prevalence,SimInf_pfilter-method {SimInf}

Extract prevalence from running a particle filter

Description

Extract prevalence from running a particle filter

Usage

## S4 method for signature 'SimInf_pfilter'
prevalence(model, formula, level, index, format = c("data.frame", "matrix"))

Arguments

model

the SimInf_pfilter object to extract 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.

format

The default (format = "data.frame") is to generate a data.frame with one row per time-step with the prevalence. Using format = "matrix" returns the result as a matrix.

Value

A data.frame if format = "data.frame", else a matrix.