SubPopulation_Population_Manager Class Reference

The class to handle all subpopulation-based ainimal population related matters in the whole landscape. More...

#include <SubPopulation_Population_Manager.h>

Inheritance diagram for SubPopulation_Population_Manager:

Public Member Functions
	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...
virtual int	calNextStage (int current_stage, double density=1)
	Return the next life stage for the given life stage. 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)
	Calculate the offspring life stage. More...
virtual void	updateDevelopmentSeason ()
	The function to update the development season. 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...
virtual unsigned	supplyDevelopmentSeason ()
	The function to supply the development season. More...
virtual void	updateMortalityArray (void)
	This function is used to update the daily mortality rate for all the ages. In this base class, it only depends on the temperature. The lowest and highest temperature that will make the species die. The optimal temperature will make the mortality rate to be 0. 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...
virtual void	initialisePopulation ()
	The function to initialise the population when starting the simulation which requires rewritten in the derived class. 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...
virtual bool	isEnoughNextLifeStage (int a_life_stage)
	The funcition to check whether it is read for the next life stage. 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...
virtual void	writeCalibrationFiles (void)
	Write probe files for calibration. 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...

Protected Member Functions
virtual void	Run (int NoTSteps)
Protected Member Functions inherited from Population_Manager_Base
	~Population_Manager_Base ()=default

Protected Attributes
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...

Private Attributes
blitz::Array< double, 1 >	m_total_num_each_stage
	Array to hold the total number of alive animals under different life stages in the whole landscape. More...
double	m_size_cell
	The size of each subpopulation cell. More...
std::vector< std::vector< int > >	m_index_next_life_stage
	The array to store the index for the ones go to the next life stage or die. -1 means nothing. More...
blitz::Array< double, 1 >	m_lowest_temperature_die
	The lowest temperature that will cause the species die. More...
blitz::Array< double, 1 >	m_highest_temperature_die
	The highest temperature that will cause the species die. More...
blitz::Array< double, 1 >	m_optimal_temperature
	The optimal development temperature for the species. (Mortality rate = 0). More...

Friends
class	Subpopulation

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...

Detailed Description

The class to handle all subpopulation-based ainimal population related matters in the whole landscape.

Constructor & Destructor Documentation

SubPopulation_Population_Manager()

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
	)

                                                                                                                                                                                                                                                                                                                        : Population_Manager_Base(L)
{
    //set the number of life stages
    m_num_life_stage = a_num_life_stage;
    m_ListNameLength = m_num_life_stage;
 
    //set the number of longest life time in calendar days
    m_max_alive_days = a_max_alive_day;
 
    //set the width and height of the grid
    m_sub_w = a_sub_w;
    m_sub_h = a_sub_h;
 
    //create the array to store the base development temperature for each life stage
    m_lowest_temp_dev.resize(m_num_life_stage);
    //create the vector to store the indix for the old enough ones for next life stage or death
    m_index_next_life_stage.resize(m_num_life_stage);
    /*
    for (int i=0; i<m_num_life_stage; i++){
        m_index_next_life_stage.at(i).push_back(-1);
    }
    */
    m_vec_subpopulation_pointers_polygon.resize(m_TheLandscape->SupplyNumberOfPolygons());
    
    //flying related parameters
    //create the movement masks
    m_current_flying_array.resize(m_max_alive_days);
    m_current_flying_array = 0.0;
    m_current_landing_array.resize(m_max_alive_days);
    m_current_landing_array = 0.0;
    m_max_long_distance = a_max_long_dist;
    m_peak_long_distance = a_peak_long_dist;
    m_scale_wind_speed = a_scale_wind_speed;
    m_max_flying_wind_speed = a_max_wind_speed;
    //the default wind direction number is 8
    m_wind_direction_num = a_wind_direc_num;
    m_wind_speed_step_size = a_wind_speed_step_size;
    //get the sampling nubmers for the wind speed with the given the step size
    m_wind_speed_num = ceil(m_max_flying_wind_speed / m_wind_speed_step_size);
 
    //resize the landing mask array
    m_landing_masks.resize(m_wind_speed_num, m_wind_direction_num);
 
    //initialise the lookup table for puting the given wind speed to a range for the sake of speed. Each range is like [) with a 1m/s resolution.
    m_wind_speed_lookup_table.resize(ceil(m_max_flying_wind_speed)+1);
    
    for(int i = 0; i<=ceil(m_max_flying_wind_speed); i++){
        m_wind_speed_lookup_table(i)= int(i/m_wind_speed_step_size);
        //cout<<m_wind_speed_lookup_table<<endl;
    }
 
    //initialise the wind direction array
    m_wind_direction_array.resize(m_wind_direction_num, 2);
    double temp_degree = 2*M_PI/m_wind_direction_num;
    for (int i=0; i<m_wind_direction_num; i++){
        m_wind_direction_array(i,0) = cos(temp_degree*i);
        m_wind_direction_array(i,1) = sin(temp_degree*i);
    }
 
    cout<<m_wind_direction_array<<endl;
 
    //convert the longest distance to the number of cells
    //we need to make it with the largest distance multiplied by the incremental factor
    m_long_move_mask_x_num_half_array.resize(m_wind_speed_num);
    m_long_move_mask_y_num_half_array.resize(m_wind_speed_num);
    for (int i=0; i<m_wind_speed_num;i++){
        m_long_move_mask_x_num_half_array(i) = m_max_long_distance*pow(a_scale_wind_speed, i)/m_sub_w;
        m_long_move_mask_y_num_half_array(i) = m_max_long_distance*pow(a_scale_wind_speed, i)/m_sub_h;
    }
 
    //initialise the landing mask arrays
    for (int i=0; i<m_wind_speed_num;i++)
        for (int j=0; j<m_wind_direction_num; j++){
            m_landing_masks(i, j).resize(2*m_long_move_mask_y_num_half_array(i)+1, 2*m_long_move_mask_x_num_half_array(i)+1);
            m_landing_masks(i, j) = 0.0;
            cout<<m_landing_masks(i,j).shape()<<endl;
    }
 
 
    double temp_longest_factored = m_max_long_distance*pow(a_scale_wind_speed, m_wind_speed_num-1);
    m_long_move_mask_x_num_half = temp_longest_factored/m_sub_w;
    m_long_move_mask_x_num = 2*m_long_move_mask_x_num_half +1;
    m_long_move_mask_y_num_half = temp_longest_factored/m_sub_h;
    m_long_move_mask_y_num = 2*m_long_move_mask_y_num_half+1;
    m_long_move_mask.resize(m_wind_speed_num, m_wind_direction_num, m_long_move_mask_y_num, m_long_move_mask_x_num);
    m_long_move_mask = 0.0;
    calLongMovementMask();
 
    //hard coded 
    m_short_move_mask_x_num = 3;
    m_short_move_mask_y_num = 3;
    m_short_move_mask.resize(m_short_move_mask_y_num, m_short_move_mask_x_num);
    m_short_move_mask = 0.0;
    if(DevReproFile==""){
        readDevReproFile("Subpopulation/subpopulation_default_info.txt");
    }
    else{
        readDevReproFile(DevReproFile);
    }
        
    // Initialize the default population size to zero
    m_total_num_each_stage.resize(m_num_life_stage);
    m_total_num_each_stage=0;
 
    //set the number of cells
    m_num_x_range = SimW/m_sub_w;
    m_num_y_range = SimH/m_sub_h;
    m_size_cell = m_sub_w*m_sub_h;
 
    //Initialize the weighted population density array with zero
    m_cell_popu_density.resize(m_num_y_range, m_num_x_range);
    m_cell_popu_density = 0.0;
 
    //Initialize the suitability for each cell with zero
    m_cell_suitability.resize(m_num_y_range, m_num_x_range);
    m_cell_suitability = 0.0;
 
    //Initialize the pointer array for the subpopulation objects
    m_the_subpopulation_array.resize(m_num_y_range, m_num_x_range); 
    m_the_subpopulation_array = NULL;
 
    m_first_flag_life_stage.resize(m_num_life_stage);
    m_first_flag_life_stage = true;
 
    //check if we need to open the base storing file
    if (cfg_Subpopu_Base_Output_Used.value()) {
        openSubpopulationBaseProbeFile();
    }
 
    m_hibernated_hatch_flag = false;
 
    //initialize the mortality related arrays
    m_current_mortality_array.resize(m_num_life_stage, m_max_alive_days);
    m_current_mortality_array = 0.0;
    m_lowest_temperature_die.resize(m_num_life_stage);
    m_lowest_temperature_die = 2;
    m_highest_temperature_die.resize(m_num_life_stage);
    m_highest_temperature_die = 40.0;
    m_optimal_temperature.resize(m_num_life_stage);
    m_optimal_temperature = 15;
 
    //create the arrays for calculation of degree days
    m_accumu_degree_days.resize(m_num_life_stage, m_max_alive_days);
    m_accumu_degree_days = 0.0;
    m_index_new_old.resize(m_num_life_stage, 2); //the first is the newest index and the second is the oldest index
    m_index_new_old = 0; //They start from zero from the beginning.
 
    //do the initialisation
    if(DevReproFile=="") initialisePopulation();
}

References calLongMovementMask(), cfg_Subpopu_Base_Output_Used, initialisePopulation(), m_accumu_degree_days, m_cell_popu_density, m_cell_suitability, m_current_flying_array, m_current_landing_array, m_current_mortality_array, m_first_flag_life_stage, m_hibernated_hatch_flag, m_highest_temperature_die, m_index_new_old, m_index_next_life_stage, m_landing_masks, Population_Manager_Base::m_ListNameLength, m_long_move_mask, m_long_move_mask_x_num, m_long_move_mask_x_num_half, m_long_move_mask_x_num_half_array, m_long_move_mask_y_num, m_long_move_mask_y_num_half, m_long_move_mask_y_num_half_array, m_lowest_temp_dev, m_lowest_temperature_die, m_max_alive_days, m_max_flying_wind_speed, m_max_long_distance, m_num_life_stage, m_num_x_range, m_num_y_range, m_optimal_temperature, m_peak_long_distance, M_PI, m_scale_wind_speed, m_short_move_mask, m_short_move_mask_x_num, m_short_move_mask_y_num, m_size_cell, m_sub_h, m_sub_w, m_the_subpopulation_array, Population_Manager_Base::m_TheLandscape, m_total_num_each_stage, m_vec_subpopulation_pointers_polygon, m_wind_direction_array, m_wind_direction_num, m_wind_speed_lookup_table, m_wind_speed_num, m_wind_speed_step_size, openSubpopulationBaseProbeFile(), readDevReproFile(), Population_Manager_Base::SimH, Population_Manager_Base::SimW, Landscape::SupplyNumberOfPolygons(), and CfgBool::value().

~SubPopulation_Population_Manager()

SubPopulation_Population_Manager::~SubPopulation_Population_Manager ( void  )

virtual

SubPopulation_Manager Destructor.

                                                                   {
    for (int i=0; i<m_num_y_range; i++){
        for (int j=0; j<m_num_x_range; j++){
            if (m_the_subpopulation_array(i,j) !=  NULL){
                delete m_the_subpopulation_array(i,j);
            }
        }
    }
    
    if(cfg_Subpopu_Base_Output_Used.value() && m_subpopulation_base_prb_file){
        m_subpopulation_base_prb_file.close();
        //delete m_subpopulation_base_prb_file;
    }
}

References cfg_Subpopu_Base_Output_Used, m_num_x_range, m_num_y_range, m_subpopulation_base_prb_file, m_the_subpopulation_array, and CfgBool::value().

Member Function Documentation

addNewDay()

void SubPopulation_Population_Manager::addNewDay

(

)

Add new day to the newest and oldest array.

                                                {
    m_index_new_old(blitz::Range::all(),0)+=1;
    //Set it to zero when they reaches the end
    for (int i=0; i < m_num_life_stage; i++){
        if (m_index_new_old(i,0) >= m_max_alive_days){
            m_index_new_old(i,0) = 0;
        }
    }
}

References m_index_new_old, m_max_alive_days, and m_num_life_stage.

Referenced by DoLast().

calLandingCurve()

double SubPopulation_Population_Manager::calLandingCurve	(	double	a_dis,
		double	a_peak,
		double	a_furthest
	)

The function to calculate the landing curve along the wind direction.

                                                                                                        {
    if(a_dis<=a_peak && a_dis>0){
        return -1*a_dis*a_dis + 2*a_peak*a_dis;
    }
    if(a_dis>a_peak && a_dis <= a_furthest){
        return a_peak*a_peak*pow(a_furthest-a_dis, 2)/pow(a_furthest-a_peak, 2);
    }
    return 0.0;
}

Referenced by calLongMovementMask().

calLongMovementMask()

void SubPopulation_Population_Manager::calLongMovementMask ( void  )

virtual

Function to calculate the movement mask.

                                                          {
 
    //fstream tempoutputfilet("result.txt", ios::app); //debug code
    for (int i=0; i<m_wind_speed_num; i++){
        for ( int x=-m_long_move_mask_x_num_half_array(i); x<m_long_move_mask_x_num_half_array(i)+1; x++){
            for (int y=m_long_move_mask_y_num_half_array(i); y>-m_long_move_mask_y_num_half_array(i)-1; y--){
                //we calculate the base mask without the consideration of the wind direction first
                double temp_mask_value = calLandingCurve(sqrt(pow(x*m_sub_w,2)+pow(y*m_sub_h,2)), m_peak_long_distance*pow(m_scale_wind_speed, i), m_max_long_distance*pow(m_scale_wind_speed, i));
                //apply the wind direction
                for(int j=0; j<m_wind_direction_num; j++){
                    //calculate the cosine value between the direction of the cell and the wind direction
                    double temp_cos = -1;
                    if(x!=0 || y!=0)
                    temp_cos = (y*m_wind_direction_array(j,1)+x*m_wind_direction_array(j,0))/(sqrt(x*x+y*y)*sqrt(m_wind_direction_array(j,0)*m_wind_direction_array(j,0)+m_wind_direction_array(j,1)*m_wind_direction_array(j,1)));
                    if (temp_cos>0.000001){
                        m_long_move_mask(i, j, m_long_move_mask_y_num_half+y, m_long_move_mask_x_num_half+x) = temp_mask_value* temp_cos;
                        m_landing_masks(i, j)(m_long_move_mask_y_num_half_array(i)-y, m_long_move_mask_x_num_half_array(i)+x) = temp_mask_value * temp_cos;
                    }
                    else{
                        m_long_move_mask(i, j, m_long_move_mask_y_num_half+y, m_long_move_mask_x_num_half+x) = 0.0;
                        m_landing_masks(i, j)(m_long_move_mask_y_num_half_array(i)-y,  m_long_move_mask_x_num_half_array(i)+x) = 0.0;
                    }
 
                    //if (i==4 && j==0) tempoutputfilet<<temp_cos<<"/t"<<temp_mask_value<<endl; //debug code
                }
            }
        }
    }
 
    //normalise the masks
    //fstream tempoutputfile("landing_mask.txt", ios::app);
 
    for (int i=0; i<m_wind_speed_num; i++){
        for (int j=0; j<m_wind_direction_num; j++){
            //cout<<m_landing_masks<<endl;
            m_landing_masks(i, j) /= sum(m_landing_masks(i,j));
            double min_value = 0.1/double(m_landing_masks(i,j).shape()(0)*m_landing_masks(i,j).shape()(1));
            for (int k=0; k<m_landing_masks(i,j).shape()(0);k++){
                for (int l=0; l<m_landing_masks(i,j).shape()(1);l++){
                    if(m_landing_masks(i, j)(k,l)<=min_value){
                        m_landing_masks(i, j)(k,l) = 0;
                    }
                }
            }
            m_landing_masks(i, j) /= sum(m_landing_masks(i,j));
            //tempoutputfile<<m_landing_masks(i,j)<<endl;
            //cout<<i<<j<<sum(m_landing_masks(i,j))<<endl;
            //cout<<m_landing_masks(i,j)<<endl;
        }
    }
    //tempoutputfile.close();
 
    /* not used
    blitz::Array<double, 1> mean_vector_temp (2);
    mean_vector_temp = 0;
    blitz::Array<double, 2> covariance_temp (2, 2);
    covariance_temp = 1,0,0,1;
 
    //We first calculate the long distance movement masks.
 
    //Get the center of the mask.
    double center_x = (m_long_move_mask_x_num-1)/2;
    double center_y = (m_long_move_mask_y_num-1)/2;
 
    //Temporary location array
    blitz::Array<double, 2> temp_local_array(m_long_move_mask_x_num, m_long_move_mask_y_num);
    blitz::firstIndex i;
    blitz::secondIndex j;
    //temp_local_array(i, blitz::Range::all())=j;
    blitz::thirdIndex k;
    blitz::fourthIndex l;
 
    m_long_move_mask_y_num = 0;
    */
    //m_long_move_mask(blitz::Range::all(), blitz::Range::all(), 0, 0) = 1.0;
    //std::cout << m_long_move_mask << std::endl;
}

References calLandingCurve(), m_landing_masks, m_long_move_mask, m_long_move_mask_x_num_half, m_long_move_mask_x_num_half_array, m_long_move_mask_y_num_half, m_long_move_mask_y_num_half_array, m_max_long_distance, m_peak_long_distance, m_scale_wind_speed, m_sub_h, m_sub_w, m_wind_direction_array, m_wind_direction_num, and m_wind_speed_num.

Referenced by SubPopulation_Population_Manager().

calNextStage()

int SubPopulation_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 in Aphid_Population_Manager.

                                                                                   {
    int next_stage;
 
    //if(current_stage == 2) //to adult, randomly choose female or male
    //{
    //  next_stage = g_rand_uni()>0.5 ? current_stage+1 :current_stage+2;
    //}
    //else 
    if (current_stage == 3 || current_stage == 4) // already adult, die next
    {
        next_stage = -1;
    }
    else if(current_stage<2)// otherwise next life stage
    {
        next_stage = current_stage+1;
    }
    else{
        if(density>=0){
            if(density<cfg_Subpopu_Density_Threshold.value()){
                next_stage = 4;
            }
            else{
                next_stage = 3; //too crowded, winged ones
            }
        }
        else{
            next_stage=-1;
        }
    }   
    return next_stage;
}

References cfg_Subpopu_Density_Threshold, and CfgFloat::value().

Referenced by SubPopulation::doDevelopment().

calOffspringStage()

int SubPopulation_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

Calculate the offspring life stage.

Reimplemented in Aphid_Population_Manager.

                                                                                                                                                                                                  {
    if(current_stage == 3 || current_stage == 4){
        *offspring_num = 1;
        return 0;
    }
    *offspring_num = 0;
    return -1;
}

Referenced by Aphid::doReproduction(), and SubPopulation::doReproduction().

CreateObjects()

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

                                                                                                                  {
   SubPopulation*  new_Sub;
   new_Sub = new SubPopulation(data->x, data->y, data->L, data->NPM, data->empty_flag, data->index_x, data->index_y, data->starting_suitability, data->starting_popu_density, number);
   // 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_Sub -> addAnimalNumGivenStageColumn(tos_Egg, 0, number);
    }
   return new_Sub;
}

References struct_SubPopulation::empty_flag, struct_SubPopulation::index_x, struct_SubPopulation::index_y, struct_SubPopulation::L, struct_SubPopulation::NPM, struct_SubPopulation::starting_popu_density, struct_SubPopulation::starting_suitability, tos_Egg, struct_SubPopulation::x, and struct_SubPopulation::y.

Referenced by initialisePopulation().

doDevelopment()

void SubPopulation_Population_Manager::doDevelopment

(

)

Function to make the development for all the subpopulation object.

                                                    {
    double current_temp = g_landscape_p->SupplyTemp();
    double current_degree_days = 0;
    //std::cout<<m_index_next_life_stage<<endl;
    //m_index_next_life_stage = -1;
 
    //update hibernate flag
    if(!m_hibernated_hatch_flag&&m_TheLandscape->SupplyMonth()==4) m_hibernated_hatch_flag = true;
    if(m_hibernated_hatch_flag &&m_TheLandscape->SupplyMonth()==11) m_hibernated_hatch_flag = false;
    for (int i=0; i < m_num_life_stage; i++){
        //clear the data from yesterday
        m_index_next_life_stage.at(i).clear();
        //First, calculate the degree days for today
        //THe degree days can only be accumulated when the curent temperature is higher than the lowest development temperature
        //for over winter eggs, no need to accumulate degree days
        if (i==0 && m_development_degree_day(0, i) < 0) {
            if (m_hibernated_hatch_flag){
                m_index_next_life_stage.at(i).push_back(0); //for the overwintering eggs, they always stay at zero.
            }
            continue;
        }
 
        else{
            if (current_temp > m_lowest_temp_dev(i)){
                current_degree_days = current_temp - m_lowest_temp_dev(i);
                //decide which ones should be added
                if(m_index_new_old(i,0)<m_index_new_old(i,1)){
                    m_accumu_degree_days(i, blitz::Range(0, m_index_new_old(i, 0))) += current_degree_days;
                    m_accumu_degree_days(i, blitz::Range(m_index_new_old(i,1), blitz::toEnd)) += current_degree_days;
                }
                else if(m_index_new_old(i, 0)==m_index_new_old(i, 1)){
                    m_accumu_degree_days(i, m_index_new_old(i, 1)) += current_degree_days;
                }
                else{
                    m_accumu_degree_days(i, blitz::Range(m_index_new_old(i, 1), m_index_new_old(i, 0))) += current_degree_days;
                }
                //check whether they need to go to next life stage or die
                while(isEnoughNextLifeStage(i)){
                    m_index_next_life_stage.at(i).push_back(m_index_new_old(i, 1));
                    //set it to zero
                    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;
                    }
                }               
            }
        }
    }
    //std::cout << current_temp <<endl;
    //std::cout << m_index_new_old <<endl;
    //for (int temp_next:m_index_next_life_stage.at(5))
    //  std::cout << temp_next <<endl;
    //std::cout << m_accumu_degree_days<<endl;
    //std::cout << m_current_mortality_array << endl;
}

References g_landscape_p, isEnoughNextLifeStage(), m_accumu_degree_days, m_development_degree_day, m_hibernated_hatch_flag, m_index_new_old, m_index_next_life_stage, m_lowest_temp_dev, m_max_alive_days, m_num_life_stage, Population_Manager_Base::m_TheLandscape, Landscape::SupplyMonth(), and Landscape::SupplyTemp().

Referenced by DoLast().

DoFirst()

void SubPopulation_Population_Manager::DoFirst ( void  )

virtual

                                              {
   updateDevelopmentSeason();
   updateMortalityArray();
   doParasitoidDevelopment();
   double current_wind_speed = g_landscape_p->SupplyWind();
    if (current_wind_speed<m_max_flying_wind_speed){
        relocatePopulation(); //let the species move when it is not too windy
    }
}

References doParasitoidDevelopment(), g_landscape_p, m_max_flying_wind_speed, relocatePopulation(), Landscape::SupplyWind(), updateDevelopmentSeason(), and updateMortalityArray().

Referenced by Run().

doFlying()

void SubPopulation_Population_Manager::doFlying	(	int	ind,
		int	index_x,
		int	index_y
	)

The function to fly the winged adults.

                                                                                {
 
    int life_stage = m_flying_life_stage_array.at(ind);
    int landing_life_stage = m_landing_life_stage_array.at(ind);
    
    m_current_flying_array = m_the_subpopulation_array(index_y, index_x)->getFlyingArray(ind);
 
    //get the wind direction and speed
    int current_wind_direction = g_landscape_p->SupplyWindDirection();
    double current_wind_speed = g_landscape_p->SupplyWind();
    int current_wind_speed_index = m_wind_speed_lookup_table(int(current_wind_speed));
    //double flying_total_num = m_the_subpopulation_array(index_y,index_x)->getNumforOneLifeStage(life_stage);
    double flying_total_num = sum(m_current_flying_array);
    if(flying_total_num>0){
        double landed_num = 0;
        int temp_index_mask_x = -1;
        int temp_index_mask_y = -1;
 
        double temp_not_landed_num = 0; //land the number samller than 1 to the peak cell
        int temp_peak_x = -1;
        int temp_peak_y = 0;
        double temp_peak = -9999999;
        for (int x = index_x-m_long_move_mask_x_num_half_array(current_wind_speed_index); x<=index_x+m_long_move_mask_x_num_half_array(current_wind_speed_index);x++){
            //out of range for x
            temp_index_mask_x++;
            if(x<0 || x>=m_num_x_range){
                continue;
            }
            temp_index_mask_y = -1;
            for (int y = index_y-m_long_move_mask_y_num_half_array(current_wind_speed_index); y<=index_y+m_long_move_mask_y_num_half_array(current_wind_speed_index);y++){
                //out of range for y
                landed_num = 0;
                temp_index_mask_y++;
                if (y<0 || y>=m_num_y_range){
                    continue;
                }
 
                //landing them
                if(m_the_subpopulation_array(y,x) !=NULL){
                    if(m_landing_masks(current_wind_speed_index, current_wind_direction)(temp_index_mask_y,temp_index_mask_x)>0.00001 && m_cell_suitability(y, x) ==1){
                        if (m_landing_masks(current_wind_speed_index, current_wind_direction)(temp_index_mask_y,temp_index_mask_x)>temp_peak){
                            temp_peak = m_landing_masks(current_wind_speed_index, current_wind_direction)(temp_index_mask_y,temp_index_mask_x);
                            temp_peak_x = x;
                            temp_peak_y = y;
                        }
                        //m_current_landing_array=m_landing_masks(current_wind_speed_index, current_wind_direction)(temp_index_mask_x,temp_index_mask_y)*m_current_flying_array;
                        landed_num = m_landing_masks(current_wind_speed_index, current_wind_direction)(temp_index_mask_y, temp_index_mask_x)*flying_total_num;
                        if(landed_num>=1){
                            //int temp_landing_age = m_index_new_old(landing_life_stage, 0) - 1;
                            //if (temp_landing_age < 0) temp_landing_age = m_max_alive_days - 1;
                            int temp_landing_age = m_index_new_old(landing_life_stage, 0);
                            
 
                            //enable local movement
                            if(m_the_subpopulation_array(y,x)->getTotalSubpopulation()<=0){
                                m_the_subpopulation_array(y,x)->setFlyLocalMovFlag(true);
                            }
                            m_the_subpopulation_array(y,x)->addAnimalNumGivenStageColumn(landing_life_stage, temp_landing_age, landed_num);
                        }
                        else if(landed_num >0 && landed_num <1){
                            temp_not_landed_num += landed_num;
                        }                                               
                    }
                }
            }
        }
 
        //land the no landing ones to the peak place
        if (temp_not_landed_num >=1 && temp_peak_x >=0 && m_the_subpopulation_array(temp_peak_y,temp_peak_x)->isFarm()&& m_cell_suitability(temp_peak_y, temp_peak_x) ==1){
            //cout<<"I am landed: "<<landing_life_stage<<endl;
            //int temp_landing_age = m_index_new_old(landing_life_stage, 0) - 1;
            //if (temp_landing_age < 0) temp_landing_age = m_max_alive_days - 1;
            int temp_landing_age = m_index_new_old(landing_life_stage, 0);
            
            if(m_the_subpopulation_array(temp_peak_y,temp_peak_x)->getTotalSubpopulation()<=0){
                m_the_subpopulation_array(temp_peak_y,temp_peak_x)->setFlyLocalMovFlag(true);
            }
            m_the_subpopulation_array(temp_peak_y,temp_peak_x)->addAnimalNumGivenStageColumn(landing_life_stage, temp_landing_age, temp_not_landed_num);
        }
        m_the_subpopulation_array(index_y, index_x)->removeAnimalNumGivenStage(life_stage);
        //m_current_flying_array *= -1;
        //m_current_flying_array = ceil(m_current_flying_array);
        //m_the_subpopulation_array(index_y, index_x)->addAnimalNumGivenStageColumn(life_stage,m_index_new_old(life_stage, 1), m_current_flying_array(i)); //land them in the old one
        //for (int i = 0; i<m_max_alive_days;){
        //  if(m_current_flying_array(i)>0){
        //      double removed_number = -1*m_current_flying_array(i);
        //      m_the_subpopulation_array(index_y, index_x)->addAnimalNumGivenStageColumn(life_stage, i, removed_number);
        //  }
        //}
    }
}

References g_landscape_p, m_cell_suitability, m_current_flying_array, m_flying_life_stage_array, m_index_new_old, m_landing_life_stage_array, m_landing_masks, m_long_move_mask_x_num_half_array, m_long_move_mask_y_num_half_array, m_num_x_range, m_num_y_range, m_the_subpopulation_array, m_wind_speed_lookup_table, Landscape::SupplyWind(), and Landscape::SupplyWindDirection().

Referenced by relocatePopulation().

DoLast()

void SubPopulation_Population_Manager::DoLast ( )

virtual

                                             {  
    doDevelopment();
    doSpecicesLastThing();
    addNewDay();
    updateWholePopulation();
    //store results if it is needed
    if(m_subpopulation_base_prb_file){
        subpopuBaseOutputProbe();
    }   
}

References addNewDay(), doDevelopment(), doSpecicesLastThing(), m_subpopulation_base_prb_file, subpopuBaseOutputProbe(), and updateWholePopulation().

Referenced by Run().

doLocalMovement()

void SubPopulation_Population_Manager::doLocalMovement	(	int	index_x,
		int	index_y,
		double	proportion
	)

The function for local movement.

                                                                                                   {
    for( int s = 0; s<m_local_moving_life_stage_array.size(); s++){
        if (m_the_subpopulation_array(index_y, index_x)->getNumforOneLifeStage(m_local_moving_life_stage_array.at(s)) && m_the_subpopulation_array(index_y, index_x)->isNewlyLanded()){
            bool temp_successed_flag = false;
            for (int i = index_x-1; i<=index_x+1; i++){
                if(i<0 || i>=m_num_x_range){
                    continue;
                }
                for (int j = index_y-1; j<=index_y+1; j++){
                    if(j<0 || j>=m_num_y_range){
                        continue;
                    }
                    if(m_the_subpopulation_array(j, i)->getTotalSubpopulation()<=0 && m_cell_suitability(j, i)>0){
                        //move half to the neighbor
                        //cout<<"I am moving to a neighbor: "<<endl;
                        for (int k=0; k<m_max_alive_days; k++){
                        
                            double mov_num = m_the_subpopulation_array(index_y, index_x)->removeAnimalPortionGivenStageColumn(s, k, proportion);
                            if (mov_num > 0){
                                m_the_subpopulation_array(j,i)->addAnimalFromAnotherCell(s, k, mov_num);
                            }
                        }
                        temp_successed_flag = true;     
                        m_the_subpopulation_array(index_y, index_x)->setFlyLocalMovFlag(false);             
                        break;
                    }
                    
                }
                if(temp_successed_flag) break;
            }
        }
    }
    
}

References m_cell_suitability, m_local_moving_life_stage_array, m_max_alive_days, m_num_x_range, m_num_y_range, and m_the_subpopulation_array.

doParasitoidDevelopment()

virtual void SubPopulation_Population_Manager::doParasitoidDevelopment ( )

inlinevirtual

The function for parasitoid calculation, it does nothing in this base class.

{;};

Referenced by DoFirst().

doSpecicesLastThing()

virtual void SubPopulation_Population_Manager::doSpecicesLastThing ( )

inlinevirtual

The special last thing for the drived species.

{;}

Referenced by DoLast().

GetLiveArraySize()

unsigned SubPopulation_Population_Manager::GetLiveArraySize ( int  a_listindex )

virtual

Must be re-implemented in descendent classes. Gets the number of 'live' objects.

Reimplemented from Population_Manager_Base.

                                                                           {
    return unsigned(supplyAllPopulationGivenStage(a_listindex));
}

References supplyAllPopulationGivenStage().

GetPopulationSize()

virtual unsigned SubPopulation_Population_Manager::GetPopulationSize ( int  a_listindex )

inlinevirtual

Must be re-implemented in descendent classes.

Reimplemented from Population_Manager_Base.

                                                       {
        return supplyAllPopulationGivenStage(a_listindex);
    }

References supplyAllPopulationGivenStage().

getSubpopulationInCellLifeStage()

double SubPopulation_Population_Manager::getSubpopulationInCellLifeStage	(	int	x_indx,
		int	y_indx,
		int	a_life_stage
	)

Supply the subpopulation size at the given life stage in the given cell.

                                                                                                                 {
    if(m_the_subpopulation_array(y_indx, x_indx)==NULL){
        return 0;
    }
    return m_the_subpopulation_array(y_indx, x_indx)->getNumforOneLifeStage(a_life_stage);
}

References m_the_subpopulation_array.

getSuitabilityInCell()

double SubPopulation_Population_Manager::getSuitabilityInCell ( int  x_indx, int  y_indx  )

inline

Supply the suitability in the given cell.

{return m_cell_suitability(y_indx, x_indx);}

References m_cell_suitability.

Referenced by Aphid::doMovement().

getTotalSubpopulationInCell()

double SubPopulation_Population_Manager::getTotalSubpopulationInCell	(	int	x_indx,
		int	y_indx
	)

Supply the total subpopulation size in the given cell.

                                                                                          {
    if(m_the_subpopulation_array(y_indx, x_indx)==NULL){
        return 0;
    }
    return m_the_subpopulation_array(y_indx, x_indx)->getTotalSubpopulation();
}

References m_the_subpopulation_array.

Referenced by Aphid::doMovement().

initialisePopulation()

void SubPopulation_Population_Manager::initialisePopulation ( )

virtual

The function to initialise the population when starting the simulation which requires rewritten in the derived class.

Reimplemented in Aphid_Population_Manager.

                                                             {
    //this is one a general subpopulation species
    m_ListNames[0]="Egg";
    m_ListNames[1]="Larva";
    m_ListNames[2]="Pupa";
    m_ListNames[3]="Adult";
    m_ListNames[4]="Adult wingless";
    m_SimulationName = "General Subpopulation Simulation";
 
    //suppose we only have one type of host
    //m_summer_hosts_tole.push_back(tole_Field);
    //m_mul_hosts_flag = false; //no host changes
    readHosts("Subpopulation/subpopulation_default_host.txt");
    
    //This needs to be changed in the decent class
    m_flying_life_stage_array.push_back(3);
    m_landing_life_stage_array.push_back(4); //by default, they don't drop theri wings
    m_local_moving_life_stage_array.push_back(3);
 
    //we add 1000 eggs to the grid when it is a suitable one
    int index_cell_i = 0;
    int index_cell_j = 0;
    struct_SubPopulation* sp;
    sp = new struct_SubPopulation;
    sp->NPM = this;
    sp->L = g_landscape_p;
    //creat the aphid in each cell
    for (int i=0; i<SimW; i=i+m_sub_w) //x, but coloumn number
    {
        index_cell_j = 0;
        for(int j=0; j<SimH; j=j+m_sub_h) //y, but row number
        {
            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 = false;
            sp->index_x = index_cell_i;
            sp->index_y = index_cell_j;
            TTypesOfLandscapeElement current_landtype = g_landscape_p->SupplyElementType(i, j);
            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));
            
            double current_biomass = g_landscape_p->SupplyVegBiomass(i, j);
 
            //for the default subpopulation species, we only have one host
            bool current_winter_host_flag = isSummerHostTole(current_landtype);
            if(current_winter_host_flag>0){
                //sp->starting_suitability = 1;
                m_the_subpopulation_array(index_cell_j, index_cell_i) = CreateObjects(NULL, sp, 1000);
                m_cell_suitability(index_cell_j, index_cell_i) = 1;
            }
            else{
                sp->empty_flag = true;
                //sp->starting_suitability = 0;
                m_the_subpopulation_array(index_cell_j, index_cell_i) = CreateObjects(NULL, sp, 0);
                m_cell_suitability(index_cell_j, index_cell_i) = 0;
            }           
            index_cell_j++;
 
            //add the pointer to its belonging polygon
            int temp_poly_id = m_TheLandscape->SupplyPolyRefIndex(sp->x, sp->y);
            m_vec_subpopulation_pointers_polygon.at(temp_poly_id).push_back(m_the_subpopulation_array(index_cell_j, index_cell_i));
        }
        index_cell_i++;
    }
    delete sp;
}

References CreateObjects(), struct_SubPopulation::empty_flag, g_landscape_p, struct_SubPopulation::h, struct_SubPopulation::index_x, struct_SubPopulation::index_y, isSummerHostTole(), struct_SubPopulation::L, m_cell_popu_density, m_cell_suitability, m_flying_life_stage_array, m_landing_life_stage_array, Population_Manager_Base::m_ListNames, m_local_moving_life_stage_array, Population_Manager_Base::m_SimulationName, m_sub_h, m_sub_w, m_the_subpopulation_array, Population_Manager_Base::m_TheLandscape, m_vec_subpopulation_pointers_polygon, struct_SubPopulation::NPM, readHosts(), Population_Manager_Base::SimH, Population_Manager_Base::SimW, struct_SubPopulation::starting_popu_density, struct_SubPopulation::starting_suitability, Landscape::SupplyElementType(), Landscape::SupplyPolyRefIndex(), Landscape::SupplyVegBiomass(), struct_SubPopulation::w, struct_SubPopulation::x, and struct_SubPopulation::y.

Referenced by SubPopulation_Population_Manager().

isEnoughNextLifeStage()

bool SubPopulation_Population_Manager::isEnoughNextLifeStage ( int  a_life_stage )

virtual

The funcition to check whether it is read for the next life stage.

Reimplemented in Aphid_Population_Manager.

                                                                            {
    return m_accumu_degree_days(a_life_stage, m_index_new_old(a_life_stage,1))>=m_development_degree_day(0, a_life_stage);
}

References m_accumu_degree_days, m_development_degree_day, and m_index_new_old.

Referenced by doDevelopment().

isSummerHostTole()

bool SubPopulation_Population_Manager::isSummerHostTole

(

TTypesOfLandscapeElement

a_ele

)

Test whether it is a summer host tole.

                                                                                     {
    if (std::count(m_summer_hosts_tole.begin(), m_summer_hosts_tole.end(), a_ele)){
        return true;
    }
 
    else {
        return false;
    }
}

References count, and m_summer_hosts_tole.

Referenced by SubPopulation::calSuitability(), initialisePopulation(), and Aphid_Population_Manager::initialiseSimWithEggs().

isSummerHostTov()

bool SubPopulation_Population_Manager::isSummerHostTov

(

TTypesOfVegetation

a_ele

)

Test whether it is a summer host tov.

                                                                              {
    if (std::count(m_summer_hosts_tov.begin(), m_summer_hosts_tov.end(), a_ele)){
        return true;
    }
 
    else {
        return false;
    }
}

References count, and m_summer_hosts_tov.

Referenced by SubPopulation::calSuitability().

isWinterHostTole()

bool SubPopulation_Population_Manager::isWinterHostTole

(

TTypesOfLandscapeElement

a_ele

)

Test whether it is a winter host tole.

                                                                                     {
    if (std::count(m_winter_hosts_tole.begin(), m_winter_hosts_tole.end(), a_ele)){
        return true;
    }
 
    else {
        return false;
    }
}

References count, and m_winter_hosts_tole.

Referenced by Aphid_Population_Manager::initialiseSimWithEggs().

isWinterHostTov()

bool SubPopulation_Population_Manager::isWinterHostTov

(

TTypesOfVegetation

a_ele

)

Test whether it is a winter host tov.

                                                                              {
    if (std::count(m_winter_hosts_tov.begin(), m_winter_hosts_tov.end(), a_ele)){
        return true;
    }
 
    else {
        return false;
    }
}

References count, and m_winter_hosts_tov.

openSubpopulationBaseProbeFile()

bool SubPopulation_Population_Manager::openSubpopulationBaseProbeFile

(

)

Open the storing file.

                                                                      {
  m_subpopulation_base_prb_file.open(cfg_Subpopu_Base_Output_Filename.value(), ios::out );
  if ( !m_subpopulation_base_prb_file) {
    g_msg->Warn( WARN_FILE, "SubPopulationPopulation_Manager::openSubpopulationBaseProbeFile(): ""Unable to open probe file",cfg_Subpopu_Base_Output_Filename.value() );
    exit( 1 );
  }
 
  #ifdef SubpopulationSpatialResult
  m_subpopulation_base_prb_file<<m_num_life_stage<<"\n";
  m_subpopulation_base_prb_file<<m_num_x_range<<"\t"<<m_num_y_range<<"\n";
  m_subpopulation_base_prb_file.flush();
  #endif
 
  return true;
}

References cfg_Subpopu_Base_Output_Filename, g_msg, m_num_life_stage, m_num_x_range, m_num_y_range, m_subpopulation_base_prb_file, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Aphid_Population_Manager::Aphid_Population_Manager(), and SubPopulation_Population_Manager().

readDevReproFile()

void SubPopulation_Population_Manager::readDevReproFile

(

string

inputfile

)

Function to read the development time and lifestage.

                                                                       {
    ifstream ist(inputfile, ios::in);
    int row_num;
    ist >> row_num;
    ist >> m_num_life_stage;
    m_development_degree_day.resize(row_num, m_num_life_stage);
 
    //load the name for life stages
    for(int j=0; j<m_num_life_stage;j++){
        string temp_name;
        ist >> temp_name;
    }
 
    //m_max_alive_days = -1;
 
    //load the development and reproducing degree days
    for (int i=0; i<row_num-1; i++){
        for(int j=0; j<m_num_life_stage;j++){
            int temp_int;
            ist >> temp_int;
            m_development_degree_day(i,j)=temp_int;
            //cout<<m_activities_priorities(i,j);
            //if(i==0){
            //  if (m_max_alive_days < temp_int){
            //      m_max_alive_days = temp_int;
            //  }
            //}
        }
    }
 
    //load the lowest development temperature
    for (int j=0; j<m_num_life_stage; j++){
        double temp_dou;
        ist >> temp_dou;
        m_lowest_temp_dev(j) = temp_dou;
    }
}

References m_development_degree_day, m_lowest_temp_dev, and m_num_life_stage.

Referenced by SubPopulation_Population_Manager().

readHosts()

void SubPopulation_Population_Manager::readHosts ( string  a_file_name )

virtual

The fuction to read the host lists for aphid.

                                                                  {
 
    //reset all the vectors
    m_winter_hosts_tole.clear();
    m_winter_hosts_tole_period.clear();
    m_winter_hosts_tole_period_map.clear();
    m_winter_hosts_tov.clear();
    m_summer_hosts_tole.clear();
    m_summer_hosts_tole_period.clear();
    m_summer_hosts_tole_period_map.clear();
    m_summer_hosts_tov.clear();
 
    ifstream ist(a_file_name, ios::in);
    string one_line;
    int host_id;
    int month_id;
 
    //get the host switch flag
    getline(ist, one_line);
    istringstream iss(one_line);
    int summer_winter;
    iss >> summer_winter;
    if (summer_winter==1) {
        m_mul_hosts_flag=false;
        m_summer_host_on=true;
        m_winter_host_on=false;
    }//only summer hosts are uses since the species does not switch hosts
 
    if (summer_winter==2) {
        m_mul_hosts_flag=true;
        m_winter_host_on=true;
        m_summer_host_on=false;
    }//start with winter host since the simulation starts from jan.
 
    //get the summer host tole
    getline(ist, one_line);
    iss = istringstream(one_line);
    int temp_index = -1;
    while(iss>>host_id){
        temp_index += 1;
        if(host_id>=0){
            m_summer_hosts_tole.push_back(TTypesOfLandscapeElement(host_id));
            m_summer_hosts_tole_period_map.insert({TTypesOfLandscapeElement(host_id), temp_index});
        }
    }
 
    //get the summer host tole period
    getline(ist, one_line);
    iss = istringstream(one_line);
    while(iss>>month_id){
        if(host_id<0){
            break;
        }
        else{
            std::vector<int> temp(2, 1);
            temp.at(0) = month_id;
            iss>>month_id;
            temp.at(1) = month_id;
            m_summer_hosts_tole_period.push_back(temp);
        }
    }
 
    //get the summer host tov
    getline(ist, one_line);
    iss = istringstream(one_line);
    string veg_str;
    while(iss>>veg_str){
        if(veg_str!="NONE"){
            m_summer_hosts_tov.push_back(g_farmmanager->TranslateVegCodes(veg_str));
        }
    }
 
    //get the winter host tole
    getline(ist, one_line);
    iss = istringstream(one_line);
    temp_index = -1;
    while(iss>>host_id){
        temp_index += 1;
        if(host_id>=0){
            m_winter_hosts_tole.push_back(TTypesOfLandscapeElement(host_id));
            m_winter_hosts_tole_period_map.insert({TTypesOfLandscapeElement(host_id), temp_index});
        }
    }
 
    //get the winter host tole period
    getline(ist, one_line);
    iss = istringstream(one_line);
    while(iss>>month_id){
        if(host_id<0){
            break;
        }
        else{
            std::vector<int> temp(2, 1);
            temp.at(0) = month_id;
            iss>>month_id;
            temp.at(1) = month_id;
            m_winter_hosts_tole_period.push_back(temp);
        }
    }
 
    //get the winter host tov
    getline(ist, one_line);
    iss = istringstream(one_line);
    while(iss>>veg_str){
        if(veg_str!="NONE"){
            m_winter_hosts_tov.push_back(g_farmmanager->TranslateVegCodes(veg_str));
        }
    }
 
}

References g_farmmanager, m_mul_hosts_flag, m_summer_host_on, m_summer_hosts_tole, m_summer_hosts_tole_period, m_summer_hosts_tole_period_map, m_summer_hosts_tov, m_winter_host_on, m_winter_hosts_tole, m_winter_hosts_tole_period, m_winter_hosts_tole_period_map, m_winter_hosts_tov, and FarmManager::TranslateVegCodes().

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

relocatePopulation()

void SubPopulation_Population_Manager::relocatePopulation

(

void

)

Relocate the population in each cell based on the suitability and movement ability.

                                                         {
 
    //local movement
    /*
    for(int ind_y=0; ind_y < m_num_y_range; ind_y++){
        for(int ind_x=0; ind_x <m_num_x_range; ind_x++){
            if(m_the_subpopulation_array(ind_y, ind_x) != NULL){
                doLocalMovement(ind_x, ind_y, 0.5);             
            }
        }
    }*/
 
        //let winged aphihds to fly
    for(int ind_y=0; ind_y < m_num_y_range; ind_y++){
        for(int ind_x=0; ind_x <m_num_x_range; ind_x++){
            if(m_the_subpopulation_array(ind_y, ind_x) != NULL){
                for(int i=0; i<m_flying_life_stage_array.size(); i++){
                    //if(m_the_subpopulation_array(ind_y, ind_x)->getFlyingNum(i)>0){
                    doFlying(i, ind_x, ind_y);
                    //}
                }
            }
        }
    }   
}

References doFlying(), m_flying_life_stage_array, m_num_x_range, m_num_y_range, and m_the_subpopulation_array.

Referenced by DoFirst().

Run()

void SubPopulation_Population_Manager::Run ( int  NoTSteps )

protectedvirtual

This is the main scheduling method for the population manager using subpopulation model.

Reimplemented from Population_Manager_Base.

                                                         {
    
  for ( int TSteps = 0; TSteps < NoTSteps; TSteps++ )
  { 
    cout<<"Day "<<m_TheLandscape->SupplyDayInYear() << endl;
    #ifdef APHID_DEBUG
    m_num_killed_by_parasitoid=0;
    m_num_parasitoid=0;
    m_num_parasitoid_egg=0;
    m_num_new_parasitoid_egg_daily=0;
    #endif  
    DoFirst();
    for (int i = 0; i < m_num_y_range; i++){
        //parallel_for(m_num_x_range[&](int start, int end){
        for (int j = 0; j < m_num_x_range; j++){
            if(m_the_subpopulation_array(i,j)!=NULL){
                m_the_subpopulation_array(i,j)->BeginStep();
            }
        }
    }
    // call the step-method of all objects
    for (int i = 0; i < m_num_y_range; i++){
    //parallel_for(m_num_x_range[&](int start, int end){
        for (int j = 0; j < m_num_x_range; j++){
            if(m_the_subpopulation_array(i,j)!=NULL){
                SubPopulation* temp_pointer = m_the_subpopulation_array(i,j);
                m_the_subpopulation_array(i,j)->Step();
            }
            else {
                std::cout<<"NULL"<<endl;
            }
        }
    }
    DoLast();
 
    #ifdef __APHID_CALIBRATION
        writeCalibrationFiles();
    #endif
 
    #ifdef APHID_BIOMASS_DEBUG
     ofstream bio_file;
     bio_file.open("biomass.txt", ios::app );
     
     for (int i = 0; i<2200; i++){
        if (g_landscape_p->SupplyElementType(i)==tole_PermPastureTussocky){
            //bio_file<<g_landscape_p->SupplyVegPhase(i)<<"\t"<<g_landscape_p->SupplyVegBiomass(i)<<"\t"<<g_landscape_p->SupplyGreenBiomass(i)<<"\t";
            bio_file<<g_landscape_p->SupplyVegBiomass(i)<<"\t"<<g_landscape_p->SupplyGreenBiomass(i)<<"\n";
            break;
        }
     }
     
    
     for (int i = 0; i<2600; i++){
        if (g_landscape_p->SupplyVegType(i)==tov_DKLegume_Beans){
            //bio_file<<g_landscape_p->SupplyVegPhase(i)<<"\t"<<g_landscape_p->SupplyVegBiomass(i)<<"\t"<<g_landscape_p->SupplyGreenBiomass(i)<<"\n";
            bio_file<<g_landscape_p->SupplyVegBiomass(i)<<"\t"<<g_landscape_p->SupplyGreenBiomass(i)<<"\n";
            break;
        }
     }
    
 
     bio_file.flush();
     bio_file.close();
    #endif
 
  } // End of time step loop
}

References DoFirst(), DoLast(), g_landscape_p, m_num_x_range, m_num_y_range, m_the_subpopulation_array, Population_Manager_Base::m_TheLandscape, Landscape::SupplyDayInYear(), Landscape::SupplyElementType(), Landscape::SupplyGreenBiomass(), Landscape::SupplyVegBiomass(), Landscape::SupplyVegType(), tole_PermPastureTussocky, tov_DKLegume_Beans, and writeCalibrationFiles().

setFirstFlagLifeStage()

void SubPopulation_Population_Manager::setFirstFlagLifeStage ( int  life_stage, bool  pvalue  )

inline

The function to set the flag indicating whether a given lifestage is the first time of existing.

{m_first_flag_life_stage(life_stage) = pvalue;}

References m_first_flag_life_stage.

Referenced by SubPopulation::doDevelopment(), and Aphid::doReproduction().

SetNoProbesAndSpeciesSpecificFunctions()

void SubPopulation_Population_Manager::SetNoProbesAndSpeciesSpecificFunctions ( int  a_pn )

virtual

Sets up probe and species specifics.

Reimplemented from Population_Manager_Base.

{
    // This function relies on the fact that g_Species has been set already
   m_TheLandscape->SetSpeciesFunctions(g_Species);
}

References g_Species, Population_Manager_Base::m_TheLandscape, and Landscape::SetSpeciesFunctions().

setOldIndex()

void SubPopulation_Population_Manager::setOldIndex	(	int	life_stage,
		int	p_value
	)

The function to set the oldest index for the given life stage.

                                                                             {
    //1 is the old one
    m_accumu_degree_days(life_stage, blitz::Range(m_index_new_old(life_stage, 1), p_value)) = 0;
    m_index_new_old(life_stage,1) = p_value;
}

References m_accumu_degree_days, and m_index_new_old.

Referenced by SubPopulation::doDevelopment(), and Aphid::doReproduction().

subpopuBaseOutputProbe()

void SubPopulation_Population_Manager::subpopuBaseOutputProbe ( )

virtual

Below are the functions for saving result.

                                                             {
    for(int i=0; i<m_num_life_stage; i++){
    m_subpopulation_base_prb_file<<m_total_num_each_stage(i)<<"\t";
    }
    m_subpopulation_base_prb_file<<g_landscape_p->SupplyDaylength()<<"\t";
    
    #ifdef APHID_DEBUG
    m_subpopulation_base_prb_file<<g_landscape_p->SupplyTemp()<<"\t"<<m_num_killed_by_parasitoid<<"\t"<<
    m_num_parasitoid<<"\t"<<m_num_parasitoid_egg<<"\t"<<m_num_new_parasitoid_egg_daily;;
    #else
    m_subpopulation_base_prb_file<<g_landscape_p->SupplyTemp();
    #endif 
 
    #ifndef SubpopulationSpatialResult
    m_subpopulation_base_prb_file<<"\n";
    #endif
 
    #ifdef SubpopulationSpatialResult
    //the population in each grid
    for (int index_y = 0; index_y < m_num_y_range; index_y++){
        for (int index_x = 0; index_x < m_num_x_range; index_x++){
            m_subpopulation_base_prb_file<<"\t";
            //for(int i=0; i<m_num_life_stage; i++){
                //store the population at each life stage
            //  m_subpopulation_base_prb_file<<m_the_subpopulation_array(index_y, index_x)->getNumforOneLifeStage(i)<<"\t";
            //}
            double temp_counter = 0;
            for (int i=5;i<9;i++){
                if(m_the_subpopulation_array(index_y, index_x) != NULL){
                    temp_counter += m_the_subpopulation_array(index_y, index_x)->getNumforOneLifeStage(i);
                }
            }
            m_subpopulation_base_prb_file<<temp_counter;
 
            // parasitoid number
            //m_subpopulation_base_prb_file<<m_the_subpopulation_array(index_y, index_x)->getPrasitoidNum()<<"\t";
            //m_subpopulation_base_prb_file<<m_the_subpopulation_array(index_y, index_x)->getPrasitoidEggNum();
        }
    }
    m_subpopulation_base_prb_file<<"\n";
    #endif
 
    m_subpopulation_base_prb_file.flush();
}

References g_landscape_p, m_num_life_stage, m_num_x_range, m_num_y_range, m_subpopulation_base_prb_file, m_the_subpopulation_array, m_total_num_each_stage, Landscape::SupplyDaylength(), and Landscape::SupplyTemp().

Referenced by DoLast().

supplyAgeInDay()

int SubPopulation_Population_Manager::supplyAgeInDay	(	int	lifestage_index,
		int	column_index
	)

The function to return the age in days given an element in the subpopulation table.

                                                                                         {
    int current_newest_index = supplyNewestIndex(lifestage_index);
    if(current_newest_index>=column_index || (current_newest_index<column_index && column_index <= current_newest_index)){
        return current_newest_index-column_index;
    }
    else{
        return m_max_alive_days-column_index+current_newest_index;
    }
}

References m_max_alive_days, and supplyNewestIndex().

Referenced by Aphid::doReproduction().

supplyAgeInDayDegree()

double SubPopulation_Population_Manager::supplyAgeInDayDegree ( int  lifestage_index, int  column_index  )

inline

{return m_accumu_degree_days(lifestage_index, column_index);}

References m_accumu_degree_days.

Referenced by Aphid::doReproduction().

supplyAllPopulationGivenStage()

double SubPopulation_Population_Manager::supplyAllPopulationGivenStage

(

int

index

)

Supply the population size at the given life stage for the who landscape.

                                                                               {
    if(index<m_num_life_stage){
        return m_total_num_each_stage(index);
    } 
    return 0;
}

References m_num_life_stage, and m_total_num_each_stage.

Referenced by GetLiveArraySize(), and GetPopulationSize().

supplyCellHeight()

double SubPopulation_Population_Manager::supplyCellHeight ( )

inline

Supply the height of a subpopulation cell.

{return m_sub_h;}

References m_sub_h.

supplyCellNumX()

int SubPopulation_Population_Manager::supplyCellNumX ( )

inline

Supply number of subpopulation in x coordinate.

{return m_num_x_range;}

References m_num_x_range.

Referenced by Aphid::doMovement().

supplyCellNumY()

int SubPopulation_Population_Manager::supplyCellNumY ( )

inline

Supply number of subpopulation in y coordinate.

{return m_num_y_range;}

References m_num_y_range.

Referenced by Aphid::doMovement().

supplyCellWidth()

double SubPopulation_Population_Manager::supplyCellWidth ( )

inline

Supply the width of a subpopulation cell.

{return m_sub_w;}

References m_sub_w.

supplyDevelopmentSeason()

virtual unsigned SubPopulation_Population_Manager::supplyDevelopmentSeason ( )

inlinevirtual

The function to supply the development season.

Reimplemented in Aphid_Population_Manager.

{return 0;};

supplyFirstFlagLifeStage()

bool SubPopulation_Population_Manager::supplyFirstFlagLifeStage ( int  life_stage )

inline

The function to supply the flag of first for the given life stage.

{return m_first_flag_life_stage(life_stage);}

References m_first_flag_life_stage.

Referenced by SubPopulation::doDevelopment(), and Aphid::doReproduction().

supplyLifeStageNum()

int SubPopulation_Population_Manager::supplyLifeStageNum ( )

inline

Supply the number of life stage.

{return m_num_life_stage;}

References m_num_life_stage.

Referenced by SubPopulation::doDevelopment(), SubPopulation::doMortality(), Aphid::doReproduction(), SubPopulation::doReproduction(), and SubPopulation::SubPopulation().

SupplyLocXY()

virtual void SubPopulation_Population_Manager::SupplyLocXY ( unsigned  , unsigned  , int &  , int &    )

inlinevirtual

A stub for identifying an individual at a location.

Reimplemented from Population_Manager_Base.

   {
      int indx = index_x;
      int indy = index_y;
      x = m_the_subpopulation_array(indy, indx)->Supply_m_Location_x();
      y = m_the_subpopulation_array(indy, indx)->Supply_m_Location_y();
   }

References m_the_subpopulation_array.

supplyMaxColNum()

int SubPopulation_Population_Manager::supplyMaxColNum ( )

inline

Supply the maximum number of column in the development array.

{return m_max_alive_days;}

References m_max_alive_days.

Referenced by SubPopulation::addAnimalNumGivenStage(), SubPopulation::doMortality(), Aphid::doReproduction(), and SubPopulation::SubPopulation().

supplyMortality()

double SubPopulation_Population_Manager::supplyMortality ( int  a_life_stage, int  a_age  )

inline

The function to supply the mortality rate for the given life stage and the age.

{return m_current_mortality_array(a_life_stage, a_age);}

References m_current_mortality_array.

supplyMortalityStageArray()

blitz::Array<double, 1> SubPopulation_Population_Manager::supplyMortalityStageArray ( int  a_life_stage )

inline

The function to supply the 1D base morality rate array for the given life stage.

{return m_current_mortality_array(a_life_stage, blitz::Range::all());}

References m_current_mortality_array.

supplyMortalityWholeArray()

blitz::Array<double, 2> SubPopulation_Population_Manager::supplyMortalityWholeArray ( void  )

inline

The function to supply the whole base mortality rate array.

{return m_current_mortality_array;}

References m_current_mortality_array.

Referenced by SubPopulation::doMortality().

supplyNewestIndex()

int SubPopulation_Population_Manager::supplyNewestIndex ( int  life_stage_index )

inline

{ return m_index_new_old(life_stage_index, 0);}

References m_index_new_old.

Referenced by SubPopulation::doDevelopment(), Aphid::doReproduction(), SubPopulation::doReproduction(), and supplyAgeInDay().

supplyNextLifeStage()

int SubPopulation_Population_Manager::supplyNextLifeStage ( int  life_circle_index, int  life_stage_index  )

inline

Supply the next life stage index for a given life stage and a given life path.

{return m_life_circle_path(life_circle_index, life_stage_index);}

References m_life_circle_path.

supplyNumFlyingLifeStages()

int SubPopulation_Population_Manager::supplyNumFlyingLifeStages ( )

inline

Supply the number of life stages that can fly.

{return m_flying_life_stage_array.size();}

References m_flying_life_stage_array.

Referenced by SubPopulation::doMovement(), and SubPopulation::SubPopulation().

supplyNumLocMovLifeStages()

int SubPopulation_Population_Manager::supplyNumLocMovLifeStages ( )

inline

Supply the number of life stages thah can do local movement.

{return m_local_moving_life_stage_array.size();}

References m_local_moving_life_stage_array.

Referenced by SubPopulation::SubPopulation().

supplyOldEnoughIndex()

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

inline

{return m_index_next_life_stage.at(life_stage_index);}

References m_index_next_life_stage.

Referenced by SubPopulation::doDevelopment().

supplySizeSubpopulationCell()

double SubPopulation_Population_Manager::supplySizeSubpopulationCell ( )

inline

Supply the size of aphid subpopulation cell.

{return m_size_cell;}

References m_size_cell.

Referenced by Aphid::calPopuDensity(), and SubPopulation::calPopuDensity().

supplySubPopulationPointer()

SubPopulation * SubPopulation_Population_Manager::supplySubPopulationPointer	(	int	indx,
		int	indy
	)

Supply the pointer of the subpopulation object in the given cell.

                                                                                             {
    return m_the_subpopulation_array(indy, indx);
}

References m_the_subpopulation_array.

Referenced by Aphid::doMovement().

supplySummerHostOn()

bool SubPopulation_Population_Manager::supplySummerHostOn ( void  )

inline

{return m_summer_host_on;}

References m_summer_host_on.

Referenced by Aphid::calSuitabilityShared().

supplySummerTolePeriod()

std::vector<int> SubPopulation_Population_Manager::supplySummerTolePeriod ( TTypesOfLandscapeElement  a_tole )

inline

The function to supply the available period vector for the given summer tole host.

{return m_summer_hosts_tole_period.at(m_summer_hosts_tole_period_map.at(a_tole)); }

References m_summer_hosts_tole_period, and m_summer_hosts_tole_period_map.

supplyTotalPopulationInCell()

double SubPopulation_Population_Manager::supplyTotalPopulationInCell	(	int	x_indx,
		int	y_indx
	)

Supply whole population size at the given cell.

supplyVecFlyingLifeStages()

std::vector<int> SubPopulation_Population_Manager::supplyVecFlyingLifeStages ( )

inline

Supply the vector of life stages for flying.

{return m_flying_life_stage_array; };

References m_flying_life_stage_array.

Referenced by SubPopulation::doMovement().

supplyVecLocMoveLifeStages()

std::vector<int> SubPopulation_Population_Manager::supplyVecLocMoveLifeStages ( )

inline

Supply the vector of life stages that can do local movement.

{return m_local_moving_life_stage_array; };

References m_local_moving_life_stage_array.

Referenced by Aphid::doMovement().

supplyWinterHostOn()

bool SubPopulation_Population_Manager::supplyWinterHostOn ( void  )

inline

{return m_winter_host_on;}

References m_winter_host_on.

Referenced by Aphid::calPopuDensity(), Aphid::calSuitabilityShared(), and Aphid::doReproduction().

supplyWinterTolePeriod()

std::vector<int> SubPopulation_Population_Manager::supplyWinterTolePeriod ( TTypesOfLandscapeElement  a_tole )

inline

The function to supply the available period vector for the given winter tole host.

{return m_winter_hosts_tole_period.at(m_winter_hosts_tole_period_map.at(a_tole)); }

References m_winter_hosts_tole_period, and m_winter_hosts_tole_period_map.

updateDevelopmentSeason()

virtual void SubPopulation_Population_Manager::updateDevelopmentSeason ( )

inlinevirtual

The function to update the development season.

Reimplemented in Aphid_Population_Manager.

{};

Referenced by DoFirst().

updateMortalityArray()

void SubPopulation_Population_Manager::updateMortalityArray ( void  )

virtual

This function is used to update the daily mortality rate for all the ages. In this base class, it only depends on the temperature. The lowest and highest temperature that will make the species die. The optimal temperature will make the mortality rate to be 0.

Reimplemented in Aphid_Population_Manager.

                                                                 {
    //get the current temperature
    double current_temperature = g_landscape_p->SupplyTemp();
    //egg will not die because of cold or hot
    m_current_mortality_array(0,blitz::Range::all()) = 0.01;
    //others will die because of too cold and too hot
    for (int i=1; i<m_num_life_stage; i++){
        if(current_temperature<m_lowest_temperature_die(i) || current_temperature>m_highest_temperature_die(i)){
            m_current_mortality_array(i,blitz::Range::all()) = 1; //all die if it is too cold or too hot
        }
        else{
            m_current_mortality_array(i,blitz::Range::all()) = 0.01;
        }
    }
    m_current_mortality_array = 0.01;
}

References g_landscape_p, m_current_mortality_array, m_highest_temperature_die, m_lowest_temperature_die, m_num_life_stage, and Landscape::SupplyTemp().

Referenced by DoFirst().

updateWholePopulation()

void SubPopulation_Population_Manager::updateWholePopulation

(

)

Update whole population info.

                                                            {
    for (int k=0; k<m_num_life_stage; k++){
        m_total_num_each_stage(k) = 0;
        for (int i = 0; i < m_num_y_range; i++){
            for (int j = 0; j < m_num_x_range; j++){
                if(m_the_subpopulation_array(i,j)!=NULL){
                    m_total_num_each_stage(k) += m_the_subpopulation_array(i,j)->getNumforOneLifeStage(k);
                }
            }
        }
    }
}

References m_num_life_stage, m_num_x_range, m_num_y_range, m_the_subpopulation_array, and m_total_num_each_stage.

Referenced by DoLast().

updateWholePopulationArray() [1/2]

void SubPopulation_Population_Manager::updateWholePopulationArray

(

blitz::Array< double, 1 >

a_array

)

                                                                                                {
    m_total_num_each_stage += a_array;
}

References m_total_num_each_stage.

updateWholePopulationArray() [2/2]

void SubPopulation_Population_Manager::updateWholePopulationArray	(	int	a_listindex,
		double	number
	)

The function to update the whole population array in the whole landscape.

{   
    double temp_number = m_total_num_each_stage(a_listindex);
    temp_number += number;
    if (temp_number < 0){
        m_total_num_each_stage(a_listindex)=0;
    }
    else
    {
        m_total_num_each_stage(a_listindex)= temp_number;
    }
}

References m_total_num_each_stage.

writeCalibrationFiles()

virtual void SubPopulation_Population_Manager::writeCalibrationFiles ( void  )

inlinevirtual

Write probe files for calibration.

Reimplemented in Aphid_Population_Manager.

{;};

Referenced by Run().

Friends And Related Function Documentation

Subpopulation

friend class Subpopulation

friend

Member Data Documentation

m_accumu_degree_days

blitz::Array<double, 2> SubPopulation_Population_Manager::m_accumu_degree_days

protected

Array for accumulated degree days for each life circle.

Referenced by Aphid_Population_Manager::calHatchChance(), doDevelopment(), Aphid_Population_Manager::doSpeciesLastThing(), Aphid_Population_Manager::initialiseSimWithEggs(), isEnoughNextLifeStage(), Aphid_Population_Manager::isEnoughNextLifeStageShared(), setOldIndex(), SubPopulation_Population_Manager(), supplyAgeInDayDegree(), and Aphid_Population_Manager::updateMortalityArrayShared().

m_cell_popu_density

blitz::Array<double, 2> SubPopulation_Population_Manager::m_cell_popu_density

protected

Array for weighted population density in each subpopulation cell.

Referenced by initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), and SubPopulation_Population_Manager().

m_cell_suitability

blitz::Array<double, 2> SubPopulation_Population_Manager::m_cell_suitability

protected

Array for suitable value in each subpopulation cell.

Referenced by doFlying(), doLocalMovement(), getSuitabilityInCell(), initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), and SubPopulation_Population_Manager().

m_current_flying_array

blitz::Array<double, 1> SubPopulation_Population_Manager::m_current_flying_array

protected

Temporal array for the flying subpopulation.

Referenced by doFlying(), and SubPopulation_Population_Manager().

m_current_landing_array

blitz::Array<double, 1> SubPopulation_Population_Manager::m_current_landing_array

protected

Temporal array for the landing subpopulation.

Referenced by SubPopulation_Population_Manager().

m_current_mortality_array

blitz::Array<double, 2> SubPopulation_Population_Manager::m_current_mortality_array

protected

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.

Referenced by SubPopulation_Population_Manager(), supplyMortality(), supplyMortalityStageArray(), supplyMortalityWholeArray(), updateMortalityArray(), and Aphid_Population_Manager::updateMortalityArrayShared().

m_development_degree_day

blitz::Array<double, 2> SubPopulation_Population_Manager::m_development_degree_day

protected

The array to store the average max and std development time for each life stage, max and std time for reproducing.

Referenced by doDevelopment(), isEnoughNextLifeStage(), and readDevReproFile().

m_first_flag_life_stage

blitz::Array<bool, 1> SubPopulation_Population_Manager::m_first_flag_life_stage

protected

Array to track whether it is the first existence for a life stage.

Referenced by setFirstFlagLifeStage(), SubPopulation_Population_Manager(), and supplyFirstFlagLifeStage().

m_flying_life_stage_array

std::vector<int> SubPopulation_Population_Manager::m_flying_life_stage_array

protected

The vector to store the life stages that can fly.

Referenced by doFlying(), Aphid_Population_Manager::initialisePopulation(), initialisePopulation(), relocatePopulation(), supplyNumFlyingLifeStages(), and supplyVecFlyingLifeStages().

m_hibernated_hatch_flag

bool SubPopulation_Population_Manager::m_hibernated_hatch_flag

protected

Flag variable to indicate hibernated eggs are ready to hatch.

Referenced by doDevelopment(), and SubPopulation_Population_Manager().

m_highest_temperature_die

blitz::Array<double, 1> SubPopulation_Population_Manager::m_highest_temperature_die

private

The highest temperature that will cause the species die.

Referenced by SubPopulation_Population_Manager(), and updateMortalityArray().

m_index_new_old

blitz::Array<int, 2> SubPopulation_Population_Manager::m_index_new_old

protected

Array for index of the newest and oldest life stages.

Referenced by addNewDay(), doDevelopment(), doFlying(), Aphid_Population_Manager::doSpeciesLastThing(), isEnoughNextLifeStage(), Aphid_Population_Manager::isEnoughNextLifeStageShared(), setOldIndex(), SubPopulation_Population_Manager(), and supplyNewestIndex().

m_index_next_life_stage

std::vector<std::vector<int> > SubPopulation_Population_Manager::m_index_next_life_stage

private

The array to store the index for the ones go to the next life stage or die. -1 means nothing.

Referenced by doDevelopment(), SubPopulation_Population_Manager(), and supplyOldEnoughIndex().

m_landing_life_stage_array

std::vector<int> SubPopulation_Population_Manager::m_landing_life_stage_array

protected

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.

Referenced by doFlying(), Aphid_Population_Manager::initialisePopulation(), and initialisePopulation().

m_landing_masks

blitz::Array<blitz::Array<double, 2>, 2> SubPopulation_Population_Manager::m_landing_masks

protected

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.

Referenced by calLongMovementMask(), doFlying(), and SubPopulation_Population_Manager().

m_life_circle_path

blitz::Array<double, 2> SubPopulation_Population_Manager::m_life_circle_path

protected

The life circle array. It could have more than one life circle paths.

Referenced by supplyNextLifeStage().

m_local_moving_life_stage_array

std::vector<int> SubPopulation_Population_Manager::m_local_moving_life_stage_array

protected

The vector to store the life stags that can move locally.

Referenced by doLocalMovement(), Aphid_Population_Manager::initialisePopulation(), initialisePopulation(), supplyNumLocMovLifeStages(), and supplyVecLocMoveLifeStages().

m_long_move_mask

blitz::Array<double, 4> SubPopulation_Population_Manager::m_long_move_mask

protected

Long distance movement mask.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_long_move_mask_x_num

int SubPopulation_Population_Manager::m_long_move_mask_x_num

protected

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

Referenced by SubPopulation_Population_Manager().

m_long_move_mask_x_num_half

int SubPopulation_Population_Manager::m_long_move_mask_x_num_half

protected

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

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_long_move_mask_x_num_half_array

blitz::Array<int,1> SubPopulation_Population_Manager::m_long_move_mask_x_num_half_array

protected

Array to store the number of cells for longest flying at different windspeed.

Referenced by calLongMovementMask(), doFlying(), and SubPopulation_Population_Manager().

m_long_move_mask_y_num

int SubPopulation_Population_Manager::m_long_move_mask_y_num

protected

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

Referenced by SubPopulation_Population_Manager().

m_long_move_mask_y_num_half

int SubPopulation_Population_Manager::m_long_move_mask_y_num_half

protected

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_long_move_mask_y_num_half_array

blitz::Array<int,1> SubPopulation_Population_Manager::m_long_move_mask_y_num_half_array

protected

Referenced by calLongMovementMask(), doFlying(), and SubPopulation_Population_Manager().

m_lowest_temp_dev

blitz::Array<double, 1> SubPopulation_Population_Manager::m_lowest_temp_dev

protected

Lowest development temperatures for each life stage. This is the last step in each day.

Referenced by doDevelopment(), Aphid_Population_Manager::initialisePopulation(), readDevReproFile(), and SubPopulation_Population_Manager().

m_lowest_temperature_die

blitz::Array<double, 1> SubPopulation_Population_Manager::m_lowest_temperature_die

private

The lowest temperature that will cause the species die.

Referenced by SubPopulation_Population_Manager(), and updateMortalityArray().

m_max_alive_days

int SubPopulation_Population_Manager::m_max_alive_days

protected

The longest alive day among all the life stages.

Referenced by addNewDay(), doDevelopment(), doLocalMovement(), Aphid_Population_Manager::doSpeciesLastThing(), SubPopulation_Population_Manager(), supplyAgeInDay(), and supplyMaxColNum().

m_max_flying_wind_speed

float SubPopulation_Population_Manager::m_max_flying_wind_speed

protected

The larget wind speed for winged adults to fly.

Referenced by DoFirst(), and SubPopulation_Population_Manager().

m_max_long_distance

int SubPopulation_Population_Manager::m_max_long_distance

protected

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

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_max_short_distance

double SubPopulation_Population_Manager::m_max_short_distance

protected

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

m_mul_hosts_flag

bool SubPopulation_Population_Manager::m_mul_hosts_flag

protected

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

Referenced by Aphid_Population_Manager::initialiseSimWithEggs(), readHosts(), and Aphid_Population_Manager::updateDevelopmentSeason().

m_num_life_stage

int SubPopulation_Population_Manager::m_num_life_stage

protected

The number of life stages for the animal.

Referenced by addNewDay(), doDevelopment(), openSubpopulationBaseProbeFile(), readDevReproFile(), subpopuBaseOutputProbe(), SubPopulation_Population_Manager(), supplyAllPopulationGivenStage(), supplyLifeStageNum(), updateMortalityArray(), and updateWholePopulation().

m_num_x_range

int SubPopulation_Population_Manager::m_num_x_range

protected

The number of subpopulation in x range.

Referenced by doFlying(), doLocalMovement(), openSubpopulationBaseProbeFile(), relocatePopulation(), Run(), subpopuBaseOutputProbe(), SubPopulation_Population_Manager(), supplyCellNumX(), updateWholePopulation(), and ~SubPopulation_Population_Manager().

m_num_y_range

int SubPopulation_Population_Manager::m_num_y_range

protected

The number of subpopulation in y range.

Referenced by doFlying(), doLocalMovement(), openSubpopulationBaseProbeFile(), relocatePopulation(), Run(), subpopuBaseOutputProbe(), SubPopulation_Population_Manager(), supplyCellNumY(), updateWholePopulation(), and ~SubPopulation_Population_Manager().

m_optimal_temperature

blitz::Array<double, 1> SubPopulation_Population_Manager::m_optimal_temperature

private

The optimal development temperature for the species. (Mortality rate = 0).

Referenced by SubPopulation_Population_Manager().

m_peak_long_distance

int SubPopulation_Population_Manager::m_peak_long_distance

protected

The distance for the peak amount of landing.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_scale_wind_speed

float SubPopulation_Population_Manager::m_scale_wind_speed

protected

The scale for wind.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_short_move_mask

blitz::Array<double, 4> SubPopulation_Population_Manager::m_short_move_mask

protected

Short distance movement mask.

Referenced by SubPopulation_Population_Manager().

m_short_move_mask_x_num

int SubPopulation_Population_Manager::m_short_move_mask_x_num

protected

Referenced by SubPopulation_Population_Manager().

m_short_move_mask_y_num

int SubPopulation_Population_Manager::m_short_move_mask_y_num

protected

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

Referenced by SubPopulation_Population_Manager().

m_size_cell

double SubPopulation_Population_Manager::m_size_cell

private

The size of each subpopulation cell.

Referenced by SubPopulation_Population_Manager(), and supplySizeSubpopulationCell().

m_sub_h

int SubPopulation_Population_Manager::m_sub_h

protected

Variable to record the height of the subpopulation cell.

Referenced by calLongMovementMask(), initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), Aphid_Population_Manager::KillAphid(), SubPopulation_Population_Manager(), Aphid_Population_Manager::SupplyAphidDensity(), and supplyCellHeight().

m_sub_w

int SubPopulation_Population_Manager::m_sub_w

protected

Variable to record the width of the subpopulation cell.

Referenced by calLongMovementMask(), initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), Aphid_Population_Manager::KillAphid(), SubPopulation_Population_Manager(), Aphid_Population_Manager::SupplyAphidDensity(), and supplyCellWidth().

m_subpopulation_base_prb_file

std::ofstream SubPopulation_Population_Manager::m_subpopulation_base_prb_file

protected

The file for the storing the data.

Referenced by DoLast(), openSubpopulationBaseProbeFile(), subpopuBaseOutputProbe(), and ~SubPopulation_Population_Manager().

m_summer_host_on

bool SubPopulation_Population_Manager::m_summer_host_on

protected

The flag to enable summer host.

Referenced by readHosts(), supplySummerHostOn(), and Aphid_Population_Manager::updateDevelopmentSeason().

m_summer_hosts_tole

std::vector<TTypesOfLandscapeElement> SubPopulation_Population_Manager::m_summer_hosts_tole

protected

The vector to hold summer host landscape type.

Referenced by isSummerHostTole(), and readHosts().

m_summer_hosts_tole_period

std::vector<std::vector<int> > SubPopulation_Population_Manager::m_summer_hosts_tole_period

protected

The vector to store the exsiting period for summer host tole.

Referenced by readHosts(), and supplySummerTolePeriod().

m_summer_hosts_tole_period_map

std::map<int, int> SubPopulation_Population_Manager::m_summer_hosts_tole_period_map

protected

The map to store the index for the summer host period.

Referenced by readHosts(), and supplySummerTolePeriod().

m_summer_hosts_tov

std::vector<TTypesOfVegetation> SubPopulation_Population_Manager::m_summer_hosts_tov

protected

The vector to hold sumber host vegetation type.

Referenced by isSummerHostTov(), and readHosts().

m_the_subpopulation_array

blitz::Array<SubPopulation*, 2> SubPopulation_Population_Manager::m_the_subpopulation_array

protected

Vector to store the all the pointers for the subpopulation object.

Referenced by doFlying(), doLocalMovement(), getSubpopulationInCellLifeStage(), getTotalSubpopulationInCell(), initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), Aphid_Population_Manager::KillAphid(), relocatePopulation(), Run(), subpopuBaseOutputProbe(), SubPopulation_Population_Manager(), Aphid_Population_Manager::SupplyAphidDensity(), SupplyLocXY(), supplySubPopulationPointer(), updateWholePopulation(), and ~SubPopulation_Population_Manager().

m_total_num_each_stage

blitz::Array<double, 1> SubPopulation_Population_Manager::m_total_num_each_stage

private

Array to hold the total number of alive animals under different life stages in the whole landscape.

Referenced by subpopuBaseOutputProbe(), SubPopulation_Population_Manager(), supplyAllPopulationGivenStage(), updateWholePopulation(), and updateWholePopulationArray().

m_vec_subpopulation_pointers_polygon

std::vector<std::vector<SubPopulation*> > SubPopulation_Population_Manager::m_vec_subpopulation_pointers_polygon

protected

The vector used to store the pointers of all the subpopulation objects in each polygon.

Referenced by initialisePopulation(), Aphid_Population_Manager::initialiseSimWithEggs(), and SubPopulation_Population_Manager().

m_wind_direction_array

blitz::Array<double, 2> SubPopulation_Population_Manager::m_wind_direction_array

protected

The array to hold the wind directions.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_wind_direction_num

int SubPopulation_Population_Manager::m_wind_direction_num

protected

The number of wind directions.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_wind_speed_lookup_table

blitz::Array<int,1> SubPopulation_Population_Manager::m_wind_speed_lookup_table

protected

The look up table for wind speed index in the flying mask.

Referenced by doFlying(), and SubPopulation_Population_Manager().

m_wind_speed_num

int SubPopulation_Population_Manager::m_wind_speed_num

protected

The number of wind speed samples.

Referenced by calLongMovementMask(), and SubPopulation_Population_Manager().

m_wind_speed_step_size

int SubPopulation_Population_Manager::m_wind_speed_step_size

protected

The sampling step size for wind speed.

Referenced by SubPopulation_Population_Manager().

m_winter_host_on

bool SubPopulation_Population_Manager::m_winter_host_on

protected

The flag to enalble winter host.

Referenced by Aphid_Population_Manager::calOffspringStageBBandPP(), readHosts(), supplyWinterHostOn(), and Aphid_Population_Manager::updateDevelopmentSeason().

m_winter_hosts_tole

std::vector<TTypesOfLandscapeElement> SubPopulation_Population_Manager::m_winter_hosts_tole

protected

The vector to hold winter host landscape type.

Referenced by isWinterHostTole(), and readHosts().

m_winter_hosts_tole_period

std::vector<std::vector<int> > SubPopulation_Population_Manager::m_winter_hosts_tole_period

protected

The vector to store the exsiting period for winter host tole.

Referenced by readHosts(), and supplyWinterTolePeriod().

m_winter_hosts_tole_period_map

std::map<int, int> SubPopulation_Population_Manager::m_winter_hosts_tole_period_map

protected

The map to store the index for the winter host period.

Referenced by readHosts(), and supplyWinterTolePeriod().

m_winter_hosts_tov

std::vector<TTypesOfVegetation> SubPopulation_Population_Manager::m_winter_hosts_tov

protected

The vector to hold winter host vegetation type.

Referenced by isWinterHostTov(), and readHosts().

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

• /builds/ALMaSS/ALMaSS_MIDox/SubPopulation/SubPopulation_Population_Manager.h
• /builds/ALMaSS/ALMaSS_MIDox/SubPopulation/SubPopulation_Population_Manager.cpp