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README

This is the repository for the rase package for R.

Current version is rase 0.2-22

It is also now one CRAN (stable version): https://cran.r-project.org/web/packages/rase/index.html

To set up###

From CRAN

install.packages('rase')

From bitbucket

In R, having installed the devtools package, type:

library(devtools)

install_bitbucket("ignacioq/rase")

Who to talk to?

Ignacio Quintero ignacio.quintero@yale.edu, Forrest Crawford forrest.crawford@yale.edu,

Reference

Quintero I, Keil P, Jetz W and Crawford F (2015). “Historical Biogeography Using Species Geographical Ranges.” Systematic Biology, 64(6), pp. 1059-1073. <URL: http://doi.org/10.1093/sysbio/syv057>.

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Version

Install

install.packages('rase')

Monthly Downloads

40

Version

0.2-22

License

GPL (>= 2)

Maintainer

Ignacio Quintero

Last Published

January 13th, 2016

Functions in rase (0.2-22)

rase-package

Range Ancestral State Estimation
bm_propose_duo

MCMC proposal for a 2-dimensional point with one daughter and one ancestor nodes
phylo.3d

Plots a Phylogenic Tree in 3D
ranges.like.bm

n-dimensional Maximumn Likelihood of Range Brownian Motion
bm_est_sigma2

Estimate Sigma and Sigma Variance
bm_propose_trio

MCMC proposal for a 2-dimensional point with two daughters and one ancestor nodes
rase

Bayesian Range Ancestral State Estimation of Polygons
tree.slice

Identify Tree Branches That Intersect With a Given Time Slice.
add.polygons

Plot the Distributions for the Phylogenetic Tips in 3D
shape.to.rase

bm_loglik_trio

Fast likelihood of a 2-dimensional point with two daughters and one ancestor nodes
rase_data

Psophia Data Used for rase Package
name.poly

Name & Order Polygons According to the Phylogeny
bm_loglik_ancestors_poly

Fast likelihood of ancestors using polygons
data.for.3d

Transform Output for 3D Plotting
bm_loglik_tree_constrained

Range Brownian motion tree likelihood
bm_loglik_duo

Likelihood of a 2-dimensional point with one daughter and one ancestor nodes
bigauss_pdf

Bivariate Gaussian PDF
bm_loglik_tree

Point Brownian motion tree likelihood
rase.slice

Ancestral State Estimation At Any Given Time Slice
post.mcmc

Post-MCMC Handling
add.dens

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

Bayesian Ancestral State Estimation with Points
bm_loglik_ancestors

Likelihood of ancestors using points
poly_center

Calculate the Polygon Center
point.like.bm

n-dimensional Maximum Likelihood of Point Brownian Motion