Getting Started
Open Rstudio and load EpiModel:
library(EpiModel)
Launch the Shiny app for EpiModel’s Individual Contact Model
class:
epiweb("icm")
Stochastic SI Model
- Replicate the Poker Chip SI model
- Set number susceptible to 9 and number infected 1
- Set time steps to 50 and simulations to 1
- Set transmission probability to 1 and act rate to 0.2
- Under the plot window, uncheck mean line and move quantile slider to
0
- Press “Run Model” button, and again…, and again…
- What changes? What stays the same? What parameters changed each time
you hit “Run Model”?
- Run lots of simulations
- Set number of simulations to 25
- Check the mean line box
- Click “Run Model”
- What are different ways that we could summarize this set of
simulations?
- Eyeball when the S and I lines cross. Enter that time step under the
Summary tab. For the disease incidence, what’s the ratio of the standard
deviation of the incidence to the mean incidence? What does that tell
you about the uncertainty in the outcomes?
Modeling the Epidemic on Larger Population
- Set number susceptible to 90 and number infected to 10
- Run 25 simulations again
- Gradually turn up the quantile band. What does this show at
50%?
- Eyeball when the S and I lines cross. Enter that time step under the
Summary tab. For the disease incidence, what’s the ratio of the standard
deviation of the incidence to the mean incidence now? What does that
tell you about the impact of population size on variability in the
outcomes?
Last updated: 2022-07-07 with EpiModel v2.3.0