plot_mcmc_bite: Plot trace and density from a log file

In bite: Bayesian Integrative Models of Trait Evolution

Description

This function plots the trace and/or density of each mcmc sample.

Usage

plot_mcmc_bite(mcmc.log, type = c("trace", "density"), burnin = 0,
  variable = NA, label = NA, col = "#000000", cex.est = 1,
  bty = "n", kp.burn = FALSE, ...)

Arguments

mcmc.log	Any mcmc sample with the saved iterations in rows and the variables in columns
type	Character taken in c("trace", "density"). If both are specified, they are plotted side by side in the same graphical device
burnin	The size of the burnin in number of iterations or the proportion of iteration you want to remove
variable	The name or number of the variable to plot. If is.na(variable), all columns of mcmc.log will be plotted except "iter" and "temperature"
label	Full variable name to be plotted
col, bty, ...	Other graphical parameters to parse to par
cex.est	The magnification to be used for estimates display
kp.burn	Logical specifying whether the plot window should adjust to the pre-burnin values (only evaluated if "trace" in type)

Author(s)

Theo Gaboriau

Examples

 ## Load test data
 data(Anolis_traits)
 data(Anolis_tree)
 data(Anolis_map)
 
 ## Run a simple MCMC chain
 my.jive <- make_jive(Anolis_tree, Anolis_traits[-3],  model.priors = list(mean="BM", logvar="OU"))
 bite_ex <- tempdir()
 logfile <- sprintf("%s/my.jive_mcmc.log", bite_ex)
 mcmc_bite(my.jive, log.file=logfile, sampling.freq=10, print.freq=10, ngen=1000) 

 ## import the results in R
 res <- read.csv(logfile, header = TRUE, sep = "\t")
 
 ## plot the results
 plot_mcmc_bite(res, burnin = 0.2, variable = NA, cex.est = .7)
 plot_mcmc_bite(res, burnin = 0.2, variable = "prior.mean", cex.est = .7)

bite documentation built on April 22, 2020, 5:09 p.m.