plot_all_acceptance_rates: Plots the acceptance rates of all parameters across MCMC...

In BEDASSLE: Quantifies Effects of Geo/Eco Distance on Genetic Differentiation

Plots the acceptance rates of all parameters across MCMC generations

Description

Creates a series of plots showing the proportion of proposed moves to accepted moves over the duration of the MCMC analysis for each parameter updated via a random-walk sampler.

Usage

plot_all_acceptance_rates(MCMC.output)

Arguments

MCMC.output

The standard MCMC output file generated from a BEDASSLE run.

Details

For optimal mixing, between ~20 samplers should be accepted. If the acceptance rates fall outside that range, this function will automatically highlight that parameter as a potential instance of poor mixing. If the acceptance rates are too low, then for subsequent analyses the user should decrease the scale of the tuning parameter (or "std," as in, e.g., aD_std), and if acceptance rates are too high, the user should increase the scale of the tuning parameter. The scale of the tuning parameter is the standard deviation of the normal distribution from which the small random variable is drawn and added to the current parameter value to propose a move. If the acceptance rate has not plateaued by the end of an analysis, it is an indication that the chain may still be "going somewhere" in parameter space, and subsequent analyses should be performed.

Author(s)

Gideon Bradburd

BEDASSLE documentation built on April 11, 2022, 1:07 a.m.