plot_all_phi_marginals {BEDASSLE}  R Documentation 
Plots the posterior marginal densities of all phi parameters. Users may specify
whether they want a histogram, a density, or both. For convenience, the F_{k}
statistic is presented in place of the phi parameter, as this is the statistic users
care about. F_{k}
is defined as \frac{1}{1+phi_{k}}
.
plot_all_phi_marginals(phi_mat, percent.burnin = 0, thinning = 1,
population.names = NULL, pop.index= NULL, histogram = TRUE, density = TRUE)
phi_mat 
The 
percent.burnin 
The percent of the sampled MCMC generations to be discarded as "burnin." If the
MCMC is run for 1,000,000 generations, and sampled every 1,000 generations, there
will be 1,000 sampled generations. A 
thinning 
The multiple by which the sampled MCMC generations are thinned. A 
population.names 
A vector of length 
pop.index 
A population index number generated to title a marginal plot if no

histogram 
A switch that controls whether or not the plot contains a histogram of the values
estimated for the parameter over the course of the MCMC. Default is 
density 
A switch that controls whether or not the plot shows the density of the values
estimated for the parameter over the course of the MCMC. Default is 
The marginal plot is another basic visual tool for MCMC diagnosis. Users should look for marginal plots that are "smooth as eggs" (indicating that the chain has been run long enough) and unimodal (indicating a single peak in the likelihood surface).
Gideon Bradburd