_starting_degree_days;
                 m_cell_suitability(index_cell_j, index_cell_i) = 1;
             }
             //else if(!sp->empty_flag){
             //  m_the_subpopulation_array[index_cell_j][index_cell_i] = CreateObjects(NULL, sp, 0);
             //  m_cell_suitability(index_cell_j, index_cell_i) = 0;
             //}
             else{
                 //m_the_subpopulation_array[index_cell_j][index_cell_i] = NULL;
                 m_the_subpopulation_array[index_cell_j][index_cell_i] = CreateObjects(NULL, sp, 0);
                 m_cell_suitability(index_cell_j, index_cell_i) = 0;
             }
  
             //add the pointer to its belonging polygon
             int temp_poly_id = m_TheLandscape->SupplyPolyRefIndex(sp->x, sp->y);
             m_vec_subpopulation_pointers_polygon[temp_poly_id].push_back(m_the_subpopulation_array[index_cell_j][index_cell_i]);        
             index_cell_j++;
         }
         index_cell_i++;
     }
     /*
     double temp_sum = different_count[0]+different_count[1]+different_count[2]+different_count[3];
     cout<<"Different: "<<different_count[0]/temp_sum<<";"<<different_count[1]/temp_sum<<";"<<different_count[2]/temp_sum<<";"<<different_count[3]/temp_sum<<";"<<temp_sum<<endl;
     exit(0);
     */
     m_current_developtype = toAphidHibernate;
     delete sp;
 }

Referenced by initialisePopulation().

◆ isEnoughNextLifeStage()

bool Aphid_Population_Manager::isEnoughNextLifeStage ( int a_life_stage )

virtual

\breif The functions to test whether it is ready for the next life stages for aphid.

Reimplemented from SubPopulation_Population_Manager.

                                                                     {
     return (this->*m_is_ready_next_liff_func_pointer)(a_life_stage);
 }

References m_is_ready_next_liff_func_pointer.

◆ isEnoughNextLifeStageShared()

bool Aphid_Population_Manager::isEnoughNextLifeStageShared ( int a_life_stage )

                                                                           {
     //Eggs only start to accumulate degree days after the first day of the simulation, always return false
     //The hatch channces are calculated in the update function
     if(a_life_stage == toa_Egg){
         return false;
     }
  
     if (a_life_stage == toa_Nymph || a_life_stage == toa_Nymph_F || a_life_stage == toa_Nymph_M) {
         if (m_accumu_degree_days(a_life_stage, m_index_new_old(a_life_stage,1)) >= m_aphid_nymph_without_wings_development_day_degrees + (g_rand_uni_fnc()-0.5)*m_aphid_nymph_without_wings_development_day_degrees_sd){
             return true;
         }
         else return false;
     }
     /*if (a_life_stage == toa_Nymph || a_life_stage == toa_Nymph_F || a_life_stage == toa_Nymph_M) {
         double threshold = m_aphid_nymph_without_wings_development_day_degrees + (g_rand_uni_fnc() - 0.5) * m_aphid_nymph_without_wings_development_day_degrees_sd;
         if(farm_flag) {
             threshold *= 0.9; //reduce development time by 10% for crops
         }
         if (m_accumu_degree_days(a_life_stage, m_index_new_old(a_life_stage, 1)) >= m_aphid_nymph_without_wings_development_day_degrees + (g_rand_uni_fnc() - 0.5) * m_aphid_nymph_without_wings_development_day_degrees_sd) {
             return true;
         }
         else return false;
     }*/
  
     if(a_life_stage == toa_Nymph_W ){
         if (m_accumu_degree_days(a_life_stage, m_index_new_old(a_life_stage,1)) >= m_aphid_nymph_with_wings_development_day_degrees + (g_rand_uni_fnc()-0.5)*m_aphid_nymph_with_wings_development_day_degrees_sd){
             return true;
         }
         else return false;
     }
  
     //the adults are contolled by the mortality
     return (m_accumu_degree_days(a_life_stage, m_index_new_old(a_life_stage,1))>=m_max_adult_dd);
 }

References g_rand_uni_fnc(), SubPopulation_Population_Manager::m_accumu_degree_days, m_aphid_nymph_with_wings_development_day_degrees, m_aphid_nymph_with_wings_development_day_degrees_sd, m_aphid_nymph_without_wings_development_day_degrees, m_aphid_nymph_without_wings_development_day_degrees_sd, SubPopulation_Population_Manager::m_index_new_old, m_max_adult_dd, toa_Egg, toa_Nymph, toa_Nymph_F, toa_Nymph_M, and toa_Nymph_W.

Referenced by initialisePopulation().

◆ KillAphid()

void Aphid_Population_Manager::KillAphid	(	int	a_x,
		int	a_y,
		double	a_num
	)

Function to kill the given number of aphids in the given location.

                                                                          {
     a_y = a_y/m_sub_h;
     a_x = a_x/m_sub_w;
     //a_num *= 1;
     return m_the_subpopulation_array[a_y][a_x]->killByPredator(a_num);
 }

References SubPopulation_Population_Manager::m_sub_h, SubPopulation_Population_Manager::m_sub_w, and SubPopulation_Population_Manager::m_the_subpopulation_array.

◆ SupplyAphidDensity()

double Aphid_Population_Manager::SupplyAphidDensity	(	int	a_x,
		int	a_y
	)

Function to supply the aphid density in the given location.

                                                                        {
     a_y = a_y/m_sub_h;
     a_x = a_x/m_sub_w;
     if(m_the_subpopulation_array[a_y][a_x]==NULL) return 0;
     return m_the_subpopulation_array[a_y][a_x]->getRawPopuDensity();
 }

References SubPopulation_Population_Manager::m_sub_h, SubPopulation_Population_Manager::m_sub_w, and SubPopulation_Population_Manager::m_the_subpopulation_array.

◆ supplyDevelopmentSeason()

virtual unsigned Aphid_Population_Manager::supplyDevelopmentSeason ( )

inlinevirtual

The function to supply the development season.

Reimplemented from SubPopulation_Population_Manager.

235 {return m_current_developtype;}

References m_current_developtype.

◆ supplyNymphNumWeight()

double Aphid_Population_Manager::supplyNymphNumWeight ( void )

inline

The function to return the daily nymph number weight.

256 {return m_nymph_produced_num_weight;}

References m_nymph_produced_num_weight.

◆ updateDevelopmentSeason()

void Aphid_Population_Manager::updateDevelopmentSeason ( )

virtual

The function to update the development season.

Reimplemented from SubPopulation_Population_Manager.

                                                       {
     // Reset the day degree sum for egg production at Jan 1st
     if (m_TheLandscape->SupplyDayInYear() < 1) m_accu_ddeg_egg_reproduction = 0;
     if(!m_mul_hosts_flag){
         return;
     }
     else{
         double current_day_length = g_landscape_ptr->SupplyDaylength();
         if(current_day_length >= m_aphid_summer_host_day_length){
             m_summer_host_on = true;
         }
         else{
             m_summer_host_on = false;
         }
  
         if(current_day_length <= m_aphid_winter_host_day_length){
             m_winter_host_on = true;
         }
         else{
             m_winter_host_on = false;
         }
     }
 }

References g_landscape_ptr, m_accu_ddeg_egg_reproduction, m_aphid_summer_host_day_length, m_aphid_winter_host_day_length, SubPopulation_Population_Manager::m_mul_hosts_flag, SubPopulation_Population_Manager::m_summer_host_on, Population_Manager_Base::m_TheLandscape, SubPopulation_Population_Manager::m_winter_host_on, Landscape::SupplyDayInYear(), and Landscape::SupplyDaylength().

◆ updateMortalityArray()

void Aphid_Population_Manager::updateMortalityArray ( void )

virtual

The fucntion to update the base mortality rate, it will call the corresponding function pointer.

Reimplemented from SubPopulation_Population_Manager.

                                                        {
     (this->*m_update_mortality_array_pointer)();
 }

References m_update_mortality_array_pointer.

◆ updateMortalityArrayShared()

void Aphid_Population_Manager::updateMortalityArrayShared ( void )

The function to calculate the base mortality rate for all aphids.

                                                              {
  
     m_current_mortality_array.setZero();
     //egg
     m_current_mortality_array.row(toa_Egg).fill(m_aphid_egg_mortality + (g_rand_uni_fnc() - 0.5) * 2 * m_aphid_egg_mortality_sd);
  
     //nymph
     //get the current temperature
     /*double total_nymph_temp_mort = 0;
     for (int time_counter=0; time_counter<24; time_counter ++) {
             double current_temp_hour = g_landscape_ptr->SupplyTempHour(time_counter);
             double nymph_temp_mort = m_aphid_nymph_mortality_para_a * current_temp_hour * current_temp_hour + m_aphid_nymph_mortality_para_b * current_temp_hour + m_aphid_nymph_mortality_para_c;
             if (nymph_temp_mort < 0) nymph_temp_mort = 0;
             if (nymph_temp_mort > 1) nymph_temp_mort = 1;
             total_nymph_temp_mort += nymph_temp_mort;
     }
     double daily_average_mort = total_nymph_temp_mort / 24;
     m_current_mortality_array.middleRows(toa_Nymph, toa_Nymph_M - toa_Nymph + 1).fill(daily_average_mort);
     //m_current_mortality_array.middleRows(toa_Nymph, toa_Nymph_M - toa_Nymph + 1).fill(m_aphid_nymph_mortality_para_a * current_temp_hour * current_temp_hour + m_aphid_nymph_mortality_para_b * current_temp_hour + m_aphid_nymph_mortality_para_c);
  
     //adults    
     double total_adult_temp_mort = 0;
     for (int time_counter = 0; time_counter < 24; time_counter++) {
         double current_temp_hour = g_landscape_ptr->SupplyTempHour(time_counter);
         double adult_temp_mort = m_aphid_adult_mortality_para_a * current_temp_hour * current_temp_hour + m_aphid_adult_mortality_para_b * current_temp_hour + m_aphid_adult_mortality_para_c;
         if (adult_temp_mort < 0) adult_temp_mort = 0;
         if (adult_temp_mort > 1) adult_temp_mort = 1;
         total_adult_temp_mort += adult_temp_mort;
     }
     double daily_average_mort_adult = total_adult_temp_mort / 24;
     m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() += daily_average_mort_adult;
     */
     //Set temperature mortalities for adults
     double current_temperature = g_landscape_ptr->SupplyTemp();
     if (current_temperature < -9 || current_temperature > 34.5){
         m_current_mortality_array.middleRows(toa_Aptera, toa_Male-toa_Aptera+1).fill(0.99);
     }
     else{
         /*
         m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() = 1.0 - (m_accumu_degree_days.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() * cfg_AphidLongevityParaA.value() + cfg_AphidLongevityParaB.value());
         //we need to rethink about this
         int current_month = m_TheLandscape->SupplyMonth();
         if(current_month >= 10 || current_month <= 2){
             m_current_mortality_array.middleRows(toa_Aptera, toa_Male-toa_Male+1) *= 2;
         }
         */
         //set 0
         m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() = (m_accumu_degree_days.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() <= m_aphid_adult_mortality_inflection_point_dd[0]).select(0, m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array());
  
         //set mortality based on the parameters
         for(int i=0; i<m_aphid_adult_mortality_inflection_point_dd.size(); i++){
             m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() = (m_accumu_degree_days.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() > m_aphid_adult_mortality_inflection_point_dd[i]).select(m_aphid_adult_mortality_vec[i], m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array());
         }
     }
     //Set temperature mortalities for adults. Add them to the mortality array
     if (current_temperature <= 4 || current_temperature >= 25) {
         m_current_mortality_array.middleRows(toa_Aptera, toa_Male - toa_Aptera + 1).array() += (m_aphid_adult_mortality_para_a * current_temperature * current_temperature + m_aphid_adult_mortality_para_b * current_temperature + m_aphid_adult_mortality_para_c);
         m_current_mortality_array.middleRows(toa_Nymph, toa_Nymph_M - toa_Nymph + 1).array() += (m_aphid_nymph_mortality_para_a * current_temperature * current_temperature + m_aphid_nymph_mortality_para_b * current_temperature + m_aphid_nymph_mortality_para_c);
     }
     // Below we remove any <0 zero elements and replace with zero
     m_current_mortality_array = (m_current_mortality_array.array() < 0).select(0, m_current_mortality_array);
  
     //cout<<"MORTALITY: "<<m_current_mortality_array<<endl;
  
     // Update the nymph production weight, it is updated in this function since it is kind of mortality rate
     double nymph_produced_weight_hourly_total = 0;
     for (int time_counter = 0; time_counter < 24; time_counter++) {
         double current_temp_hour = g_landscape_ptr->SupplyTempHour(time_counter);
         double nymph_produced_weight_hourly = m_aphid_nymph_production_temp_weight_para_a * (current_temp_hour +2) * (current_temp_hour +2) + m_aphid_nymph_production_temp_weight_para_b * (current_temp_hour +2) + m_aphid_nymph_production_temp_weight_para_c;
         if (nymph_produced_weight_hourly < 0) nymph_produced_weight_hourly = 0;
         if (nymph_produced_weight_hourly > 1) nymph_produced_weight_hourly = 1;
         nymph_produced_weight_hourly_total += nymph_produced_weight_hourly;
     }
     m_nymph_produced_num_weight = nymph_produced_weight_hourly_total / 24;
     //m_nymph_produced_num_weight = m_aphid_nymph_production_temp_weight_para_a* (current_temperature + 4) * (current_temperature + 4) + m_aphid_nymph_production_temp_weight_para_b * (current_temperature + 4) + m_aphid_nymph_production_temp_weight_para_c;
  
     //cout<<current_temperature << "   "<<m_nymph_produced_num_weight<<endl;
     if(m_nymph_produced_num_weight<0) m_nymph_produced_num_weight=0;
     if(m_nymph_produced_num_weight>1) m_nymph_produced_num_weight=1;
  
     //update the egg reproduction flag
     if(m_first_egg_hatch_flag){
         if(current_temperature>0){
             m_accu_ddeg_egg_reproduction += current_temperature;
         }
         if(m_accu_ddeg_egg_reproduction >= m_aphid_sexual_reproduction_average_add+2*(g_rand_uni_fnc()-0.5)*m_aphid_sexual_reproduction_add_sd){
             m_egg_reproduction_flag = true;
             m_first_egg_hatch_flag = false;
             m_accu_ddeg_egg_reproduction = 0;
         }
     }
 }

References g_landscape_ptr, g_rand_uni_fnc(), m_accu_ddeg_egg_reproduction, SubPopulation_Population_Manager::m_accumu_degree_days, m_aphid_adult_mortality_inflection_point_dd, m_aphid_adult_mortality_para_a, m_aphid_adult_mortality_para_b, m_aphid_adult_mortality_para_c, m_aphid_adult_mortality_vec, m_aphid_egg_mortality, m_aphid_egg_mortality_sd, m_aphid_nymph_mortality_para_a, m_aphid_nymph_mortality_para_b, m_aphid_nymph_mortality_para_c, m_aphid_nymph_production_temp_weight_para_a, m_aphid_nymph_production_temp_weight_para_b, m_aphid_nymph_production_temp_weight_para_c, m_aphid_sexual_reproduction_add_sd, m_aphid_sexual_reproduction_average_add, SubPopulation_Population_Manager::m_current_mortality_array, m_egg_reproduction_flag, m_first_egg_hatch_flag, m_nymph_produced_num_weight, Landscape::SupplyTemp(), Landscape::SupplyTempHour(), toa_Aptera, toa_Egg, toa_Male, toa_Nymph, and toa_Nymph_M.

Referenced by initialisePopulation().

◆ writeCalibrationFiles()

void Aphid_Population_Manager::writeCalibrationFiles ( void )

virtual

Write probe files for calibration.

Reimplemented from SubPopulation_Population_Manager.

                                                         {
     #ifdef __APHID_CALIBRATION
         writeAphidCalibData();
     #endif
 }

Member Data Documentation

◆ m_accu_ddeg_egg_reproduction

double Aphid_Population_Manager::m_accu_ddeg_egg_reproduction

private

The accumulated day degrees to enable sexual development.

Referenced by Aphid_Population_Manager(), updateDevelopmentSeason(), and updateMortalityArrayShared().

◆ m_aphid_adult_longevity_para_a

double Aphid_Population_Manager::m_aphid_adult_longevity_para_a

private

The variable to store the adult longevity parameter A.

Referenced by initialisePopulation().

◆ m_aphid_adult_longevity_para_b

double Aphid_Population_Manager::m_aphid_adult_longevity_para_b

private

The variable to store the adult longevity parameter B.

Referenced by initialisePopulation().

◆ m_aphid_adult_mortality_inflection_point_dd

vector<double> Aphid_Population_Manager::m_aphid_adult_mortality_inflection_point_dd

private

The vector to store inflection point of accumulated day degrees for adult mortality.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_adult_mortality_para_a

double Aphid_Population_Manager::m_aphid_adult_mortality_para_a

private

The variable to store the adult mortality parameter A.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_adult_mortality_para_b

double Aphid_Population_Manager::m_aphid_adult_mortality_para_b

private

The variable to store the adult mortality parameter B.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_adult_mortality_para_c

double Aphid_Population_Manager::m_aphid_adult_mortality_para_c

private

The variable to store the adult mortality parameter C.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_adult_mortality_vec

vector<double> Aphid_Population_Manager::m_aphid_adult_mortality_vec

private

The vector to store the adult mortality for the inflection point.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_alate_proportion_para_a

double Aphid_Population_Manager::m_aphid_alate_proportion_para_a

private

The variable to store alate proportion calculation parameter A.

Referenced by calOffspringStageBBandPP(), calOffspringStageEGandPEA(), and initialisePopulation().

◆ m_aphid_alate_proportion_para_b

double Aphid_Population_Manager::m_aphid_alate_proportion_para_b

private

The variable to store alate proportion calculation parameter B.

Referenced by calOffspringStageBBandPP(), calOffspringStageEGandPEA(), and initialisePopulation().

◆ m_aphid_alate_proportion_para_c

double Aphid_Population_Manager::m_aphid_alate_proportion_para_c

private

The variable to store alate proportion calculation parameter C.

Referenced by calOffspringStageBBandPP(), calOffspringStageEGandPEA(), and initialisePopulation().

◆ m_aphid_egg_hatch_chance_max_degree_days

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_max_degree_days

private

The variable to store the largest degree days for egg hatch chance being one.

Referenced by calHatchChance().

◆ m_aphid_egg_hatch_chance_para_a

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_para_a

private

The variable to store the egg hatch chance parameter A.

Referenced by Aphid_Population_Manager(), calHatchChance(), and initialisePopulation().

◆ m_aphid_egg_hatch_chance_para_a_after_threshold

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_para_a_after_threshold

private

The variable to store the egg hatch chance parameter A after threshold.

Referenced by Aphid_Population_Manager(), and calHatchChance().

◆ m_aphid_egg_hatch_chance_para_b

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_para_b

private

The variable to store the egg hatch chance parameter B.

Referenced by Aphid_Population_Manager(), calHatchChance(), and initialisePopulation().

◆ m_aphid_egg_hatch_chance_para_b_after_threshold

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_para_b_after_threshold

private

The variable to store the egg hatch chance parameter B after threshold.

Referenced by Aphid_Population_Manager(), and calHatchChance().

◆ m_aphid_egg_hatch_chance_threshold

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_threshold

private

The threshold of hatch value to start the delay of egg hatch, this is to avoid the eggs hatching from the same day.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_hatch_chance_turing_degree_days

double Aphid_Population_Manager::m_aphid_egg_hatch_chance_turing_degree_days

private

The variable to store the turning degree day for egg hatch chance.

Referenced by Aphid_Population_Manager(), and calHatchChance().

◆ m_aphid_egg_hatch_delay_degree_days

double Aphid_Population_Manager::m_aphid_egg_hatch_delay_degree_days

private

The number of degree days to delay the egg's hatch.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_mortality

double Aphid_Population_Manager::m_aphid_egg_mortality

private

The variable to store the aphid egg mortality.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_egg_mortality_sd

double Aphid_Population_Manager::m_aphid_egg_mortality_sd

private

The variable to store the standard deviation of the gee mortality.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_egg_production_para_a

double Aphid_Population_Manager::m_aphid_egg_production_para_a

private

The variable to store the egg production parameter A.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_production_para_b

double Aphid_Population_Manager::m_aphid_egg_production_para_b

private

The variable to store the egg production parameter B.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_production_para_c

double Aphid_Population_Manager::m_aphid_egg_production_para_c

private

The variable to store the egg production parameter C.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_production_para_sd

double Aphid_Population_Manager::m_aphid_egg_production_para_sd

private

The variable to store the egg production parameter's standard deviation.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_egg_starting_degree_days

double Aphid_Population_Manager::m_aphid_egg_starting_degree_days

private

The variable to store the egg's starting degree days when the simulation starts.

Referenced by initialisePopulation(), and initialiseSimWithEggs().

◆ m_aphid_female_reproduction_day_length

double Aphid_Population_Manager::m_aphid_female_reproduction_day_length

private

The day length in minutes for female reproduction. This is used for EG and PEA.

Referenced by calOffspringStageEGandPEA(), and initialisePopulation().

◆ m_aphid_male_reproduction_day_length

double Aphid_Population_Manager::m_aphid_male_reproduction_day_length

private

The day length in minutes for male reproduction. This is used for EG and PEA.

Referenced by initialisePopulation().

◆ m_aphid_nymph_mortality_para_a

double Aphid_Population_Manager::m_aphid_nymph_mortality_para_a

private

The variable to store the nymph temperature based mortality parameter A.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_mortality_para_b

double Aphid_Population_Manager::m_aphid_nymph_mortality_para_b

private

The variable to store the nymph temperature based mortality parameter B.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_mortality_para_c

double Aphid_Population_Manager::m_aphid_nymph_mortality_para_c

private

The variable to store the nymph temperature based mortality parameter C.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_production_changing_add

double Aphid_Population_Manager::m_aphid_nymph_production_changing_add

private

The variable to store the nymph production changing accumulated degree days.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_nymph_production_para_a1

double Aphid_Population_Manager::m_aphid_nymph_production_para_a1

private

The variable to store the nymph production parameter A1.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_nymph_production_para_a2

double Aphid_Population_Manager::m_aphid_nymph_production_para_a2

private

The variable to store the nymph production parameter A2.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_nymph_production_para_b1

double Aphid_Population_Manager::m_aphid_nymph_production_para_b1

private

The variable to store the nymph production parameter B1.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_nymph_production_para_b2

double Aphid_Population_Manager::m_aphid_nymph_production_para_b2

private

The variable to store the nymph production parameter B2.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_nymph_production_temp_weight_para_a

double Aphid_Population_Manager::m_aphid_nymph_production_temp_weight_para_a

private

The variable to store the temperature weighted nymph production parameter A.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_production_temp_weight_para_b

double Aphid_Population_Manager::m_aphid_nymph_production_temp_weight_para_b

private

The variable to store the temperature weighted nymph production parameter B.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_production_temp_weight_para_c

double Aphid_Population_Manager::m_aphid_nymph_production_temp_weight_para_c

private

The variable to store the temperature weighted nymph production parameter C.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_nymph_with_wings_development_day_degrees

double Aphid_Population_Manager::m_aphid_nymph_with_wings_development_day_degrees

private

The variable to store the nymph with wings development day degrees.

Referenced by initialisePopulation(), and isEnoughNextLifeStageShared().

◆ m_aphid_nymph_with_wings_development_day_degrees_sd

double Aphid_Population_Manager::m_aphid_nymph_with_wings_development_day_degrees_sd

private

The variable to store the nymph with wings development day degrees's standard deviation.

Referenced by initialisePopulation(), and isEnoughNextLifeStageShared().

◆ m_aphid_nymph_without_wings_development_day_degrees

double Aphid_Population_Manager::m_aphid_nymph_without_wings_development_day_degrees

private

The variable to store the nymph without wings development day degrees.

Referenced by initialisePopulation(), and isEnoughNextLifeStageShared().

◆ m_aphid_nymph_without_wings_development_day_degrees_sd

double Aphid_Population_Manager::m_aphid_nymph_without_wings_development_day_degrees_sd

private

The variable to store the nymph without wings development day degrees's standard deviation.

Referenced by initialisePopulation(), and isEnoughNextLifeStageShared().

◆ m_aphid_sexual_reproduction_add_sd

double Aphid_Population_Manager::m_aphid_sexual_reproduction_add_sd

private

The standard deviation of the required accumulated degree days to enable sexual reproduction after the first egg hatches.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_sexual_reproduction_average_add

double Aphid_Population_Manager::m_aphid_sexual_reproduction_average_add

private

The average required accumulated degree days to enable sexual reproduction after the first egg hatches.

Referenced by initialisePopulation(), and updateMortalityArrayShared().

◆ m_aphid_specie_name

string Aphid_Population_Manager::m_aphid_specie_name

private

This is to store the aphid species name.

Referenced by Aphid_Population_Manager(), and initialisePopulation().

◆ m_aphid_summer_host_day_length

double Aphid_Population_Manager::m_aphid_summer_host_day_length

private

The day length in minutes to turn on summer host. This is used for BB and PP.

Referenced by initialisePopulation(), and updateDevelopmentSeason().

◆ m_aphid_winter_host_day_length

double Aphid_Population_Manager::m_aphid_winter_host_day_length

private

THe day length in minutes to turn on winter host. This is used for BB and PP.

Referenced by initialisePopulation(), and updateDevelopmentSeason().

◆ m_current_developtype

TTypesOfAphidDevelopmentSeason Aphid_Population_Manager::m_current_developtype

private

The variable to show the development season.

Referenced by initialiseSimWithEggs(), and supplyDevelopmentSeason().

◆ m_egg_per_day

vector<double> Aphid_Population_Manager::m_egg_per_day

private

The vector to store the age (in degree days) related reproduction offspring egg.

Referenced by Aphid_Population_Manager(), calOffspringStageBBandPP(), and calOffspringStageEGandPEA().

◆ m_egg_reproduction_flag

bool Aphid_Population_Manager::m_egg_reproduction_flag

private

The flag to enable sexual development.

Referenced by Aphid_Population_Manager(), calNextStageShared(), calOffspringStageBBandPP(), calOffspringStageEGandPEA(), and updateMortalityArrayShared().

◆ m_first_egg_hatch_flag

bool Aphid_Population_Manager::m_first_egg_hatch_flag

private

The flag to show the first hatch of egg.

Referenced by Aphid_Population_Manager(), calNextStageShared(), and updateMortalityArrayShared().

◆ m_is_ready_next_liff_func_pointer

bool(Aphid_Population_Manager::* Aphid_Population_Manager::m_is_ready_next_liff_func_pointer) (int a_life_stage)

private

THe function pointer for testing whether the given life stage is ready for the next one.

Referenced by initialisePopulation(), and isEnoughNextLifeStage().

◆ m_max_adult_dd

int Aphid_Population_Manager::m_max_adult_dd

private

THe variable to store the maximum number of degree days for aphid.

Referenced by Aphid_Population_Manager(), initialisePopulation(), and isEnoughNextLifeStageShared().

◆ m_max_day_degree_adult

double Aphid_Population_Manager::m_max_day_degree_adult

private

The longest day degrees that a adult can have.

Referenced by doSpeciesLastThing(), and initialisePopulation().

◆ m_next_life_func_pointer

int(Aphid_Population_Manager::* Aphid_Population_Manager::m_next_life_func_pointer) (int current_stage)

private

The function pointer for calculation of next life stage.

Referenced by calNextStage(), and initialisePopulation().

◆ m_nymph_per_day

vector<double> Aphid_Population_Manager::m_nymph_per_day

private

The vector to store the age (in degree days) related reproduction offsping nymph.

Referenced by Aphid_Population_Manager(), calOffspringStageBBandPP(), and calOffspringStageEGandPEA().

◆ m_nymph_produced_num_weight

double Aphid_Population_Manager::m_nymph_produced_num_weight

private

The weight to regulate the number of nymph produced per day based on temperature.

Referenced by calOffspringStageBBandPP(), calOffspringStageEGandPEA(), supplyNymphNumWeight(), and updateMortalityArrayShared().

◆ m_offspring_func_pointer

int(Aphid_Population_Manager::* Aphid_Population_Manager::m_offspring_func_pointer) (int current_stage, double *offspring_num, double a_age, double a_density, double a_growth_stage, double *a_propotion, bool winter_host_flag)

private

The function pointer for calculation of the offsrping stage number.

Referenced by calOffspringStage(), and initialisePopulation().

◆ m_update_mortality_array_pointer

void(Aphid_Population_Manager::* Aphid_Population_Manager::m_update_mortality_array_pointer) ()

private

The function pointer for calculation of the shared base mortality rate for the whole landscape.

Referenced by initialisePopulation(), and updateMortalityArray().

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

/builds/ALMaSS/ALMaSS_MIDox/Aphid/Aphid_Population_Manager.h
/builds/ALMaSS/ALMaSS_MIDox/Aphid/Aphid_Population_Manager.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Aphid_Population_Manager()

◆ ~Aphid_Population_Manager()

Member Function Documentation

◆ calHatchChance()

◆ calNextStage()

◆ calNextStageShared()

◆ calOffspringStage()

◆ calOffspringStageBBandPP()

◆ calOffspringStageEGandPEA()

◆ CreateObjects()

◆ doSpeciesLastThing()

◆ initialisePopulation()

◆ initialiseSimWithEggs()

◆ isEnoughNextLifeStage()

◆ isEnoughNextLifeStageShared()

◆ KillAphid()

◆ SupplyAphidDensity()

◆ supplyDevelopmentSeason()

◆ supplyNymphNumWeight()

◆ updateDevelopmentSeason()

◆ updateMortalityArray()

◆ updateMortalityArrayShared()

◆ writeCalibrationFiles()

Member Data Documentation

◆ m_accu_ddeg_egg_reproduction

◆ m_aphid_adult_longevity_para_a

◆ m_aphid_adult_longevity_para_b

◆ m_aphid_adult_mortality_inflection_point_dd

◆ m_aphid_adult_mortality_para_a

◆ m_aphid_adult_mortality_para_b

◆ m_aphid_adult_mortality_para_c

◆ m_aphid_adult_mortality_vec

◆ m_aphid_alate_proportion_para_a

◆ m_aphid_alate_proportion_para_b

◆ m_aphid_alate_proportion_para_c

◆ m_aphid_egg_hatch_chance_max_degree_days

◆ m_aphid_egg_hatch_chance_para_a

◆ m_aphid_egg_hatch_chance_para_a_after_threshold

◆ m_aphid_egg_hatch_chance_para_b

◆ m_aphid_egg_hatch_chance_para_b_after_threshold

◆ m_aphid_egg_hatch_chance_threshold

◆ m_aphid_egg_hatch_chance_turing_degree_days

◆ m_aphid_egg_hatch_delay_degree_days

◆ m_aphid_egg_mortality

◆ m_aphid_egg_mortality_sd

◆ m_aphid_egg_production_para_a

◆ m_aphid_egg_production_para_b

◆ m_aphid_egg_production_para_c

◆ m_aphid_egg_production_para_sd

◆ m_aphid_egg_starting_degree_days

◆ m_aphid_female_reproduction_day_length

◆ m_aphid_male_reproduction_day_length

◆ m_aphid_nymph_mortality_para_a

◆ m_aphid_nymph_mortality_para_b

◆ m_aphid_nymph_mortality_para_c

◆ m_aphid_nymph_production_changing_add

◆ m_aphid_nymph_production_para_a1

◆ m_aphid_nymph_production_para_a2

◆ m_aphid_nymph_production_para_b1

◆ m_aphid_nymph_production_para_b2

◆ m_aphid_nymph_production_temp_weight_para_a

◆ m_aphid_nymph_production_temp_weight_para_b

◆ m_aphid_nymph_production_temp_weight_para_c

◆ m_aphid_nymph_with_wings_development_day_degrees

◆ m_aphid_nymph_with_wings_development_day_degrees_sd

◆ m_aphid_nymph_without_wings_development_day_degrees

◆ m_aphid_nymph_without_wings_development_day_degrees_sd

◆ m_aphid_sexual_reproduction_add_sd

◆ m_aphid_sexual_reproduction_average_add

◆ m_aphid_specie_name

◆ m_aphid_summer_host_day_length

◆ m_aphid_winter_host_day_length

◆ m_current_developtype

◆ m_egg_per_day

◆ m_egg_reproduction_flag