make.all.bedassle.plots makes figures from the output from a
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The filename (in quotes, with the full file
path) of the data.block R object (.Robj) file output by a
A character vector to be prepended to all figures.
This function takes the file output from a BEDASSLE analysis and generates a number of plots for visualizing results and diagnosing MCMC performance.
This function produces a variety of plots that can be useful for visualizing results or diagnosing MCMC performance. The plots made are by no means exhaustive, and users are encouraged to make further plots, or customize these plots as they see fit. The plots generated (as .pdf files) are:
model.fit.CIs - A plot of the sample allelic covariance
shown with the 95% credible interval of the parametric
covariance for each entry in the matrix. Only generated
if either the
run.bedassle function call are specified. One
plot is produced for each chain.
Trace plots - Plots of parameter values over the MCMC.
lpd - A plot of the log posterior probability over the MCMC.
nuggets - A plot of estimates of the nugget parameters over the MCMC.
alpha parameters - Plots of estimates of the various parameters (all or some of alpha0,alphaD,alphaE,alpha2, depending on the model specified) over the MCMC.
This function has only invisible return values.
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