Generates force-of-infection indexes for heterogeneous age groups

Generates a list of integers indexing together the time/age intervals for which FOI values will be estimated in fit_seromodel. The max value in foi_index corresponds to the number of FOI values to be estimated when sampling. The serofoi approach to fitting serological data currently supposes that FOI is piecewise-constant across either groups of years or ages, and this function creates a Data Frame that communicates this grouping to the Stan model

Usage

get_foi_index(serosurvey, group_size, model_type)

Arguments

serosurvey

survey_year

Year in which the survey took place (only needed to plot time models)

age_min

Floor value of the average between age_min and age_max

age_max

The size of the sample

n_sample

Number of samples for each age group

n_seropositive

Number of positive samples for each age group

group_size

Age groups size

model_type

Type of the model. Either "age" or "time"

Value

A Data Frame which describes the grouping of years or ages (dependent on model) into pieces within which the FOI is assumed constant when performing model fitting. A single FOI value will be estimated for ages/years assigned with the same index

Examples

data(chagas2012)
foi_index <- get_foi_index(chagas2012, group_size = 25, model_type = "time")