mcmc

psophia_tree

psophia_shp

psophia_poly

Data used for Quintero et al, (2015) extracted from Ribas et al (2012). It contains the phylogenetic tree and current geographic distributions for the genus Psophia.

datasets

rase_data

The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015). Historical Biogeography Using Species Geographical Ranges. Systematic biology, 64(6), 1059-1073. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.

Ignacio Quintero

rase

Range Ancestral State Estimation for Phylogeography and
        Comparative Analyses

rase_data function

<code>psophia_shp</code> contains the distributions of Psophia species as shapefiles in the format 
 <code><a href="/link/SpatialPolygonsDataFrame?package=rase&version=0.2-21&to=sp" rd-options="sp" data-mini-rdoc="sp::SpatialPolygonsDataFrame">SpatialPolygonsDataFrame</a></code>. 
<code>psophia_poly</code> contains the distributions of Psophia species as a list of polygons in <code><a href="/link/owin.object?package=rase&version=0.2-21&to=spatstat" rd-options="spatstat" data-mini-rdoc="spatstat::owin.object">owin.object</a></code> format used as input for <code><a href="/link/rase?package=rase&version=0.2-21" rd-options="" data-mini-rdoc="rase::rase">rase</a></code>.
<code>psophia_tree</code> contains Psophia's phylogenetic tree in <code><a href="/link/phylo?package=rase&version=0.2-21&to=ape" rd-options="ape" data-mini-rdoc="ape::phylo">phylo</a></code> format. 
<code>mcmc</code> contains the MCMC chain of rase run over the Psophia data after a 2000 burnin period and sampling every 10 iterations.

format

Ribas, C. C., Aleixo, A., Nogueira, A. C. R., Miyaki, C. Y., and Cracraft, J. 2011 A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proc. R. Soc. B.Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057

rase_data: Psophia Data Used for rase Package

Description

Usage

Arguments

format

source