vaccination_scenario: Calculate number of influenza cases given a vaccination...

In MJomaba/flu-evidence-synthesis: Flu Evidence Synthesis: Analysing Effectiveness of Vaccine Strategies

Calculate number of influenza cases given a vaccination strategy

Description

Calculate number of influenza cases given a vaccination strategy

Usage

vaccination_scenario(vaccine_calendar, parameters, contact_ids,
  incidence_function, time_column, parameter_map, ..., verbose = T)

Arguments

vaccine_calendar	A vaccine calendar valid for that year
parameters	The parameters to use. Both a vector or a data frame with each row a set of parameters (e.g. a batch of inferred parameters by adaptive_mcmc$batch) are accepted.
contact_ids	Optional: The contact_ids used to infer the contact matrix. Similar to the parameters this can be a vector or a data frame.
incidence_function	An optional function that takes a vaccine_calendar, parameters and optionally contact_ids and returns the incidence over time. If none is provided then the default infectionODEs is used. In that case both polymod_data and demography data need to be provided as well.
time_column	An optional time column that will be removed from the data returned by the incidence_function
parameter_map	Optional: mapping for the parameters (by description and age group) to the relevant index in the parameter vector. Needed parameters are: transmissibility, psi (infection from outside sources), susceptibility (with a value per age group) and log of initial_infected population parameter_mapping.
...	Further parameters that will be passed to the incidence_function
verbose	Whether to display warnings. Default is TRUE.

Value

The total incidence in a year per age and risk group

See Also

infectionODEs

MJomaba/flu-evidence-synthesis documentation built on April 26, 2022, 11:12 p.m.