Model parameters¶

This page provides a high-level summary of the simulation parameters types, format and definition used across the three models.

❗ Please refer to each model's source documentation. The information provided here is indicative only and may not reflect the latest updates of each model.

EMOD includes a large and detailed set of parameters that control vector biology, host immunity, climate effects, and simulation configuration. These parameters are mostly configured via JSON or campaign scripts.
malariasimulation parameters are implemented in R and used to define host immunity, infection progression, and clinical outcomes. Emphasis is placed on age-structured immunity and probabilistic outcomes.
OpenMalaria parameters are implemented in XML.

EMOD¶

Example parameter names obtained from config.json.

Category	Description	Example Parameters
Climate & Environmental	Governs temperature, rainfall, humidity, and seasonality effects	`Air_Temperature_Offset` `Base_Rainfall` `Climate_Model`
Vector Biology	Controls larval habitat, vector aging, migration, and mortality	`Enable_Vector_Aging` `Vector_Sampling_Type` `Egg_Hatch_Density_Dependence`
Host Immunity	Models maternal antibodies, immunity acquisition, and decay	`Enable_Maternal_Protection` `Antibody_Memory_Level` `Antibody_CSP_Decay_Days`
Infection Dynamics	Defines parameters for parasitemia, detectability, and transmission	`Fever_Severe_Threshold` `Antigen_Switch_Rate` `Simulated EIR`
Mortality & Health Outcomes	Parameters influencing severe disease and mortality	`Fever_Mortality_Threshold` `Anemia_Mortality_Threshold`
Simulation Configuration	Core runtime and structural settings	`Simulation_Timestep` `Start_Time` `Serialized_Population_Writing_Type`
Reporting	Enables or disables built-in reporters and custom reports	`Enable_Default_Reporting` `Custom_Reports_Filename`
Demographics & Population	Includes aging, birth/death processes, and risk profiles	`Enable_Birth` `Demographics_Filenames` `x_Base_Population`

malariasimulation¶

Example parameter names obtained from get_parameters function to view defined parameters in the model.
Note list not exhaustive, and indicative only.

Category	Description	Example Parameters
Fixed State Transitions	Time lags between disease states	`du`
Immunity Boost Grace Periods	Time windows where immunity cannot be boosted again	`ub` `uc` `ud` `uv`
Immunity Decay Rates	Decay of maternal or acquired immunity	`rm` `rvm`
Detection Probability Modifiers	How age and immunity influence detectability of infection	`ad` `d1` `gammad`
Infectivity Towards Mosquitoes	Transmission potential depending on disease status	`cd` `cu` `gamma1`
Probability of Clinical/Severe Disease	Likelihood of clinical/severe cases given immunity and age	`ic0` `phi0` `theta0`
Pre-erythrocytic Infection Probabilities	Probability of initial infection post bite	`b0` `ib0` `kb`
Mortality Parameters	Influence of immunity on disease-related mortality	`pcm` `pvm`

OpenMalaria¶

Example parameter names and definitions obtained from OpenMalaria’s XML base file.
Note table not exhaustive, and indicative only, a full table has been published in Reiker et al 2021.

Category	Description	Example Parameters
Infection Success & Inoculation	Defines probabilities of successful infection based on exposure	`'-ln(1-Sinf)'` `Estar` `Xstar_p`
Host Variability & Immunity Dynamics	Describes host heterogeneity and maternal/immune decay	`sigma2i` `decay_m` `alpha`
Cumulative Exposure Thresholds	Thresholds for developing immunity or changing infection risk	`CumulativeYstar` `CumulativeHstar`
Density Bias & Detection	Adjusts parasitemia thresholds and density measurements	`Density bias` `Ystar1` `Idete multiplier`
Mortality Risk Factors	Factors influencing case fatality and indirect mortality from comorbidities	`log oddsr CF community` `Indirect risk cofactor` `comorbidity intercept`
Parasite Density & Immune Response	Models the parasite dynamics and immune clearance rates	`Ystar half life` `Immune effector decay` `Asexual immunity decay`