SimInf (version 11.1.0)

nodes: Example data with spatial distribution of nodes

Description

Example data containing spatial coordinates for 1600 nodes, used to initialize spatially distributed population models and visualize simulation results.

Usage

data(nodes)

Format

A data.frame with 1600 rows and 2 columns:

x

Numeric vector of x-coordinates.

y

Numeric vector of y-coordinates.

Examples

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

## 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.
## For reproducibility, specify the seed.
result <- run(model, seed = 22)

## 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, format = "matrix")) > 0

## Display infected nodes in 'blue' and non-infected nodes in 'yellow'.
data("nodes", package = "SimInf")
plot(
    y ~ x,
    nodes,
    col = ifelse(infected, "blue", "yellow"),
    pch = 20,
    asp = 1
)