An R package with utility functions to work with MCMCtree
You can install the package by typing in an R prompt:
devtools::install_github("dosreislab/mcmc3r")
The packge can be used to plot the L and B calibration densities used by MCMCtree. Note you can use the sn
package (available from CRAN) to plot the Skew-normal and Skew-t calibration densities. For example, suppose you have a minimum bound calibration L(10, .1, 1, .025)
, you can plot this with:
curve(dL(x, 10, .1, 1, .025), n=5e2, from=0, to=100)
and suppose you have the joint calibration B(5, 10, .01, .05)
, this can be plotted with:
curve(dB(x, 5, 10, .01, .05), n=5e2, from=0, to=20)
The package can be used to prepare control files for marginal likelihood calculation with MCMCtree to, for example, select the relaxed-clock model. Marginal likelihood calculation can be carried out by the thermodynamic integration or stepping-stones methods. A tutorial is available here.
The package is also useful for working with quantitative morphological characters. It can:
MCMCtree
.MCMCtree
.If using the package for marginal likelihood calculation please cite:
The block bootstrap used to estimate the error of marginal likelihood estimates is described in:
The continuous morphological models are described in: