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rase (version 0.2-21)

Range Ancestral State Estimation for Phylogeography and Comparative Analyses

Description

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.

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Version

Install

install.packages('rase')

Monthly Downloads

12

Version

0.2-21

License

GPL (>= 2)

Maintainer

Ignacio Quintero

Last Published

November 9th, 2015

Functions in rase (0.2-21)

add.dens

Plot the Posterior Density for each Ancestor in 3D Space
bm_loglik_tree_constrained

Range Brownian motion tree likelihood
rase

Bayesian Range Ancestral State Estimation of Polygons
poly_center

Calculate the Polygon Center
rase_data

Psophia Data Used for rase Package
bm_loglik_trio

Fast likelihood of a 2-dimensional point with two daughters and one ancestor nodes
shape.to.rase

Transform a Shapefile into owin.object Format
bm_propose_trio

MCMC proposal for a 2-dimensional point with two daughters and one ancestor nodes
name.poly

Name & Order Polygons According to the Phylogeny
phylo.3d

Plots a Phylogenic Tree in 3D
bm_est_sigma2

Estimate Sigma and Sigma Variance
ranges.like.bm

n-dimensional Maximumn Likelihood of Range Brownian Motion
tree.slice

Identify Tree Branches That Intersect With a Given Time Slice.
point.like.bm

n-dimensional Maximum Likelihood of Point Brownian Motion
random_rase3d

Apply rase to Randomly Generated Data
bm_loglik_tree

Point Brownian motion tree likelihood
data.for.3d

Transform Output for 3D Plotting
bm_loglik_duo

Likelihood of a 2-dimensional point with one daughter and one ancestor nodes
add.polygons

Plot the Distributions for the Phylogenetic Tips in 3D
rase-package

Range Ancestral State Estimation
bm_loglik_ancestors_poly

Fast likelihood of ancestors using polygons
bm_ase

Bayesian Ancestral State Estimation with Points
bigauss_pdf

Bivariate Gaussian PDF
bm_loglik_ancestors

Likelihood of ancestors using points
post.mcmc

Post-MCMC Handling
bm_propose_duo

MCMC proposal for a 2-dimensional point with one daughter and one ancestor nodes
rase.slice

Ancestral State Estimation At Any Given Time Slice