plot_all_joint_marginals: Plots the joint marginals for all parameter pairs

Description Usage Arguments Details Author(s)


For each sampled MCMC generation, the values estimated for a pair of parameters are logged and plotted against one another. Points are color coded by when in the analysis they were sampled, so that users can visually assess mixing. A joint marginal plot is generated for all combinations of parameters, excluding the phi parameters estimated in the beta-binomial model.


plot_all_joint_marginals(MCMC.output, percent.burnin = 0, thinning = 1)



The standard MCMC output file generated from a BEDASSLE run.


The percent of the sampled MCMC generations to be discarded as "burn-in." If the MCMC is run for 1,000,000 generations, and sampled every 1,000 generations, there will be 1,000 sampled generations. A percent.burnin of 20 will discard the first 200 sampled parameter values from that sample.


The multiple by which the sampled MCMC generations are thinned. A thinning of 5 will sample every 5th MCMC generation.


Visualizations of the joint marginal distributions allow users to (1) assess how well the MCMC is mixing, and (2) potentially diagnose instances of non-identifiability in the model. Strong linear trends in the joint marginal, or visible "ridges" in the likelihood surface, may be indicative of parameter non-identifiability, in which multiple combinations of values of these two parameters provide equally reasonable fits to the data.


Gideon Bradburd

BEDASSLE documentation built on May 2, 2019, 6:10 a.m.