Using the P. vivax model | Model details | Parameters | Structure | New Infections | Immunity | Infectivity of LM-detectable infections | Hypnozoites | Drug treatment | Equilibrium | Key Model References

Estimating variation in parameters

Variation and population size | Parameterisation | Simulations | Stochastic elimination | Estimating variation

Setting bed net parameters | Parameterisation | A note on mosquito species | Simulation | Visualisation | Comparing coverage and population bed net usage | Using the netz package

Issues | Git | Code organisation | Pull Requests | Microbenchmarks | Wishlist

Introduction | Using set_antimalarial_resistance() to parameterise resistance | Simulating static resistance | Parameterisation | Simulation | Visualisation | Simulating dynamic resistance | Simulating antimalarial resistance with multiple resistance outcomes | References

Age group rendering | Set custom demography | Simulation | Visualisation | Set dynamic demography | Parameterisation

Mass Drug Administration | Parameterisation | Interventions | Simulation | Visualisation | Seasonal Malaria Chemoprevention | Simulations

PfPR~2-10~ matching using malariaEquilibrium | PfPR~2-10~ matching using malariasimulation | Establish malariasimulation parameters | Run the simulations and calculate PfPR~2-10~ | Fit line of best fit relating initial EIR values to PfPR~2-10~ | Visualisation | Matching EIR to PfPR~2-10~ values | Calibrating PfPR~2-10~ using the cali package

Run metapopulation simulation | Parameterisation | Simulation | Visualisation

Model structure | Human Biology | States | Parameters | Mosquito Biology | Key Model References (structure and dynamics) | Run simulation | Code | Output | Additional outputs | Output visualisation | Set equilibrium | Override parameters | Seasonality | Individual mosquitoes | Vignettes

Seasonality | Custom modification of the mosquito carrying capacity | Larval source management | Invasive species | Full flexibility

Setting mosquito species parameters | Single endophilic mosquito species | Single exophilic mosquito species | Plot adult female infectious mosquitoes by species over time | Setting multiple mosquito species

Setting drugs and clinical treatment | Parameterisation and simulation | Visualisation

Parameterisation | Mass RTS,S | Simulation | Visualisation | Seasonal mass vaccination | RTS,S EPI | RTS,S EPI with seasonal boosters | RTS,S dosing | TBV

Setting IRS parameters | Parameterisation | A note on mosquito species | Simulation | Visualisation

Introduction | Bitset | Prefabs | C++ Prefabs

Introduction | Usage | Practical example | Caveats | Restoring random number generator state | Saving and restoring events

Introduction | Resizing variables | Birth and death processes | Simulation

Introduction | Variables | Categorical Variable | Integer Variable | Double Variable | Processes | Render | Events | Targeted Events | Simulate

Introduction | Specification | Processes | Events | Rendering | Simulation