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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

618

Version

2.8.0

License

GPL-2

Maintainer

Pasquale Raia

Last Published

June 4th, 2023

Functions in RRphylo (2.8.0)

distNodes

Finding distance between nodes and tips
evo.dir

Phylogenetic vector analysis of phenotypic change
getGenus

Taxonomic inspection of the tree at the genus level
RRphylo

Evolutionary rates computation along phylogenies
fix.poly

Resolving polytomies to non-zero length branches
angle.matrix

Ontogenetic shape vectors analysis
StableTraitsR

Run StableTraits from within R
conv.map

Mapping morphological convergence on 3D surfaces
colorbar

Draw colorbar on a plot
cutPhylo

Cut the phylogeny at a given age or node
makeL

Matrix of branch lengths along root-to-tip paths
move.lineage

Move tips or clades
lollipoPlot

Lollipop charts
namesCompare

Checking species names for misspelling and synonyms
makeL1

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

Tracing nodes along paths
getMommy

Upward tip or node to root path
overfitRR

Testing RRphylo methods overfit
makeFossil

Make fossil species on a phylogeny
getSis

Get sister clade
plotRR

Plot the RRphylo output onto the phylogenetic tree
plotConv

Graphical representation of search.conv results
plotTrend

Graphical representation of search.trend results
retrieve.angles

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

Graphical representation of search.shift results
phyloclust

Test for phylogenetic clustering
rate.map

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

Plot RRphylo rates at a specified node
rescaleRR

Rescaling phylogenetic trees
random.evolvability.test

Randomization test for phylogenetic structuring in evolvability
tips

Get descending tips
search.conv

Searching for morphological convergence among species and clades
setBM

Producing simulated phenotypes with trends
sig2BM

Brownian Motion rate computation
search.trend

Searching for evolutionary trends in phenotypes and rates
tree.merger

Fast addition of tips and clades on an existing tree
swapONE

Create alternative phylogenies from a given tree
search.shift

Locating shifts in phenotypic evolutionary rates
scaleTree

Phylogenetic tree calibration
sizedsubtree

Find a node subtending to a clade of desired size
treeCompare

Visualize the difference between phylogenetic trees
treedataMatch

Cross-reference tree and data
DataSimians

Example dataset
RRphylo-defunct

Defunct functions in Package RRphylo
DataUng

Example dataset
DataCetaceans

Example dataset
RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies
DataFelids

Example dataset
PGLS_fossil

Phylogenetic Generalized Least Square with phylogenies including fossils
RRphylo-deprecated

Deprecated functions in Package RRphylo
DataApes

Example dataset
DataOrnithodirans

Example dataset