ALMaSS Bembidion ODdox  1.1
The bembidion model description following ODdox protocol
Bembidion_all.cpp File Reference
#include <string.h>
#include <iostream>
#include <fstream>
#include "../Landscape/ls.h"
#include "../BatchALMaSS/PopulationManager.h"
#include "../BatchALMaSS/AOR_Probe.h"
#include "../BatchALMaSS/MovementMap.h"
#include "../BatchALMaSS/positionmap.h"
#include "../Bembidion/bembidion_all.h"
#include "../BatchALMaSS/BoostRandomGenerators.h"

Go to the source code of this file.

Variables

boost::variate_generator< base_generator_type &, boost::uniform_real<> > g_rand_uni
 
CfgInt cfg_pm_eventfrequency
 
CfgInt cfg_pm_eventsize
 
CfgBool cfg_RipleysOutput_used
 
CfgBool cfg_AOROutput_used
 
CfgBool cfg_ReallyBigOutput_used
 
CfgBool cfg_ReallyBigOutputMonthly_used
 
const int Vector_x [8]
 
const int Vector_y [8]
 
static CfgFloat cfg_BemAdultPPPElimiationRate ("BEM_ADPPPELIMIATIONRATE", CFG_CUSTOM, 0.0, 0.0, 1.0)
 Pesticide body burden is multiplied by this daily. More...
 
static CfgFloat cfg_BemAdultPPPThreshold ("BEM_ADPPPTHRESHOLD", CFG_CUSTOM, 9999999999.9)
 Adult PPP threshold for effect. More...
 
static CfgFloat cfg_BemAdultPPPEffectProb ("BEM_ADPPPEFFECTPROB", CFG_CUSTOM, 0, 0.0, 1.0)
 The probability of daily effect per day on threshold excedence. More...
 
static CfgFloat cfg_BemAdultPPPEffectProbDecay ("BEM_ADPPPEFFECTPROBDECAY", CFG_CUSTOM, 0, 0.0, 1.0)
 The probability of daily effect per day on threshold excedence. More...
 
static CfgBool cfg_SavePesticideMortLocation ("BEM_SAVEPESTMORTLOC", CFG_CUSTOM, false)
 Controls whether pesticide mortality location should be recorded. More...
 
static CfgBool cfg_SaveInfieldLocation ("BEM_SAVEINFIELDLOC", CFG_CUSTOM, false)
 Controls whether in-field off-field location should be recorded. More...
 
static CfgInt cfg_InCropRef ("BEM_INCROPREF", CFG_CUSTOM, 603)
 Defines the crop reference for in-crop if pest mort location or in-field locations are switched on. More...
 
static CfgInt cfg_SaveInfieldLocationInterval ("BEM_INCROPREFINTERVAL", CFG_CUSTOM, 10000)
 Interval for recording in-crop locations - > 364 is ignored. More...
 
static CfgInt cfg_SaveInfieldLocationStartDay ("BEM_INCROPREFSTARTDAY", CFG_CUSTOM, -2)
 Start day in year to record in-field locations. More...
 
static CfgInt cfg_beetlestartnos ("BEM_STARTNO", CFG_CUSTOM, 10000)
 Controls the numbers of adults entering the simulation. More...
 
static CfgInt cfg_DDepRange ("BEM_DDEPRANGE", CFG_CUSTOM, 3)
 Adult/Larve density dependent range. More...
 
static CfgInt cfg_LDDepMort0 ("BEM_LDDEPMORTZERO", CFG_CUSTOM, 3)
 Larval density dependent mortality. More...
 
static CfgInt cfg_LDDepMort1 ("BEM_LDDEPMORTONE", CFG_CUSTOM, 0)
 Larval density dependent mortality. More...
 
static CfgInt cfg_ADDepMort0 ("BEM_ADDEPMORTZERO", CFG_CUSTOM, 2)
 Adult density dependent mortality constant. More...
 
static CfgInt cfg_ADDepMort1 ("BEM_ADDEPMORTONE", CFG_CUSTOM, 10)
 Chance of death if there is another adult within the density-dependent range square this beetle is in. More...
 
static CfgInt cfg_MaxDailyMovement ("BEM_MAXDAILYMOVEMENT", CFG_CUSTOM, 14)
 Max daily movement in m. More...
 
const char * SimulationName ="Bembidion lampros"
 
double g_SpeedyDivides [2001]
 Facilitating array for divisions by integers (= *1/N) More...
 
const double DailyEggMort = 0.007
 Daily fixed mortality probability. More...
 
const double DailyLarvaeMort = 0.001
 Daily fixed mortality probability. More...
 
const double DailyPupaeMort = 0.001
 Daily fixed mortality probability. More...
 
const double DailyAdultMort = 0.001
 Daily fixed mortality probability. More...
 
const double LarvalDailyMort [3][6]
 Daily fixed mortality probability based on three larval stages and temperature. More...
 
const double DevelopmentInflectionPoint = 12.0
 Inflection point in larval day degree calculations. More...
 
const double DevelConst1 = 3.0
 Day degree threshold constant for all stages. More...
 
const double EggDevelConst2 = 178.58
 Day degree constant. More...
 
const double LDevelConst2 [3] = {101.4,107.4,190.4}
 Day degree constant. More...
 
const double PupaDevelConst2 = 147.7
 Day degree constant. More...
 
const double above12Egg = EggDevelConst2/124.9
 Day degree constant above inflection point. More...
 
const double above12Larvae [3] = {(LDevelConst2[0]/87.5),(LDevelConst2[1]/95.2),(LDevelConst2[2]/189.3)}
 Day degree constant above inflection point. More...
 
const double above12Pupae = EggDevelConst2/132.3
 Day degree constant above inflection point. More...
 
const double AdultEggLayingThreshold = 3
 Temperature threshold for egg laying. More...
 
const double EggProductionSlope = 0.6
 
static CfgInt cfg_TotalNoEggs ("BEM_TOTALEGGS", CFG_CUSTOM, 256)
 The maximum number of eggs it is possible to produce per female. More...
 
const float DispersalThreshold = 6.0
 Adult dispersal temp threshold for DD calcuation. More...
 
const int DipsersalDayDegrees = 8
 
const int FieldHibernateChance = 25
 
int MaxDailyMovement
 
const int AdultTurnRate = 80
 
const int StartAggregatingDay = 270
 
const int StartAggregatingDayProb = 260
 
const int StopAggregationDay = 280
 
static CfgFloat cfg_BeetleStriglingMort ("BEM_STRIGLINGMORT", CFG_CUSTOM, 0.250)
 
static CfgFloat cfg_BeetleHarvestMort ("BEM_HARVESTMORT", CFG_CUSTOM, 0.290)
 
static CfgFloat cfg_Egg_SoilCultivationMortality ("BEM_EGGSOILMORT", CFG_CUSTOM, 0.500)
 
static CfgFloat cfg_Larva_SoilCultivationMortality ("BEM_LARVAESOILMORT", CFG_CUSTOM, 0.500)
 
static CfgFloat cfg_Pupa_SoilCultivationMortality ("BEM_PUPAESOILMORT", CFG_CUSTOM, 0.500)
 
static CfgFloat cfg_Adult_SoilCultivationMortality ("BEM_ADULTSOILMORT", CFG_CUSTOM, 0.270)
 
static CfgFloat cfg_Egg_InsecticideApplication ("BEM_EGGINSECTICIDEMORT", CFG_CUSTOM, 0)
 
static CfgFloat cfg_Larva_InsecticideApplication ("BEM_LARVAEINSECTICIDEMORT", CFG_CUSTOM, 0.800)
 
static CfgFloat cfg_Pupa_InsecticideApplication ("BEM_PUPAEINSECTICIDEMORT", CFG_CUSTOM, 0.800)
 
static CfgFloat cfg_Adult_InsecticideApplication ("BEM_ADULTINSECTICIDEMORT", CFG_CUSTOM, 0.800)
 
static CfgInt cfg_PesticideTrialEggTreatmentMort ("BEM_PTRIALEGGMORT", CFG_CUSTOM, 0)
 
static CfgInt cfg_PesticideTrialLarvaeTreatmentMort ("BEM_PTRIALLARVAEMORT", CFG_CUSTOM, 0)
 
static CfgInt cfg_PesticideTrialPupaeTreatmentMort ("BEM_PTRIALPUPAEMORT", CFG_CUSTOM, 0)
 
static CfgInt cfg_PesticideTrialAdultTreatmentMort ("BEM_PTRIALADULTMORT", CFG_CUSTOM, 0)
 
const int PesticideTrialAdultToxicMort = 0
 
const int PesticideTrialPupaeToxicMort = 0
 
const int PesticideTrialLarvaeToxicMort = 0
 
const int PesticideTrialEggToxicMort = 0
 

Variable Documentation

◆ above12Egg

const double above12Egg = EggDevelConst2/124.9

Day degree constant above inflection point.

Definition at line 128 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ above12Larvae

const double above12Larvae[3] = {(LDevelConst2[0]/87.5),(LDevelConst2[1]/95.2),(LDevelConst2[2]/189.3)}

Day degree constant above inflection point.

Definition at line 130 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ above12Pupae

const double above12Pupae = EggDevelConst2/132.3

Day degree constant above inflection point.

Definition at line 132 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ AdultEggLayingThreshold

const double AdultEggLayingThreshold = 3

Temperature threshold for egg laying.

Definition at line 134 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ AdultTurnRate

const int AdultTurnRate = 80

brief Turning rate of adults

Definition at line 147 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::DailyMovement().

◆ cfg_ADDepMort0

CfgInt cfg_ADDepMort0("BEM_ADDEPMORTZERO", CFG_CUSTOM, 2)
static

Adult density dependent mortality constant.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager().

◆ cfg_ADDepMort1

CfgInt cfg_ADDepMort1("BEM_ADDEPMORTONE", CFG_CUSTOM, 10)
static

Chance of death if there is another adult within the density-dependent range square this beetle is in.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager().

◆ cfg_Adult_InsecticideApplication

CfgFloat cfg_Adult_InsecticideApplication("BEM_ADULTINSECTICIDEMORT", CFG_CUSTOM, 0.800)
static

brief Farm Operation Mortality

Referenced by Bembidion_Adult::OnFarmEvent().

◆ cfg_Adult_SoilCultivationMortality

CfgFloat cfg_Adult_SoilCultivationMortality("BEM_ADULTSOILMORT", CFG_CUSTOM, 0.270)
static

brief Farm Operation Mortality

Referenced by Bembidion_Adult::OnFarmEvent().

◆ cfg_AOROutput_used

◆ cfg_BeetleHarvestMort

CfgFloat cfg_BeetleHarvestMort("BEM_HARVESTMORT", CFG_CUSTOM, 0.290)
static

brief Farm Operation Mortality

Referenced by Bembidion_Adult::OnFarmEvent().

◆ cfg_beetlestartnos

CfgInt cfg_beetlestartnos("BEM_STARTNO", CFG_CUSTOM, 10000)
static

Controls the numbers of adults entering the simulation.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_BeetleStriglingMort

CfgFloat cfg_BeetleStriglingMort("BEM_STRIGLINGMORT", CFG_CUSTOM, 0.250)
static

brief Farm Operation Mortality

Referenced by Bembidion_Adult::OnFarmEvent().

◆ cfg_BemAdultPPPEffectProb

CfgFloat cfg_BemAdultPPPEffectProb("BEM_ADPPPEFFECTPROB", CFG_CUSTOM, 0, 0.0, 1.0)
static

The probability of daily effect per day on threshold excedence.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_BemAdultPPPEffectProbDecay

CfgFloat cfg_BemAdultPPPEffectProbDecay("BEM_ADPPPEFFECTPROBDECAY", CFG_CUSTOM, 0, 0.0, 1.0)
static

The probability of daily effect per day on threshold excedence.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_BemAdultPPPElimiationRate

CfgFloat cfg_BemAdultPPPElimiationRate("BEM_ADPPPELIMIATIONRATE", CFG_CUSTOM, 0.0, 0.0, 1.0)
static

Pesticide body burden is multiplied by this daily.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_BemAdultPPPThreshold

CfgFloat cfg_BemAdultPPPThreshold("BEM_ADPPPTHRESHOLD", CFG_CUSTOM, 9999999999.9)
static

Adult PPP threshold for effect.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_DDepRange

CfgInt cfg_DDepRange("BEM_DDEPRANGE", CFG_CUSTOM, 3)
static

Adult/Larve density dependent range.

Referenced by Bembidion_Adult::DDepMort(), and Bembidion_Larvae::st_Develop().

◆ cfg_Egg_InsecticideApplication

CfgFloat cfg_Egg_InsecticideApplication("BEM_EGGINSECTICIDEMORT", CFG_CUSTOM, 0)
static

brief Farm Operation Mortality

Referenced by Bembidion_Egg_List::DailyMortality().

◆ cfg_Egg_SoilCultivationMortality

CfgFloat cfg_Egg_SoilCultivationMortality("BEM_EGGSOILMORT", CFG_CUSTOM, 0.500)
static

brief Farm Operation Mortality

Referenced by Bembidion_Egg_List::DailyMortality().

◆ cfg_InCropRef

CfgInt cfg_InCropRef("BEM_INCROPREF", CFG_CUSTOM, 603)
static

Defines the crop reference for in-crop if pest mort location or in-field locations are switched on.

Referenced by Bembidion_Population_Manager::Init().

◆ cfg_Larva_InsecticideApplication

CfgFloat cfg_Larva_InsecticideApplication("BEM_LARVAEINSECTICIDEMORT", CFG_CUSTOM, 0.800)
static

brief Farm Operation Mortality

Referenced by Bembidion_Larvae::OnFarmEvent().

◆ cfg_Larva_SoilCultivationMortality

CfgFloat cfg_Larva_SoilCultivationMortality("BEM_LARVAESOILMORT", CFG_CUSTOM, 0.500)
static

brief Farm Operation Mortality

Referenced by Bembidion_Larvae::OnFarmEvent().

◆ cfg_LDDepMort0

CfgInt cfg_LDDepMort0("BEM_LDDEPMORTZERO", CFG_CUSTOM, 3)
static

Larval density dependent mortality.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager().

◆ cfg_LDDepMort1

CfgInt cfg_LDDepMort1("BEM_LDDEPMORTONE", CFG_CUSTOM, 0)
static

Larval density dependent mortality.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager().

◆ cfg_MaxDailyMovement

CfgInt cfg_MaxDailyMovement("BEM_MAXDAILYMOVEMENT", CFG_CUSTOM, 14)
static

Max daily movement in m.

Referenced by Bembidion_Population_Manager::Bembidion_Population_Manager().

◆ cfg_PesticideTrialAdultTreatmentMort

CfgInt cfg_PesticideTrialAdultTreatmentMort("BEM_PTRIALADULTMORT", CFG_CUSTOM, 0)
static

brief Farm Operation Mortality

Referenced by Bembidion_Adult::OnFarmEvent().

◆ cfg_PesticideTrialEggTreatmentMort

CfgInt cfg_PesticideTrialEggTreatmentMort("BEM_PTRIALEGGMORT", CFG_CUSTOM, 0)
static

brief Farm Operation Mortality

Referenced by Bembidion_Egg_List::DailyMortality().

◆ cfg_PesticideTrialLarvaeTreatmentMort

CfgInt cfg_PesticideTrialLarvaeTreatmentMort("BEM_PTRIALLARVAEMORT", CFG_CUSTOM, 0)
static

brief Farm Operation Mortality

Referenced by Bembidion_Larvae::OnFarmEvent().

◆ cfg_PesticideTrialPupaeTreatmentMort

CfgInt cfg_PesticideTrialPupaeTreatmentMort("BEM_PTRIALPUPAEMORT", CFG_CUSTOM, 0)
static

brief Farm Operation Mortality

Referenced by Bembidion_Pupae::OnFarmEvent().

◆ cfg_pm_eventfrequency

CfgInt cfg_pm_eventfrequency

◆ cfg_pm_eventsize

CfgInt cfg_pm_eventsize

◆ cfg_Pupa_InsecticideApplication

CfgFloat cfg_Pupa_InsecticideApplication("BEM_PUPAEINSECTICIDEMORT", CFG_CUSTOM, 0.800)
static

brief Farm Operation Mortality

Referenced by Bembidion_Pupae::OnFarmEvent().

◆ cfg_Pupa_SoilCultivationMortality

CfgFloat cfg_Pupa_SoilCultivationMortality("BEM_PUPAESOILMORT", CFG_CUSTOM, 0.500)
static

brief Farm Operation Mortality

Referenced by Bembidion_Pupae::OnFarmEvent().

◆ cfg_ReallyBigOutput_used

◆ cfg_ReallyBigOutputMonthly_used

CfgBool cfg_ReallyBigOutputMonthly_used

◆ cfg_RipleysOutput_used

◆ cfg_SaveInfieldLocation

CfgBool cfg_SaveInfieldLocation("BEM_SAVEINFIELDLOC", CFG_CUSTOM, false)
static

Controls whether in-field off-field location should be recorded.

Referenced by Bembidion_Population_Manager::DoLast(), and Bembidion_Population_Manager::Init().

◆ cfg_SaveInfieldLocationInterval

CfgInt cfg_SaveInfieldLocationInterval("BEM_INCROPREFINTERVAL", CFG_CUSTOM, 10000)
static

Interval for recording in-crop locations - > 364 is ignored.

Referenced by Bembidion_Population_Manager::DoLast().

◆ cfg_SaveInfieldLocationStartDay

CfgInt cfg_SaveInfieldLocationStartDay("BEM_INCROPREFSTARTDAY", CFG_CUSTOM, -2)
static

Start day in year to record in-field locations.

Referenced by Bembidion_Population_Manager::DoLast().

◆ cfg_SavePesticideMortLocation

CfgBool cfg_SavePesticideMortLocation("BEM_SAVEPESTMORTLOC", CFG_CUSTOM, false)
static

Controls whether pesticide mortality location should be recorded.

◆ cfg_TotalNoEggs

CfgInt cfg_TotalNoEggs("BEM_TOTALEGGS", CFG_CUSTOM, 256)
static

The maximum number of eggs it is possible to produce per female.

Referenced by Bembidion_Adult::Step().

◆ DailyAdultMort

const double DailyAdultMort = 0.001

Daily fixed mortality probability.

Definition at line 112 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::DailyMortality().

◆ DailyEggMort

const double DailyEggMort = 0.007

Daily fixed mortality probability.

Definition at line 106 of file Bembidion_all.cpp.

Referenced by Bembidion_Egg_List::DailyMortality().

◆ DailyLarvaeMort

const double DailyLarvaeMort = 0.001

Daily fixed mortality probability.

Definition at line 108 of file Bembidion_all.cpp.

Referenced by Bembidion_Larvae::DailyMortality().

◆ DailyPupaeMort

const double DailyPupaeMort = 0.001

Daily fixed mortality probability.

Definition at line 110 of file Bembidion_all.cpp.

Referenced by Bembidion_Pupae::DailyMortality().

◆ DevelConst1

const double DevelConst1 = 3.0

Day degree threshold constant for all stages.

Definition at line 120 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ DevelopmentInflectionPoint

const double DevelopmentInflectionPoint = 12.0

Inflection point in larval day degree calculations.

Definition at line 118 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ DipsersalDayDegrees

const int DipsersalDayDegrees = 8

brief Day degrees required before dispersal

Definition at line 141 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::st_Hibernate().

◆ DispersalThreshold

const float DispersalThreshold = 6.0

Adult dispersal temp threshold for DD calcuation.

Definition at line 139 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::st_Hibernate().

◆ EggDevelConst2

const double EggDevelConst2 = 178.58

Day degree constant.

Definition at line 122 of file Bembidion_all.cpp.

Referenced by Bembidion_Egg_List::st_Develop().

◆ EggProductionSlope

const double EggProductionSlope = 0.6

Definition at line 135 of file Bembidion_all.cpp.

Referenced by Bembidion_Population_Manager::DoFirst().

◆ FieldHibernateChance

const int FieldHibernateChance = 25

brief Probability of hibernation in field

Definition at line 143 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::MoveToAggr().

◆ g_rand_uni

◆ g_SpeedyDivides

double g_SpeedyDivides[2001]

Facilitating array for divisions by integers (= *1/N)

Facilitating array for divisions by integers (= *1/N)

Definition at line 250 of file Landscape.cpp.

Referenced by Landscape::Landscape(), and Bembidion_Pupae::st_Develop().

◆ LarvalDailyMort

const double LarvalDailyMort[3][6]
Initial value:
= {{0.0855,0.0855,0.1036,0.0563,0.0515,0.0657},
{0.0626,0.0626,0.0940,0.0529,0.0492,0.0633},
{0.0631,0.0631,0.0545,0.0268,0.0236,0.0295}}

Daily fixed mortality probability based on three larval stages and temperature.

Definition at line 114 of file Bembidion_all.cpp.

Referenced by Bembidion_Larvae::TempRelatedLarvalMortality().

◆ LDevelConst2

const double LDevelConst2[3] = {101.4,107.4,190.4}

Day degree constant.

Definition at line 124 of file Bembidion_all.cpp.

Referenced by Bembidion_Larvae::st_Develop().

◆ MaxDailyMovement

int MaxDailyMovement

◆ PesticideTrialAdultToxicMort

const int PesticideTrialAdultToxicMort = 0

brief Farm Operation Mortality

Definition at line 187 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::OnFarmEvent().

◆ PesticideTrialEggToxicMort

const int PesticideTrialEggToxicMort = 0

brief Farm Operation Mortality

Definition at line 193 of file Bembidion_all.cpp.

Referenced by Bembidion_Egg_List::DailyMortality().

◆ PesticideTrialLarvaeToxicMort

const int PesticideTrialLarvaeToxicMort = 0

brief Farm Operation Mortality

Definition at line 191 of file Bembidion_all.cpp.

Referenced by Bembidion_Larvae::OnFarmEvent().

◆ PesticideTrialPupaeToxicMort

const int PesticideTrialPupaeToxicMort = 0

brief Farm Operation Mortality

Definition at line 189 of file Bembidion_all.cpp.

Referenced by Bembidion_Pupae::OnFarmEvent().

◆ PupaDevelConst2

const double PupaDevelConst2 = 147.7

Day degree constant.

Definition at line 126 of file Bembidion_all.cpp.

Referenced by Bembidion_Pupae::st_Develop().

◆ SimulationName

const char* SimulationName ="Bembidion lampros"

Definition at line 93 of file Bembidion_all.cpp.

◆ StartAggregatingDay

const int StartAggregatingDay = 270

brief Start of aggregation behaviour

Definition at line 149 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::st_Forage().

◆ StartAggregatingDayProb

const int StartAggregatingDayProb = 260

brief Chance of starting aggregating on StartAggregatingDay

Definition at line 151 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::st_Forage().

◆ StopAggregationDay

const int StopAggregationDay = 280

brief Day at which hibernation can start if in the correct habitat type

Definition at line 153 of file Bembidion_all.cpp.

Referenced by Bembidion_Adult::MoveToAggr().

◆ Vector_x

const int Vector_x[8]

◆ Vector_y

const int Vector_y[8]