fbseqDebug
is a companion package for debugging the fbseq
and fbseqCUDA
packages, available on GitHub. You will need both of these packages installed, and fbseqCUDA
requires CUDA. See the fbseqCUDA
package vignette for more details.
The full_conditionals
function uses both real maize data and simulated data to check each MCMC parameter against its true full conditional distribution and output relevant plots. For the histograms, MCMC samples are plotted with the true full conditional density overlayed as a line. Traceplots are also output.
The fbseq
package estimates credible intervals using posterior means and posterior variances of parameters. This approach saves hundreds of megabytes of memory relative to calculations involving quantiles of Monte Carlo samples. However, the required distributional assumptions only approximately hold, so these credible intervals are only approximately correct. To that end, the credible_debug
function checks the memory-efficient credible intervals with conventional quantile-intensive ones to make sure the two match well enough. Multiple plots are produced for that purpose.
The paschold_mcmc
and simulated_mcmc
functions run fbseq
on real and simulated data, respectively, and produce output to assess how well the program is working.
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