events_SEIR: Example data to initialize events for the 'SEIR' model

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

Example data to initialize events for the ‘SEIR’ model

Description

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

Usage

events_SEIR()

Details

Example data to initialize scheduled events (see SimInf_events) for a population of 1600 nodes and demonstrate the SEIR model. The dataset contains 466692 events for 1600 nodes distributed over 4 * 365 days. The events are divided into three types: ‘Exit’ events remove individuals from the population (n = 182535), ‘Enter’ events add individuals to the population (n = 182685), and ‘External transfer’ events move individuals between nodes in the population (n = 101472). The vignette contains a detailed description of how scheduled events operate on a model.

Value

A data.frame

Examples

## 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. Add one infected individual
## to the first node.
u0 <- u0_SEIR()
u0$I[1] <- 1
tspan <- seq(from = 1, to = 4*365, by = 1)
model <- SEIR(u0      = u0,
              tspan   = tspan,
              events  = events_SEIR(),
              beta    = 0.16,
              epsilon = 0.25,
              gamma   = 0.01)

## Display the number of individuals affected by each event type
## per day.
plot(events(model))

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

## Summarize the trajectory. The summary includes the number of
## events by event type.
summary(result)

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