plot.epimcmc: Plot the output of 'epimcmc' object

In EpiILM: Spatial and Network Based Individual Level Models for Epidemics

Description

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

Usage

## 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.

Value

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)

EpiILM documentation built on Jan. 13, 2021, 1:07 p.m.