Table of Contents | Preface | Custom Numerical Routines | Step Function | Test Simulation | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Euler Method Solutions | Default ODE Solutions | Analysis | Tips and Tricks

Table of Contents | Preface | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: Tau-leaping Solutions | References

Table of Contents | Preface | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: Chemical Langevin Equation Solutions | References

Table of Contents | Preface | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Stochastic: Tau Leaping Solutions | References

Table of Contents | Preface | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: Decoupled ODE model | Stochastic: Tau Leaping Solutions

Table of Contents | Preface | Time-Inhomogeneous Adult Mortality | Time-dependent Rate Functions | Mathematical Considerations | Programming Time-Dependent Rates in MGDrivE2 | Petri Net Setup | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Simulation: ODE Models | Simulation: CTMC Models | Results | References

Table of Contents | Preface | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: Tau-leaping Solutions

Table of Contents | Preface | Example: Logistic Density Dependence | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: Tau-leaping Solutions | Example: Lotka-Volterra Density Dependence | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: CLE Solutions

Table of Contents | Preface | One Node Simulations | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: Tau-leaping Solutions | Metapopulation Network Simulations | Parameterization | Initialization of the Petri Net | Equilibrium Conditions and Hazard Functions | Simulation of Fully Specified SPN Model | Deterministic: ODE Solutions | Stochastic: CLE Solutions | References

Landscape Setup | Single Population | Two Populations | n Populations | Realistic Location | Inheritance Simulations | Mendelian Inheritance Simulations, Single Population | Deterministic | Deterministic, With Fitness Cost | Stochastic | Mendelian Inheritance Simulations, Two Populations | Deterministic, No Migration | Deterministic, Small Migration | Stochastic, Small Migration | Stochastic, Small Migration and Fitness Cost | Reciprocal Translocation Gene Drive Simulations, One Population | Deterministic, Below Threshold | Deterministic, Above Threshold | Stochastic, "Above" Threshold

Introduction | Brief Description | Previous Work: | Notation and Conventions | Mathematical Framework | Inheritance Cube | Drive-specific Cubes | Population Dynamics | Larval Stages | Adult Stages | Gene Drive Releases and Effects | Migration | Stochasticity | Mosquito Biology | References

MGDrivE, One Run | Mendelian Inheritance, Stochastic, Multiple Populations | Full Code | Load Libraries | Setup Folder Directory | Simulation Parameters | Inheritance Pattern | Releases | Setup and Run | Post Processing | Plotting