Scatterplot of number of individuals in each compartment

A matrix of scatterplots with the number of individuals in each compartment is produced. The ijth scatterplot contains x[,i] plotted against x[,j].

Usage

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

Arguments

x

The model to plot

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) includes all compartments.

index

indices specifying the nodes to include when plotting data. Default index = NULL include all nodes in the model.

...

Additional arguments affecting the plot produced.

Examples

## For reproducibility, call the set.seed() function and specify
## the number of threads to use. To use all available threads,
## remove the set_num_threads() call.
set.seed(123)
set_num_threads(1)

## Create an 'SIR' model with 10 nodes and initialise
## it with 99 susceptible individuals and one infected
## individual. Let the model run over 100 days.
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 and save the result.
result <- run(model)

## Create a scatter plot that includes all compartments in all
## nodes.
pairs(result)


## Create a scatter plot that includes the S and I compartments in
## nodes 1 and 2.
pairs(result, ~S+I, 1:2)