u0_SEIR: Example data to initialize the 'SEIR' model

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

Example data to initialize the ‘SEIR’ model

Description

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

Usage

u0_SEIR()

Details

A data.frame with the number of individuals in the ‘S’, ‘E’, ‘I’ and ‘R’ compartments in 1600 nodes. Note that the ‘E’, ‘I’ and ‘R’ compartments are zero.

Value

A data.frame

Examples

## Not run: 
## 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 'SEIR' model with 1600 nodes and initialize it to
## run over 4*365 days and record data at weekly time-points.
## Add ten infected individuals to the first node.
u0 <- u0_SEIR()
u0$I[1] <- 10
tspan <- seq(from = 1, to = 4*365, by = 7)
model <- SEIR(u0      = u0,
              tspan   = tspan,
              events  = events_SEIR(),
              beta    = 0.16,
              epsilon = 0.25,
              gamma   = 0.01)

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

## Summarize trajectory
summary(result)

## End(Not run)

stewid/SimInf documentation built on April 26, 2024, 5:14 a.m.