nodes {SimInf} | R Documentation

## Example data with spatial distribution of nodes

### Description

Example data to initialize a population of 1600 nodes and demonstrate various models.

### Usage

    data(nodes)

### Format

A `data.frame`

### Examples

    ## Create an 'SIR' model with 1600 nodes and initialize
    ## it to run over 4*365 days. Add one infected individual
    ## to the first node.
    u0 <- u0_SIR()
    u0$I[1] <- 1
    tspan <- seq(from = 1, to = 4*365, by = 1)
    model <- SIR(u0     = u0,
                 tspan  = tspan,
                 events = events_SIR(),
                 beta   = 0.16,
                 gamma  = 0.077)

    ## Run the model to generate a single stochastic trajectory.
    result <- run(model, threads = 1)

    ## Determine nodes with one or more infected individuals in the
    ## trajectory. Extract the 'I' compartment and check for any
    ## infected individuals in each node.
    infected <- colSums(trajectory(result, ~ I, as.is = TRUE)) > 0

    ## Display infected nodes in 'blue' and non-infected nodes in 'yellow'.
    data("nodes", package = "SimInf")
    col <- ifelse(infected, "blue", "yellow")
    plot(y ~ x, nodes, col = col, pch = 20, cex = 2)

[Package SimInf version 6.3.0 Index]