get_foi_index: Generates Force-of-Infection indexes for heterogeneous age...

In serofoi: Bayesian Estimation of the Force of Infection from Serological Data

Generates Force-of-Infection indexes for heterogeneous age groups

Description

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")

serofoi documentation built on April 3, 2025, 11:40 p.m.