Example data to initialize events for the ‘SIS’ model

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

Usage

events_SIS()

Value

A data.frame

Details

Example data to initialize scheduled events (see SimInf_events) for a population of 1600 nodes and demonstrate the SIS 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.

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 'SIS' model with 1600 nodes and initialize
## it to run over 4*365 days. Add one infected individual
## to the first node.
u0 <- u0_SIS()
u0$I[1] <- 1
tspan <- seq(from = 1, to = 4*365, by = 1)
model <- SIS(u0     = u0,
             tspan  = tspan,
             events = events_SIS(),
             beta   = 0.16,
             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)
#> Model: SIS
#> Number of nodes: 1600
#> 
#> Transitions
#> -----------
#>  S -> upsilon*S*I -> I
#>  I -> gamma*I -> S
#> 
#> Global data
#> -----------
#>  - None
#> 
#> Local data
#> ----------
#>  Parameter Value
#>  beta      0.16 
#>  gamma     0.01 
#> 
#> Scheduled events
#> ----------------
#>  Exit: 182535
#>  Enter: 182685
#>  Internal transfer: 0
#>  External transfer: 101472
#> 
#> Network summary
#> ---------------
#>             Min. 1st Qu. Median Mean 3rd Qu. Max.
#>  Indegree:  40.0    57.0   62.0 62.1    68.0 90.0
#>  Outdegree: 36.0    57.0   62.0 62.1    67.0 89.0
#> 
#> Compartments
#> ------------
#>     Min. 1st Qu. Median  Mean 3rd Qu.  Max.
#>  S   0.0     7.0   10.0  44.2    96.0 218.0
#>  I   0.0     0.0   96.0  80.3   125.0 228.0