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RRphylo

The goal of RRphylo is to compute phenotypic evolutionary rates, estimate ancestral states, locate rate shifts on the tree, and compare vectors of phenotypes and evolutionary rates among species. RRphylo is not based on any evolutionary model, and is best suited to work with phylogenies of fossil species.

Installation from CRAN

You can install the released version of RRphylo from CRAN with:

install.packages("RRphylo")

Installation from github

You can install RRphylo from github by using the R package devtools:

install.packages("devtools")

devtools::install_github("pasraia/RRphylo",build_vignettes = TRUE,dependencies=TRUE)

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Version

Install

install.packages('RRphylo')

Monthly Downloads

452

Version

2.5.0

License

GPL-2

Maintainer

Pasquale Raia

Last Published

December 3rd, 2020

Functions in RRphylo (2.5.0)

StableTraitsR

Run StableTraits from within R
PGLS_fossil

Phylogenetic Generalized Least Square with fossil phylogenies
DataUng

Example dataset
RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies
RRphylo

Evolutionary rates computation along phylogenies
DataOrnithodirans

Example dataset
DataSimians

Example dataset
DataFelids

Example dataset
DataCetaceans

Example dataset
DataApes

Example dataset
makeFossil

Make fossil species on a phylogeny
makeL

Matrix of branch lengths along root-to-tip paths
getSis

Get sister clade
getMommy

Upward tip or node to root path
evo.dir

Phylogenetic vector analysis of phenotypic change
fix.poly

Resolving polytomies to non-zero length branches
plotRates

Plot RRphylo rates at a specified node
distNodes

Finding distance between nodes and tips
cutPhylo

Cut the phylogeny at a given age or node
phyloclust

Test for phylogenetic clustering
makeL1

Matrix of branch lengths along a root-to-node path
angle.matrix

Ontogenetic shape vectors analysis
conv.map

Mapping morphological convergence on 3D surfaces
overfitRR

Testing RRphylo methods overfit
search.conv

Searching for morphological convergence among species and clades
scaleTree

Phylogenetic tree calibration
random.evolvability.test

Randomization test for phylogenetic structuring in evolvability
setBM

Producing simulated phenotypes with trends
sizedsubtree

Find a node subtending to a clade of desired size
swap.phylo

Test the effect of phylogenetic uncertainty on rate shifts found at a particular node
retrieve.angles

Extracting a user-specified subset of the evo.dir results
search.trend

Searching for evolutionary trends in phenotypes and rates
search.shift

Locating shifts in phenotypic evolutionary rates
tree.merger

Fast addition of tips and clades on an existing tree
swapONE

Create alternative phylogenies from a given tree