Function reference • MicroWNV

Bloodmeal

The bloodmeal function computes bites taken by mosquitoes on hosts relevant for pathogen transmission between species over a time step. After it is computed, the various components can be updated independently. This function overrides compute_bloodmeal from Micro-MoB

compute_bloodmeal(): Compute bloodmeals taken by mosquitoes on hosts

Adult mosquito component

Certain S3 methods are overridden to account for specific behavior for West Nile virus.

compute_q(): Compute human blood feeding fraction (\(q\))

compute_q(<RM>): Compute human blood feeding fraction for RM model (\(q\))

Adult bird component

The adult bird component is responsible for updating adult bird populations and their pathogen dynamics. Any model of adult birds in MicroWNV is required to implement the following interface methods.

step_birds(): Update bird population

compute_WB(): Compute available birds (\(W_{B}\))

compute_wfB(): Compute bird biting weights (\(w_{f_{B}}\))

compute_xB(): Compute net infectiousness of birds (\(x_{B}\))

compute_B_pop(): Compute total bird population (\(B_{pop}\))

compute_PsiB(): Compute time at risk matrix (\(\Psi\))

compute_clutch(): Compute number of eggs laid from birds for each patch

SIRS adult bird model

This model implements a simple SIRS model of adult birds with risk distributed accross a “home range”.

setup_birds_SIRS(): Setup birds with SIRS infection model

step_birds(<SIRS>): Update SIRS bird population

step_birds(<SIRS_deterministic>): Update SIRS bird population (deterministic)

step_birds(<SIRS_stochastic>): Update SIRS bird population (stochastic)

compute_WB(<SIRS>): Compute available SIRS bird population (\(W_{B}\))

compute_wfB(<SIRS>): Compute bird biting weights of SIRS birds (\(w_{f_{B}}\))

compute_xB(<SIRS>): Compute net infectiousness of SIRS birds (\(x_{B}\))

compute_B_pop(<SIRS>): Compute total SIRS bird population (\(B_{pop}\))

compute_PsiB(<SIRS>): Compute SIRS bird time at risk matrix (\(\Psi\))

compute_clutch(<SIRS>): Compute SIRS egg clutches

Fledgling (immature) bird component

The fledgling component is responsible for updating fledgling bird populations which live in nests. It must calculate how many eggs clutches are laid by adults per day, add them to nests, update the fledglings, and calculate the number of new adults. Any model of fledglings in MicroWNV is required to implement the following interface methods.

step_fledge(): Update fledgling populations

compute_fledge(): Compute number of new fledglings

Trace (forced) fledgling model

This is a model of fledglings where birth is passed as a trace (forcing) term and it is not affected by endogenous dynamics.

setup_fledge_trace(): Setup fledglings with trace (forced) births

step_fledge(<trace>): Update fledgling populations for forced births

compute_fledge(<trace>): Compute number of new fledglings from trace

compute_fledge(<trace_deterministic>): Compute number of new fledglings from trace (deterministic)

compute_fledge(<trace_stochastic>): Compute number of new fledglings from trace (stochastic)