rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses
Version 0.3-2

Implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015) . 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.

Browse man pages Browse package API and functions Browse package files

AuthorIgnacio Quintero [aut, cre], Forrest W. Crawford [aut], Petr Keil [aut]
Date of publication2017-03-22 14:11:51 UTC
MaintainerIgnacio Quintero <ignacio.quintero@yale.edu>
LicenseGPL (>= 2)
Version0.3-2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rase")

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_loglik_ancestors: Likelihood of ancestors using points
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
make_bm_est_sigma2: Estimate Sigma and Sigma Variance
make_bm_loglik_ancestors_poly: Fast likelihood of ancestors using polygons
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
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...

Functions

add.dens Man page Source code
add.polygons Man page Source code
bigauss_pdf Man page Source code
bm_ase Man page Source code
bm_loglik_ancestors Man page Source code
bm_loglik_duo Man page Source code
bm_loglik_tree Man page Source code
bm_loglik_tree_constrained Man page Source code
bm_loglik_trio Man page Source code
bm_propose_duo Man page Source code
bm_propose_trio Man page Source code
data.for.3d Man page Source code
make_bm_est_sigma2 Man page Source code
make_bm_loglik_ancestors_poly Man page Source code
mcmc Man page
name.poly Man page Source code
phylo.3d Man page Source code
point.like.bm Man page Source code
poly_center Man page Source code
psophia_poly Man page
psophia_shp Man page
psophia_tree Man page
ranges.like.bm Man page Source code
rase Man page Source code
rase-package Man page
rase.slice Man page Source code
shape.to.rase Man page Source code
tree.slice Man page Source code

Files

inst
inst/CITATION
NAMESPACE
data
data/rase_data.rda
R
R/rase_source.r
README.md
MD5
DESCRIPTION
man
man/rase.Rd
man/bm_loglik_duo.Rd
man/add.polygons.Rd
man/add.dens.Rd
man/rase_data.Rd
man/phylo.3d.Rd
man/bm_loglik_tree_constrained.Rd
man/bm_propose_duo.Rd
man/name.poly.Rd
man/bm_loglik_ancestors.Rd
man/bm_propose_trio.Rd
man/shape.to.rase.Rd
man/bm_loglik_tree.Rd
man/bm_loglik_trio.Rd
man/ranges.like.bm.Rd
man/data.for.3d.Rd
man/make_bm_est_sigma2.Rd
man/rase-package.Rd
man/rase.slice.Rd
man/bm_ase.Rd
man/poly_center.Rd
man/bigauss_pdf.Rd
man/point.like.bm.Rd
man/make_bm_loglik_ancestors_poly.Rd
man/tree.slice.Rd
rase documentation built on May 19, 2017, 8:48 a.m.