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

In SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations

Scatterplot of number of individuals in each compartment

Description

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 signature '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

## 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)

SimInf documentation built on Jan. 23, 2023, 5:43 p.m.