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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

818

Version

2.5.9

License

GPL-2

Maintainer

Pasquale Raia

Last Published

November 4th, 2021

Functions in RRphylo (2.5.9)

evo.dir

Phylogenetic vector analysis of phenotypic change
distNodes

Finding distance between nodes and tips
cutPhylo

Cut the phylogeny at a given age or node
angle.matrix

Ontogenetic shape vectors analysis
conv.map

Mapping morphological convergence on 3D surfaces
getSis

Get sister clade
node.paths

Tracing nodes along paths
makeL1

Matrix of branch lengths along a root-to-node path
getMommy

Upward tip or node to root path
makeL

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

Phylogenetic tree calibration
makeFossil

Make fossil species on a phylogeny
plotRates

Plot RRphylo rates at a specified node
random.evolvability.test

Randomization test for phylogenetic structuring in evolvability
fix.poly

Resolving polytomies to non-zero length branches
phyloclust

Test for phylogenetic clustering
StableTraitsR

Run StableTraits from within R
overfitRR

Testing RRphylo methods overfit
search.trend

Searching for evolutionary trends in phenotypes and rates
swap.phylo

Test the effect of phylogenetic uncertainty on rate shifts found at a particular node
sizedsubtree

Find a node subtending to a clade of desired size
search.conv

Searching for morphological convergence among species and clades
search.shift

Locating shifts in phenotypic evolutionary rates
rescaleRR

Rescaling phylogenetic trees according to RRphylo rates
rate.map

Mapping rate and direction of phenotypic change on 3D surfaces.
swapONE

Create alternative phylogenies from a given tree
tree.merger

Fast addition of tips and clades on an existing tree
setBM

Producing simulated phenotypes with trends
retrieve.angles

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

Example dataset
DataSimians

Example dataset
PGLS_fossil

Phylogenetic Generalized Least Square with fossil phylogenies
RRphylo

Evolutionary rates computation along phylogenies
RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies
DataCetaceans

Example dataset
DataUng

Example dataset
DataOrnithodirans

Example dataset
DataFelids

Example dataset