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RRphylo

The RRphylo package collects tools to compute branch-wise evolutionary rates, estimate ancestral states, locate rate shifts, assess temporal trends in phenotypes and rates, evaluate morphological convergence, along with some useful functions to easily visualize analyses results, assess statistical robustness, and build/manipulate phylogenetic trees.

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

392

Version

3.0.1

License

GPL-2

Maintainer

Silvia Castiglione

Last Published

July 12th, 2025

Functions in RRphylo (3.0.1)

colorbar

Draw colorbar on a plot
angle.matrix

Ontogenetic shape vectors analysis
namesCompare

Checking species names for misspelling and synonyms
getGenus

Taxonomic inspection of the tree at the genus level
plotShift

Graphical representation of search.shift results
conv.map

Mapping morphological convergence on 3D surfaces
makeFossil

Make fossil species on a phylogeny
makeL

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

Plot RRphylo rates at a specified node
overfitSC

Testing search.conv overfit
getMommy

Upward tip or node to root path
overfitSS

Testing search.shift overfit
overfitPGLS

Testing PGLS_fossil overfit
getSis

Get sister clade
lollipoPlot

Lollipop charts
overfitRR

Testing RRphylo overfit
node.paths

Tracing nodes along paths
plotRR

Plot the RRphylo output onto the phylogenetic tree
plotConv

Graphical representation of search.conv results
search.conv

Searching for morphological convergence among species and clades
overfitST

Testing search.trend overfit
phyloclust

Test for phylogenetic clustering
move.lineage

Move tips or clades
makeL1

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

Altering phylogenetic trees
retrieve.angles

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

Phylogenetic tree calibration
rescaleRR

Rescaling phylogenetic trees
setBM

Producing simulated phenotypes with trends
plotTrend

Graphical representation of search.trend results
random.evolvability.test

Randomization test for phylogenetic structuring in evolvability
search.trend

Searching for evolutionary trends in phenotypes and rates
sizedsubtree

Find a node subtending to a clade of desired size
sig2BM

Brownian Motion rate computation
search.shift

Locating shifts in phenotypic evolutionary rates
rate.map

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

Cross-reference tree and data
rateHistory

Computing historical rates
swapONE

Create alternative phylogenies from a given tree
tips

Get descending tips
treeCompare

Visualize the difference between phylogenetic trees
tree.merger

Fast construction of phylogenetic trees
DataSimians

Example dataset
DataUng

Example dataset
RRphylo-deprecated

Deprecated functions in Package RRphylo
RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies
PGLS_fossil

Phylogenetic Generalized Least Square with phylogenies including fossils
RRphylo-defunct

Defunct functions in Package RRphylo
cutPhylo

Cut the phylogeny at a given age or node
StableTraitsR

Run StableTraits from within R
compRates

Comparing average absolute rates between clades
fix.poly

Resolving polytomies to non-zero length branches
RRphylo

Evolutionary rates computation along phylogenies
evo.dir

Phylogenetic vector analysis of phenotypic change
DataCetaceans

Example dataset
DataFelids

Example dataset
DataOrnithodirans

Example dataset
DataApes

Example dataset
distNodes

Finding distance between nodes and tips