Default parameters¶
Depending on latest stable calibration used.
EMOD¶
config.json
| Parameter | Estimate |
|---|---|
| Age_Dependent_Biting_Risk_Type | SURFACE_AREA_DEPENDENT |
| Age_Initialization_Distribution_Type | DISTRIBUTION_COMPLEX |
| Air_Temperature_Filename | climate/seasonal_air_temperature_daily.bin |
| Air_Temperature_Offset | 0 |
| Anemia_Mortality_Inverse_Width | 1 |
| Anemia_Mortality_Threshold | 0.654726663 |
| Anemia_Severe_Inverse_Width | 10 |
| Anemia_Severe_Threshold | 4.50775825 |
| Antibody_CSP_Decay_Days | 90 |
| Antibody_CSP_Killing_Inverse_Width | 1.5 |
| Antibody_CSP_Killing_Threshold | 20 |
| Antibody_Capacity_Growth_Rate | 0.09 |
| Antibody_IRBC_Kill_Rate | 1.596 |
| Antibody_Memory_Level | 0.34 |
| Antibody_Stimulation_C50 | 30 |
| Antigen_Switch_Rate | 7.65E-10 |
| Base_Air_Temperature | 27 |
| Base_Gametocyte_Fraction_Male | 0.2 |
| Base_Gametocyte_Mosquito_Survival_Rate | 0.002011099 |
| Base_Gametocyte_Production_Rate | 0.06150582 |
| Base_Land_Temperature | 27 |
| Base_Rainfall | 10 |
| Base_Relative_Humidity | 0.75 |
| Base_Sporozoite_Survival_Fraction | 0.25 |
| Birth_Rate_Dependence | POPULATION_DEP_RATE |
| Birth_Rate_Time_Dependence | NONE |
| Campaign_Filename | campaign.json |
| Climate_Model | CLIMATE_BY_DATA |
| Climate_Update_Resolution | CLIMATE_UPDATE_DAY |
| Clinical_Fever_Threshold_High | 1.5 |
| Clinical_Fever_Threshold_Low | 0.5 |
| Config_Name | |
| Custom_Coordinator_Events | [] |
| Custom_Individual_Events | [‘Received_Treatment’, ‘Received_Severe_Treatment’] |
| Custom_Node_Events | [] |
| Custom_Reports_Filename | custom_reports.json |
| Cytokine_Gametocyte_Inactivation | 0.01667 |
| Death_Rate_Dependence | NONDISEASE_MORTALITY_BY_AGE_AND_GENDER |
| Demographics_Filenames | [‘demographics.json’] |
| Egg_Hatch_Delay_Distribution | NO_DELAY |
| Egg_Hatch_Density_Dependence | NO_DENSITY_DEPENDENCE |
| Egg_Saturation_At_Oviposition | SATURATION_AT_OVIPOSITION |
| Enable_Aging | 1 |
| Enable_Birth | 1 |
| Enable_Climate_Stochasticity | 0 |
| Enable_Default_Reporting | 1 |
| Enable_Demographics_Birth | 0 |
| Enable_Demographics_Builtin | 0 |
| Enable_Demographics_Reporting | 0 |
| Enable_Demographics_Risk | 1 |
| Enable_Disease_Mortality | 0 |
| Enable_Drought_Egg_Hatch_Delay | 0 |
| Enable_Egg_Mortality | 0 |
| Enable_Infectivity_Reservoir | 0 |
| Enable_Initial_Prevalence | 1 |
| Enable_Interventions | 1 |
| Enable_Maternal_Antibodies_Transmission | 1 |
| Enable_Maternal_Infection_Transmission | 0 |
| Enable_Maternal_Protection | 0 |
| Enable_Natural_Mortality | 1 |
| Enable_Property_Output | 0 |
| Enable_Skipping | 0 |
| Enable_Spatial_Output | 0 |
| Enable_Superinfection | 1 |
| Enable_Susceptibility_Scaling | 0 |
| Enable_Temperature_Dependent_Egg_Hatching | 0 |
| Enable_Termination_On_Zero_Total_Infectivity | 0 |
| Enable_Vector_Aging | 0 |
| Enable_Vector_Migration | 1 |
| Enable_Vector_Migration_Local | 0 |
| Enable_Vector_Migration_Regional | 0 |
| Enable_Vector_Mortality | 1 |
| Enable_Vector_Species_Report | 0 |
| Enable_Vital_Dynamics | 1 |
| Erythropoiesis_Anemia_Effect | 3.5 |
| Falciparum_MSP_Variants | 32 |
| Falciparum_Nonspecific_Types | 76 |
| Falciparum_PfEMP1_Variants | 1070 |
| Fever_IRBC_Kill_Rate | 1.4 |
| Fever_Mortality_Inverse_Width | 1895.519716 |
| Fever_Mortality_Threshold | 3.400500856 |
| Fever_Severe_Inverse_Width | 27.56535804 |
| Fever_Severe_Threshold | 3.983542997 |
| Gametocyte_Stage_Survival_Rate | 0.588569307 |
| Human_Feeding_Mortality | 0.1 |
| Incubation_Period_Constant | 7 |
| Incubation_Period_Distribution | CONSTANT_DISTRIBUTION |
| Individual_Sampling_Type | TRACK_ALL |
| Infection_Updates_Per_Timestep | 8 |
| Infectious_Period_Exponential | 6 |
| Infectious_Period_Gaussian_Mean | 6 |
| Infectious_Period_Gaussian_Std_Dev | 1 |
| Infectious_Period_Kappa | 1 |
| Infectious_Period_Lambda | 1 |
| Infectious_Period_Log_Normal_Mu | 6 |
| Infectious_Period_Log_Normal_Sigma | 1 |
| Infectious_Period_Max | 1 |
| Infectious_Period_Mean_1 | 1 |
| Infectious_Period_Mean_2 | 1 |
| Infectious_Period_Min | 0 |
| Infectious_Period_Peak_2_Value | 1 |
| Infectious_Period_Poisson_Mean | 6 |
| Infectious_Period_Proportion_0 | 1 |
| Infectious_Period_Proportion_1 | 1 |
| Infectivity_Scale_Type | CONSTANT_INFECTIVITY |
| Innate_Immune_Variation_Type | NONE |
| Insecticides | [] |
| Inset_Chart_Has_IP | [] |
| Inset_Chart_Has_Interventions | [] |
| Inset_Chart_Include_Pregnancies | 0 |
| Inset_Chart_Reporting_Include_30Day_Avg_Infection_Duration | 1 |
| Land_Temperature_Filename | climate/seasonal_air_temperature_daily.bin |
| Land_Temperature_Offset | 0 |
| Larval_Density_Dependence | UNIFORM_WHEN_OVERPOPULATION |
| Load_Balance_Filename | |
| MSP1_Merozoite_Kill_Fraction | 0.511735322 |
| Malaria_Model | MALARIA_MECHANISTIC_MODEL |
| Malaria_Strain_Model | FALCIPARUM_RANDOM_STRAIN |
| Maternal_Antibodies_Type | SIMPLE_WANING |
| Maternal_Antibody_Decay_Rate | 0.01 |
| Maternal_Antibody_Protection | 0.1327 |
| Max_Individual_Infections | 3 |
| Max_MSP1_Antibody_Growthrate | 0.045 |
| Mean_Egg_Hatch_Delay | 0 |
| Mean_Sporozoites_Per_Bite | 11 |
| Memory_Usage_Halting_Threshold_Working_Set_MB | 8000 |
| Memory_Usage_Warning_Threshold_Working_Set_MB | 7000 |
| Merozoites_Per_Hepatocyte | 15000 |
| Merozoites_Per_Schizont | 16 |
| Min_Adapted_Response | 0.05 |
| Min_Days_Between_Clinical_Incidents | 14 |
| Nonspecific_Antibody_Growth_Rate_Factor | 0.5 |
| Nonspecific_Antigenicity_Factor | 0.415111634 |
| Number_Basestrains | 1 |
| Number_Of_Asexual_Cycles_Without_Gametocytes | 1 |
| Parasite_Mortality_Inverse_Width | 327.5159451 |
| Parasite_Mortality_Threshold | 851138.0382 |
| Parasite_Severe_Inverse_Width | 56.5754896 |
| Parasite_Severe_Threshold | 851031.2877 |
| Parasite_Switch_Type | RATE_PER_PARASITE_7VARS |
| PfHRP2_Boost_Rate | 0.018 |
| PfHRP2_Decay_Rate | 0.167 |
| Population_Density_Infectivity_Correction | CONSTANT_INFECTIVITY |
| Population_Scale_Type | FIXED_SCALING |
| Pyrogenic_Threshold | 15000 |
| RBC_Destruction_Multiplier | 3.29 |
| Rainfall_Filename | climate/seasonal_rainfall_daily.bin |
| Rainfall_In_mm_To_Fill_Swamp | 1000 |
| Rainfall_Scale_Factor | 1 |
| Random_Number_Generator_Policy | ONE_PER_CORE |
| Random_Number_Generator_Type | USE_PSEUDO_DES |
| Relative_Humidity_Filename | climate/seasonal_relative_humidity_daily.bin |
| Relative_Humidity_Scale_Factor | 1 |
| Report_Coordinator_Event_Recorder | 0 |
| Report_Detection_Threshold_Blood_Smear_Gametocytes | 40 |
| Report_Detection_Threshold_Blood_Smear_Parasites | 40 |
| Report_Detection_Threshold_Fever | 1 |
| Report_Detection_Threshold_PCR_Gametocytes | 0.05 |
| Report_Detection_Threshold_PCR_Parasites | 0.05 |
| Report_Detection_Threshold_PfHRP2 | 5 |
| Report_Detection_Threshold_True_Parasite_Density | 0 |
| Report_Gametocyte_Smear_Sensitivity | 0.1 |
| Report_Node_Event_Recorder | 0 |
| Report_Parasite_Smear_Sensitivity | 0.1 |
| Report_Surveillance_Event_Recorder | 0 |
| Run_Number | 2 |
| Semipermanent_Habitat_Decay_Rate | 0.01 |
| Serialized_Population_Reading_Type | NONE |
| Serialized_Population_Writing_Type | NONE |
| Simulation_Duration | 5475 |
| Simulation_Timestep | 1 |
| Simulation_Type | MALARIA_SIM |
| Start_Time | 1 |
| Temporary_Habitat_Decay_Factor | 0.05 |
| Vector_Larval_Rainfall_Mortality | NONE |
| Vector_Migration_Food_Modifier | 0 |
| Vector_Migration_Habitat_Modifier | 0 |
| Vector_Migration_Modifier_Equation | LINEAR |
| Vector_Migration_Stay_Put_Modifier | 0 |
| Vector_Sampling_Type | VECTOR_COMPARTMENTS_NUMBER |
| Wolbachia_Infection_Modification | 1 |
| Wolbachia_Mortality_Modification | 1 |
| x_Base_Population | 1 |
| x_Birth | 1 |
| x_Other_Mortality | 1 |
| x_Temporary_Larval_Habitat | 1.3484 |
| x_Vector_Migration_Local | 1 |
malariasimulation¶
malariasimulation offers a get_parameters function to view all parameters in the model. Default values were determined by using the median across 50 random sets of parameter draws.
| Parameter Symbol | Parameter Type | Parameter Description | Parameter Default | Parameter Min | Parameter Max |
|---|---|---|---|---|---|
| du | fixed state transitions | the delay for humans to move from state U to S | 110 | 69.5898 | 146.062 |
| ub | immunity boost grace periods | period in which pre-erythrocytic immunity cannot be boosted | 7.2 | 1.06229 | 25.8764 |
| uc | immunity boost grace periods | period in which clinical immunity cannot be boosted | 6.06 | 1.48711 | 13.58 |
| ud | immunity boost grace periods | period in which immunity to detectability cannot be boosted | 9.44512 | 1.05122 | 26.5402 |
| uv | immunity boost grace periods | period in which severe immunity cannot be boosted | 11.4321 | 0.0409431 | 117.171 |
| rm | immunity decay rates | decay rate for maternal immunity to clinical disease | 67.6952 | 56.0482 | 93.1118 |
| rvm | immunity decay rates | decay rate for maternal immunity to severe disease | 76.8365 | 37.8859 | 139.677 |
| ad | immunity reducing probability of detection | scale parameter relating age to immunity | 7993.5 | 6554.22 | 10094.6 |
| d1 | immunity reducing probability of detection | minimum probability due to immunity | 0.160527 | 0.0540254 | 0.314522 |
| fd0 | immunity reducing probability of detection | time-scale at which immunity changes with age | 0.007055 | 0.00000471 | 0.042121 |
| gammad | immunity reducing probability of detection | shape parameter relating age to immunity | 4.8183 | 3.11894 | 8.16328 |
| id0 | immunity reducing probability of detection | scale parameter | 1.577533 | 0.0567825 | 15.44549 |
| kd | immunity reducing probability of detection | shape parameter | 0.476614 | 0.190643 | 1.26744 |
| cd | infectivity towards mosquitoes | infectivity of clinically diseased humans towards mosquitoes | 0.068 | 0.0262169 | 0.193139 |
| cu | infectivity towards mosquitoes | infectivity of sub-patent infection | 0.0062 | 0.0000708 | 0.029169 |
| gamma1 | infectivity towards mosquitoes | parameter for infectivity of asymptomatic humans | 1.82425 | 0.123118 | 16.5369 |
| pcm | mortality parameters | new-born clinical immunity relative to mother’s | 0.774368 | 0.420769 | 0.998944 |
| pvm | mortality parameters | new-born severe immunity relative to mother’s | 0.195768 | 0.0925639 | 0.855581 |
| ic0 | probability of clinical infection | scale parameter | 18.02366 | 10.63586 | 36.79639 |
| kc | probability of clinical infection | shape parameter | 2.36949 | 1.76969 | 3.21076 |
| phi0 | probability of clinical infection | maximum probability due to no immunity | 0.792 | 0.352825 | 0.986045 |
| phi1 | probability of clinical infection | maximum reduction due to immunity | 0.00074 | 0.00000228 | 0.003369 |
| b0 | probability of pre-erythrocytic infection | maximum probability due to no immunity | 0.59 | 0.349146 | 0.989847 |
| ib0 | probability of pre-erythrocytic infection | scale parameter | 43.9 | 13.25245 | 148.795 |
| kb | probability of pre-erythrocytic infection | shape parameter | 2.16 | 0.908016 | 3.44781 |
| av | probability of severe infection | age dependent modifier | 2493.41 | 924.234 | 5067.72 |
| fv0 | probability of severe infection | age dependent modifier | 0.141195 | 0.0043904 | 0.994957 |
| gammav | probability of severe infection | age dependent modifier | 2.91282 | 0.272665 | 5.95187 |
| iv0 | probability of severe infection | scale parameter | 1.09629 | 0.3073822 | 3.734202 |
| kv | probability of severe infection | shape parameter | 2.00048 | 1.27469 | 3.17738 |
| theta0 | probability of severe infection | maximum probability due to no immunity | 0.074989 | 0.0085529 | 0.204342 |
| theta1 | probability of severe infection | maximum reduction due to immunity | 0.000119 | 0.0000077 | 0.000846 |
OpenMalaria¶
Table layout adapted from supplementary file from Reiker et al 2021
| Parameter | Meaning | Unit/ dimension | Estimate |
|---|---|---|---|
| ‘-ln(1-Sinf)’ | Lower limit of success probability of inoculations | Proportion | 0.050736 |
| Estar | Inoculations/personnight | 0.03247 | |
| Simm | Lower limit of success probability of inoculations in immune individuals | Proportion | 0.092699 |
| Xstar_p | Critical value of cumulative number of entomologic inoculations | Inoculations | 4158.408 |
| gamma_p | Steepness of relationship between success of inoculation | Dimensionless constant | 0.607779 |
| sigma2i | Variation between hosts on parasite densities (variance of log-normal distribution) | 8.731388 | |
| CumulativeYstar | Critical value of cumulative number of parasite days | 3.42E+09 | |
| CumulativeHstar | Critical value of cumulative number of infections | Infections | 79.63425 |
| ‘-ln(1-alpha_m)’ | Maternal protection at birth | Dimensionless | 5.459868 |
| decay_m | Decay of maternal protection | Per year | 5.273989 |
| sigma2_0 | Fixed variance component for densities | 0.963133 | |
| Xstar_v | Critical value of cumulative number of infections for variance in parasite densities | Infections | 0.889578 |
| Ystar2 | Parasites/microliter | 26.2003 | |
| alpha | Factor determining increase in | 147000.4 | |
| Density bias (non Garki) | Density bias (non Garki) | Dimensionless | 0.177379 |
| sigma2 | Mass action parameter | Dimensionless | 0.05 |
| log oddsr CF community | Case fatality for severe episodes in the community compared to hospital | Log odds | 1.86078 |
| Indirect risk cofactor | Co-morbidity intercept relevant to indirect mortality | Proportion | 0.004234 |
| Non-malaria infant mortality | Non-malaria intercept for infant mortality | Deaths / 1000 live births | 61.75034 |
| Density bias (Garki) | Density bias (Garki) | Dimensionless | 4.796108 |
| Severe Malaria Threshhold | Parasitaemia threshold for severe episodes type Y/ | 14753690 | |
| Immunity Penalty | Immune penalty | 1 | |
| Immune effector decay | Immune effector decay | 0 | |
| comorbidity intercept | Prevalence of comorbidity/susceptibility at birth relevant to severe episodes | proportion | 0.006827 |
| Ystar half life | Years | 1.383771 | |
| Ystar1 | 1177.043 | ||
| Asexual immunity decay | 0 | ||
| Ystar0 | 68.86192 | ||
| Idete multiplier | Dimensionless | 2.797524 | |
| critical age for comorbidity | Years | 0.152848 |