epinet (version 0.0-7)

EpiPlot: Plot the spread of an epidemic

Description

Plot the spread of an epidemic over a contact network.

Usage

plotepi(epi)
plotepimcmc(mcmcoutput,num=iterations)

Arguments

epi

a simulated epidemic, in the form of the output produced by SEIR.simulator.

mcmcoutput

output from epibayesmcmc.

num

a number indicating which of the MCMC samples to plot. Defaults to the final sample in the chain.

Value

• returns no value. Strictly invoked for the plotting side effect.

Details

Takes as input either a simulated epidemic, or the output from an MCMC output (which itself infers the epidemic times) and plots them, indicating the path that the infection took during the epidemic (the transmission tree) and the times that each node entered the Exposed, Infectious, and Removed states.

Examples

# Simulate an epidemic through a network of 30
set.seed(1)
examplenet <- buildER(30,0.1)
exampleepidemic <- SEIR.simulator(examplenet,30,0.3,2,5,latencydist="gamma")
# Plot the simulated epidemic
plotepi(exampleepidemic)
# Run MCMC algorithm on this epidemic
examplemcmc <- epibayesmcmc(exampleepidemic,nsamp=100000,
	thinning=1000, bprior=c(0,1), tiprior=c(0,5),teprior=c(0,5),kiprior=c(0,10),
	keprior=c(0,10), N=30, priordists="uniform",extrathinning=10,inferEtimes=TRUE, 
	inferItimes=TRUE)
# Plot starting state of epidemic from chain 
plotepimcmc(examplemcmc,1)
# Plot final state of epidemic from chain 
plotepimcmc(examplemcmc)