R/carnivores.R

In dosreislab/mcmc3r: Tools to work with MCMCtree

#' Carnivores dataset
#' 
#' @description 
#' Dataset of carnivores containing alignments of morphlogical continuous
#' characters, a phylogeny, and an MCMC matrix produced by MCMCtree.
#' 
#' @format \code{carnivores} is a list with elements:
#'
#' \code{C.raw}, a matrix of 29 3D-landmarks measurements from 19 species;
#'
#' \code{V.raw}, a matrix of 29 3D-landmarks for 21 common foxes (Vulpes
#' vulpes);
#'
#' \code{C.proc} and \code{V.proc}, the corresponding matrices after Procrustes
#' alignment;
#'
#' \code{var.foxes} and \code{R.sh}, with estimates of the variance vector and
#' correlation matrix for the landmarks in the 21 foxes;
#'
#' \code{M}, a matrix of transformed landmarks (using the foxes variances
#' and correlation matrix, with Cholesky metric) for the 19 carnivores;
#' 
#' \code{pairedLM}, a matrix describing the symmetry of the landmarks;
#'
#' \code{tree}, the phylogeny of the 19 carnivores; and
#'
#' \code{mcmc}, an MCMC sample of divergence times and morphological and
#' molecular rates from an MCMCtree analysis.
#' 
#' @source 
#' Alvarez-Carretero S, Goswami A, Yang Z and dos Reis M. (2018) Bayesian
#' estimation of species divergence times using correlated quantitative
#' characters. \emph{Syst. Biol.,} 68: 967--986.
"carnivores"