plot.epimcmc function

Plot the output of epimcmc object

plot.epimcmc is an S3 method that plots the output of an S3 object of class epimcmc.

## S3 method for class 'epimcmc'
plot(x, partype, start = 1, end = NULL, thin = 1, ...)

Arguments

• x: An S3 object of class epimcmc (i.e. the output of the epimcmc function).
• partype: Determines which of two options to plot the output of the epimcmc function are used: parameter'' produces trace plots for each of the model parameters, and loglik'' produces trace plot of the log-likelihood of the MCMC samples.
• start, end, thin: options for creating mcmc object.
• ...: additional arguments that are passed to the generic plot function.

Returns

plot.

See Also

epimcmc, summary.epimcmc, mcmc, plot.mcmc.

Examples

## Example :  spatial SI model
# generate 100 individuals

set.seed(59991)

x <- runif(100, 0, 10)

y <- runif(100, 0, 10)

covariate <- runif(100, 0, 2)

out1 <- epidata(type = "SI", n = 100, Sformula = ~covariate, tmax = 15,
               sus.par = c(0.1, 0.3), beta = 5.0, x = x, y = y)

alphapar1 <- matrix(c(1, 1, 1, 1), ncol = 2, nrow = 2)

betapar1 <- c(10, 2)

epi <- epimcmc(object = out1, tmin = 1, tmax = 15,
               niter = 1000, sus.par.ini = c(0.1, 0.1), beta.ini = 5,
               Sformula = ~covariate, pro.sus.var = c(0.2, 0.3), pro.beta.var = 0.8,
               prior.sus.dist = c("gamma", "gamma"), prior.beta.dist = "gamma",
               prior.sus.par = alphapar1, prior.beta.par = betapar1,
               adapt = TRUE, acc.rate = 0.5)

# plot estimates
plot(epi, partype = "parameter", start = 100)