Box plot of number of individuals in each compartment

Produce box-and-whisker plots summarizing the distribution of the number of individuals in specified model compartments. The plots aggregate data across all time points in tspan and the selected nodes (specified by index).

Usage

# S4 method for class 'SimInf_model'
boxplot(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 boxplot().

Details

This function is useful for visualizing the variability and range of compartment counts across the entire simulation trajectory.

Examples

## For reproducibility, set the seed and number of threads.
set.seed(123)
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.
result <- run(model)

## Create a boxplot for all compartments across all nodes and time
## points.
boxplot(result)


## Create a boxplot for the S and I compartments, but only for
## nodes 1 and 2.
boxplot(result, compartments = c("S", "I"), index = 1:2)