plot_chains: Plot MCMC chains
In sppmix: Modeling Spatial Poisson and Related Point Processes

Description Usage Arguments Author(s) See Also Examples

Plot the MCMC chains for all component means and probabilities, generated by est_mix_damcmc or est_mix_bdmcmc.

For examples see

http://faculty.missouri.edu/~micheasa/sppmix/sppmix_all_examples.html#plot_chains

1 2	plot_chains(fit, burnin = floor(fit$L/10), chain = c("p", "x", "y"), ncol = fit$m%%3 + 1, separate = TRUE, open_new_window = FALSE)

`fit`	Object of class `damcmc_res` or `bdmcmc_res`.
`burnin`	Number of initial realizations to discard. By default, it is 1/10 of the total number of iterations.
`chain`	Character vector choosing from c("p", "x", "y"). Multiple choices are supported. This will plot the MCMC chain for the requested variables.
`ncol`	Number of columns in each plot.
`separate`	Logical flag to request the the chains should be shown in separate plots or shown in one plot with different colors per component. The latter (`separate=FALSE`) is useful for spotting label switching visually.
`open_new_window`	Open a new window for the plot.

Jiaxun Chen, Sakis Micheas

PlotUSAStates, normmix, rsppmix, est_mix_damcmc, FixLS_da

fit <- est_mix_damcmc(pp = spatstat::redwood, m = 10)
plot(fit)
plot_chains(fit)
#plot the chains in the same plot with different colors
plot_chains(fit, separate = FALSE)
# Only plot the realizations for the component means
plot_chains(fit, chain = c("x", "y"))
#check labels
check_labels(fit)
#fix labels and plot the chains again
post_fixed = FixLS_da(fit, plot_result = TRUE)
plot_chains(post_fixed)
plot_chains(post_fixed, separate = FALSE)
#We work with the California Earthquake data. We fit an IPPP with intensity surface
#modeled by a mixture with 8 normal components.
CAfit=est_mix_damcmc(CAQuakes2014.RichterOver3.0, m=5, L = 20000)
#Now retrieve the surface of Maximum a Posteriori (MAP) estimates of the mixture parameter.
#Note that the resulting surface is not affected by label switching.
MAPsurf=GetMAPEst(CAfit)
#Plot the states and the earthquake locations along with the fitted MAP IPPP intensity surface
ret=PlotUSAStates(states=c('California','Nevada','Arizona'), showcentroids=FALSE,
 shownames=TRUE, main= "Earthquakes in CA, 2014", pp=CAQuakes2014.RichterOver3.0, surf=MAPsurf,
 boundarycolor="white", namescolor="white")
CAfit=est_mix_damcmc(pp = CAQuakes2014.RichterOver3.0, m = 5)
plot(CAfit)
check_labels(CAfit)
plot_chains(CAfit, separate = FALSE)
#fix labels and plot the chains again
post_fixedCA = FixLS_da(CAfit, plot_result = TRUE)
plot_chains(post_fixedCA, separate = FALSE)