prevalence: Generic function to calculate prevalence from trajectory data
In SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations

prevalence

R Documentation

Generic function to calculate prevalence from trajectory data

Description

Calculate the proportion of individuals with disease in the population, or the proportion of nodes with at least one diseased individual, or the proportion of individuals with disease in each node.

Usage

prevalence(model, formula, level = 1, index = NULL, ...)

Arguments

`model`	The `model` with trajectory data to calculate the prevalence from.
`formula`	A formula that specifies the compartments that define the cases with a disease or that have a specific characteristic (numerator), and the compartments that define the entire population of interest (denominator). The left-hand-side of the formula defines the cases, and the right-hand-side defines the population, for example, `I~S+I+R` in a ‘SIR’ model (see ‘Examples’). The `.` (dot) is expanded to all compartments, for example, `I~.` is expanded to `I~S+I+R` in a ‘SIR’ model (see ‘Examples’). The formula can also contain a condition (indicated by `\|`) for each node and time step to further control the population to include in the calculation, for example, `I ~ . \| R == 0` to calculate the prevalence when the recovered is zero in a ‘SIR’ model. The condition must evaluate to `TRUE` or `FALSE` in each node and time step. Note that if the denominator is zero, the prevalence is `NaN`.
`level`	The level at which the prevalence is calculated at each time point in `tspan`. 1 (population prevalence): calculates the proportion of the individuals (cases) in the population. 2 (node prevalence): calculates the proportion of nodes with at least one case. 3 (within-node prevalence): calculates the proportion of cases within each node. Default is `1`.
`index`	indices specifying the subset of nodes to include when extracting data. Default (`index = NULL`) is to extract data from all nodes.
`...`	Additional arguments, see `prevalence,SimInf_model-method`