plot.epictmcmc {EpiILMCT}

Plot the output of epictmcmc object

Description

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

Usage

## S3 method for class 'epictmcmc'
plot(x, epi = NULL, plottype = NULL, start = NULL, end = NULL, 
thin = NULL, ...)

Arguments

x

an S3 object of class epictmcmc (i.e. the output of the epictmcmc function).

epi

epidemic data of class datagen.

plottype

determines which of three options to plot the output of the epictmcmc function are used: “parameter” produces trace plots for each of the model parameters, and “inf.times” (“rem.times”) produces plots of the average posterior and 95% CI of the unobserved infection (removal) times when datatype set to “known removal” (“unknown removal”).

start, end, thin

options for creating mcmc object.

...

additional arguments that are passed to the generic plot function.

Value

The argument plottype is used to specify the kind of plot produced. Trace and density plots of the posterior distribution of the model parameters can be obtained by setting plottype = “parameter”. Additionally, in the case of unobserved infection (removal) times, a plot of the average posterior and 95% percentile intervals of the inferred infection (removal) times are produced by setting plottype = “inf.times” (“rem.times”).

See Also

epictmcmc, print.epictmcmc, summary.epictmcmc, mcmc, plot.mcmc.