rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses

Implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015) <DOI:10.1093/sysbio/syv057>. 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.

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.