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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

2.8.1

License

GPL-2

Maintainer

Silvia Castiglione

Last Published

August 22nd, 2024

Functions in RRphylo (2.8.1)

colorbar

Draw colorbar on a plot
getGenus

Taxonomic inspection of the tree at the genus level
node.paths

Tracing nodes along paths
namesCompare

Checking species names for misspelling and synonyms
getMommy

Upward tip or node to root path
overfitRR

Testing RRphylo methods overfit
move.lineage

Move tips or clades
getSis

Get sister clade
makeL1

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

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

Rescaling phylogenetic trees
retrieve.angles

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

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

Plot the RRphylo output onto the phylogenetic tree
phyloclust

Test for phylogenetic clustering
random.evolvability.test

Randomization test for phylogenetic structuring in evolvability
plotRates

Plot RRphylo rates at a specified node
plotConv

Graphical representation of search.conv results
plotTrend

Graphical representation of search.trend results
plotShift

Graphical representation of search.shift results
makeFossil

Make fossil species on a phylogeny
setBM

Producing simulated phenotypes with trends
search.shift

Locating shifts in phenotypic evolutionary rates
lollipoPlot

Lollipop charts
sig2BM

Brownian Motion rate computation
search.trend

Searching for evolutionary trends in phenotypes and rates
tips

Get descending tips
tree.merger

Fast addition of tips and clades on an existing tree
swapONE

Create alternative phylogenies from a given tree
sizedsubtree

Find a node subtending to a clade of desired size
treedataMatch

Cross-reference tree and data
treeCompare

Visualize the difference between phylogenetic trees
search.conv

Searching for morphological convergence among species and clades
scaleTree

Phylogenetic tree calibration
DataFelids

Example dataset
distNodes

Finding distance between nodes and tips
DataOrnithodirans

Example dataset
evo.dir

Phylogenetic vector analysis of phenotypic change
DataSimians

Example dataset
DataUng

Example dataset
DataCetaceans

Example dataset
DataApes

Example dataset
fix.poly

Resolving polytomies to non-zero length branches
RRphylo

Evolutionary rates computation along phylogenies
StableTraitsR

Run StableTraits from within R
RRphylo-deprecated

Deprecated functions in Package RRphylo
RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies
RRphylo-defunct

Defunct functions in Package RRphylo
PGLS_fossil

Phylogenetic Generalized Least Square with phylogenies including fossils
angle.matrix

Ontogenetic shape vectors analysis
conv.map

Mapping morphological convergence on 3D surfaces
cutPhylo

Cut the phylogeny at a given age or node