Artifacts using Phylobase (11)

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An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Last Release on May 1, 2022
BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss ...
Last Release on Apr 30, 2022
Analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. This package can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of heritability from its parents. Parameters are estimated by maximum likelihood. Users need to enter a comparative data set, a phylogeny, and information on gene flow leading to hybrids. See Jhwueng and O'Meara (2017) <DOI:10.1101/023986>.
Last Release on May 12, 2022
The BMhyd package analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. This package can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of heritability from its parents. Parameters are estimated by maximum likelihood. Users need to enter a comparative data set, a phylogeny, and information on gene flow leading to hybrids.
Last Release on May 1, 2022
Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Last Release on Apr 30, 2022
This package enhancements to phylobase classes. It provides classes and methods which help uses manipulate branch-annotated trees and provides supports for a few other extra features.
Last Release on May 1, 2022
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
Last Release on May 12, 2022
Create and customize interactive phylogenetic trees using the 'phylocanvas' JavaScript library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps, and in R Markdown documents. See <http://phylocanvas.org/> for more information on the 'phylocanvas' library.
Last Release on May 1, 2022
Tools for calculating and viewing topological properties of phylogenetic trees.
Last Release on May 29, 2022
This wraps the 'Phylotastic' services APIs <https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.
Last Release on Apr 30, 2022