View source: R/plot_phi_trace.R
plot_phi_trace  R Documentation 
This function plots the phi parameter value estimated in each sampled generation of the MCMC against the index of that sampled generation. 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_phi_trace(phi, percent.burnin = 0, thinning = 1, population.names = NULL, pop.index = NULL)
phi 
The vector of phi values estimated for a single population from an MCMC run. 
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 
The name of the population/individual for which the marginal density of the phi
parameter is being plotted. This will be used to title the marginal plot. If

pop.index 
A population index number generated to title a marginal plot if no

A trace plot is a basic visual tool for assessing MCMC mixing. If the chain is mixing well, the trace plot will resemble a "fuzzy caterpillar." If the trace plot has not plateaued, it is an indication that the chain has not converged on the stationary posterior distribution, and must be run longer. If the trace plot of a parameter exhibits high autocorrelation, the user may wish to either increase or decrease the scale of the tuning parameter on that parameter, to decrease or increase acceptance rates, respectively. If the chain appears to be bouncing between areas of "fuzzy caterpillardom," it may be an indication of a multimodal likelihood surface.
Gideon Bradburd
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