Setup | Scenarios of contact reduction

Use case | What we have | What we assume | Defining a value for $R_0$ | Getting population estimates | Modelling population susceptibility | Running final_size | A short-cut for homogeneous populations | References

Use case | What we have | What we assume | Getting $R_0$, contact and demography data, and susceptibility | Running final_size over $R_0$ samples | Iterate final_size() | With base R | With | Visualise uncertainty in final size

Use case | What we have | What we assume | Modelling the initial epidemic | Modelling waning immunity and influx of susceptibles | Projected estimates of effective $R$ | References

Use case | What we have | What we assume | Primer on heterogeneous susceptibility | Getting $R_0$ and contact and demography data | Susceptibility variation between age groups | Calculate the effective $R_0$ | Calculate the final epidemic size | Susceptibility variation within and between age groups | Getting data on within-group susceptibility differences | Heterogeneous susceptibility without social contact heterogeneity | References

From SIR to final size with homogeneous mixing | Varying susceptibility | Final size equation with heterogeneous mixing | References

Use case | What we have | What we assume | Primer on susceptibility matrices | Susceptibility matrix | Demography-in-susceptibility matrix | Homogeneous susceptibility | Case 1: Uniform susceptibility | Heterogeneous susceptibility | Case 2: Susceptibility varies between groups | Case 3: Susceptibility varies both between and within groups | Case 4: Susceptibility varies within groups in different proportion | Case 5: Susceptibility varies within three groups | References

Use case | What we have | What we assume | Defining a value for $R_0$ | Heterogeneous social mixing | Getting and preparing contact and demography data | Population susceptibility | Why susceptibility and p_susceptibility are matrices | Running final_size | Visualise final sizes | Final size proportions to counts | References

SIR model definition | Final size in a uniformly mixing population | Final size with heterogeneous mixing | Prepare population data | Susceptibility varies between groups | Susceptibility varies within groups in different proportions | Complete immunity to infection in part of the population