SimInf (version 11.1.0)

pairs,SimInf_model-method: Scatterplot matrix of number of individuals in each compartment

Description

Produce a matrix of scatterplots showing the relationship between the number of individuals in different model compartments. The ijth panel displays the counts of compartment j plotted against compartment i.

Usage

# S4 method for SimInf_model
pairs(x, compartments = NULL, index = NULL, ...)

Arguments

x

The SimInf_model object containing the trajectory data.

compartments

Specify the names of the compartments to include. Can be a character vector (e.g., c("S", "I", "R")) or a formula (e.g., ~S + I + R). If NULL (default), all compartments in the model are included.

index

Indices of the nodes to include in the plot. If NULL (default), data from all nodes are pooled together. If a vector (e.g., 1:2), only data from those specific nodes are used.

...

Additional graphical arguments passed to pairs().

Details

Data is aggregated across all time points in tspan and the selected nodes (specified by index). This allows for visualizing the correlation structure between compartments throughout the simulation.

Examples

## For reproducibility, specify the number of threads.
set_num_threads(1)

## Create an 'SIR' model with 10 nodes.
model <- SIR(
  u0 = data.frame(
    S = rep(99, 10),
    I = rep(1, 10),
    R = rep(0, 10)
  ),
  tspan = 1:100,
  beta = 0.16,
  gamma = 0.077
)

## Run the model with a fixed seed for reproducibility.
result <- run(model, seed = 22)

## Create a scatterplot matrix for all compartments across all
## nodes.
pairs(result)

## Create a scatterplot matrix for the S and I compartments,
## using only data from nodes 1 and 2.
pairs(result, compartments = c("S", "I"), index = 1:2)