u0_SISe: Example data to initialize the 'SISe' model

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

Example data to initialize the ‘SISe’ model

Description

Example data to initialize a population of 1600 nodes and demonstrate the SISe model.

Usage

u0_SISe()

Details

A data.frame with the number of individuals in the ‘S’ and ‘I’ compartments in 1600 nodes. Note that the ‘I’ compartment is zero.

Value

A data.frame

Examples

## Create an 'SISe' model with 1600 nodes and initialize it to
## run over 4*365 days and record data at weekly time-points.

## Load the initial population and add ten infected individuals to
## the first node.
u0 <- u0_SISe()
u0$I[1] <- 10

## Define 'tspan' to run the simulation over 4*365 and record the
## state of the system at weekly time-points.
tspan <- seq(from = 1, to = 4*365, by = 7)

## Load scheduled events for the population of nodes with births,
## deaths and between-node movements of individuals.
events <- events_SISe()

## Create an 'SISe' model
model <- SISe(u0 = u0, tspan = tspan, events = events_SISe(),
              phi = 0, upsilon = 1.8e-2, gamma = 0.1, alpha = 1,
              beta_t1 = 1.0e-1, beta_t2 = 1.0e-1, beta_t3 = 1.25e-1,
              beta_t4 = 1.25e-1, end_t1 = 91, end_t2 = 182,
              end_t3 = 273, end_t4 = 365, epsilon = 0)

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

## Summarize trajectory
summary(result)

## Plot the proportion of nodes with at least one infected
## individual.
plot(result, I~S+I, level = 2, type = "l")

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