make.all.bedassle.plots: Make output plots

In gbradburd/bedassle: Quantifies Effects of Geographic and Ecological Distance on Genetic Differentiation

Make output plots

Description

make.all.bedassle.plots makes figures from the output from a BEDASSLE analysis.

Usage

make.all.bedassle.plots(
  results.files,
  data.block.file,
  prefix,
  chain.cols = NULL
)

Arguments

results.files	A vector of the filenames (in quotes, with the full file path) of the posterior results files output by the different chains of a BEDASSLE run. Can also be a single filename if user wants to visualize only a single run.
data.block.file	The filename (in quotes, with the full file path) of the data.block R object (.Robj) file output by a BEDASSLE run.
prefix	A character vector to be prepended to all figures.
chain.cols	A vector of colors to be used in plotting results from different MCMC chains. There should be one color specified for each chain. If NULL, the plots will use the required set or subset of 12 pre-specified colors. If there are more than 12 chains, users must supply their own colors.

Details

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 geoDist or envDist arguments in 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.

Value

This function has only invisible return values.

gbradburd/bedassle documentation built on May 20, 2022, 1 p.m.