R/salamanders.R

In rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

#' MrBayes output from analysis of Williams et al. data
#' 
#' This is the output from a MrBayes run of 25,000,000 generations using the analysis settings from the original .nex files.  
#' Sampling is one tree per 100,000 generations.  Data is from alignments of three separate sequences, two chains per alignment, each with its associated log file.
#'
#' @references Study reference: Williams JS, Niedzwiecki JH, Weisrock DW (2013) Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Molecular Phylogenetics and Evolution 68(3): 671-682. http://dx.doi.org/10.1016/j.ympev.2013.04.013
#' 
#' Dryad reference: Williams JS, Niedzwiecki JH, Weisrock DW (2013) Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2gq14
#' 
#' http://datadryad.org/resource/doi:10.5061/dryad.2gq14
#' 
#' @docType data
#' @keywords datasets
#' @name salamanders
#' @usage data(salamanders)
#' @format A data frame with six chains (two each from three separate alignments) of 251 phylogenetic trees and associated likelihood and parameter values.

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