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from v1.4 host immunity was added to the model. host immunity has been added in a simple SEIR approach to the original model, using a scheme that closely follows [#!laneri:10!#]. In the default immunity scheme, immunity is gained as a result of infectious bites, with an e-folding scale set such that 95% of individuals receiving 100 infectious bites per year (EIRa=100) will be clinically immune [#!filipe:07!#,#!doolan:09!#]. A Newtonian relaxation loss term is applied so that 95% of individuals lose immunity after 3 years. In addition to clinical immunity, the model also accounts for transmission blocking immunity in the same way as [#!klein:08!#,#!laneri:10!#], by reducing the host to vector transmission probability in immune individuals [#!boudin:05!#], (and see review in supplementary tables 5 and 7 in [#!ermert:11a!#]).
| parameter | definition | default | units |
| rhostclear | clearance rate for non-immune adults | 150 | days |
| rpthost2vect | probability of infected transmission from infected host to vector | 0.2 | |
| rptvect2host | probability of infected transmission from infected vector to host | 0.3 | |
| rimmune_gain_eira | Annual EIR required to gain full immunity | 100 | bites pppd |
| rimmune_loss_tau | E-folding timescale for immunity loss | 365 | days |
| rpop_death_rate | dead and replacement rate | 0.02 | fraction per year |
| rpopdensity_min | minimum population density for code to run | 5e.-7 | per km |
| rbitehighrisk | ratio of rate of bites for high risk (E) to low risk (S) categories | 5 |