trajectory,SimInf_pfilter-method {SimInf}

Extract filtered trajectory from running a particle filter

Description

Extract filtered trajectory from running a particle filter

Usage

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

Arguments

model

the SimInf_pfilter object to extract the result from.

compartments

specify the names of the compartments to extract data from. The compartments can be specified as a character vector e.g. compartments = c('S', 'I', 'R'), or as a formula e.g. compartments = ~S+I+R (see ‘Examples’). Default (compartments=NULL) is to extract the number of individuals in each compartment i.e. the data from all discrete state compartments in the model. In models that also have continuous state variables e.g. the SISe model, they are also included.

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 node and time-step with the number of individuals in each compartment. Using format = "matrix" returns the result as a matrix, which is the internal format (see ‘Details’ in trajectory,SimInf_model-method).

Value

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