rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses

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.

Author
Ignacio Quintero [aut, cre], Forrest W. Crawford [aut], Petr Keil [aut]
Date of publication
2016-01-13 22:41:22
Maintainer
Ignacio Quintero <ignacio.quintero@yale.edu>
License
GPL (>= 2)
Version
0.2-22

View on CRAN

Man pages

add.dens
Plot the Posterior Density for each Ancestor in 3D Space
add.polygons
Plot the Distributions for the Phylogenetic Tips in 3D
bigauss_pdf
Bivariate Gaussian PDF
bm_ase
Bayesian Ancestral State Estimation with Points
bm_est_sigma2
Estimate Sigma and Sigma Variance
bm_loglik_ancestors
Likelihood of ancestors using points
bm_loglik_ancestors_poly
Fast likelihood of ancestors using polygons
bm_loglik_duo
Likelihood of a 2-dimensional point with one daughter and one...
bm_loglik_tree
Point Brownian motion tree likelihood
bm_loglik_tree_constrained
Range Brownian motion tree likelihood
bm_loglik_trio
Fast likelihood of a 2-dimensional point with two daughters...
bm_propose_duo
MCMC proposal for a 2-dimensional point with one daughter and...
bm_propose_trio
MCMC proposal for a 2-dimensional point with two daughters...
data.for.3d
Transform Output for 3D Plotting
name.poly
Name & Order Polygons According to the Phylogeny
phylo.3d
Plots a Phylogenic Tree in 3D
point.like.bm
n-dimensional Maximum Likelihood of Point Brownian Motion
poly_center
Calculate the Polygon Center
post.mcmc
Post-MCMC Handling
ranges.like.bm
n-dimensional Maximumn Likelihood of Range Brownian Motion
rase
Bayesian Range Ancestral State Estimation of Polygons
rase_data
Psophia Data Used for rase Package
rase-package
Range Ancestral State Estimation
rase.slice
Ancestral State Estimation At Any Given Time Slice
shape.to.rase
Transform a Shapefile into 'owin.object' Format
tree.slice
Identify Tree Branches That Intersect With a Given Time...

Files in this package

rase
rase/inst
rase/inst/CITATION
rase/NAMESPACE
rase/data
rase/data/rase_data.rda
rase/R
rase/R/rase_source.r
rase/README.md
rase/MD5
rase/DESCRIPTION
rase/man
rase/man/rase.Rd
rase/man/bm_loglik_duo.Rd
rase/man/bm_est_sigma2.Rd
rase/man/add.polygons.Rd
rase/man/add.dens.Rd
rase/man/rase_data.Rd
rase/man/phylo.3d.Rd
rase/man/bm_loglik_tree_constrained.Rd
rase/man/bm_propose_duo.Rd
rase/man/name.poly.Rd
rase/man/bm_loglik_ancestors.Rd
rase/man/bm_propose_trio.Rd
rase/man/shape.to.rase.Rd
rase/man/bm_loglik_tree.Rd
rase/man/bm_loglik_trio.Rd
rase/man/ranges.like.bm.Rd
rase/man/data.for.3d.Rd
rase/man/rase-package.Rd
rase/man/rase.slice.Rd
rase/man/bm_ase.Rd
rase/man/poly_center.Rd
rase/man/bigauss_pdf.Rd
rase/man/bm_loglik_ancestors_poly.Rd
rase/man/point.like.bm.Rd
rase/man/post.mcmc.Rd
rase/man/tree.slice.Rd