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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

618

Version

3.0.0

License

GPL-2

Maintainer

Silvia Castiglione

Last Published

March 23rd, 2025

Functions in RRphylo (3.0.0)

Phylogenetic vector analysis of phenotypic change

Run StableTraits from within R

Resolving polytomies to non-zero length branches

Cut the phylogeny at a given age or node

Mapping morphological convergence on 3D surfaces

Evolutionary rates computation along phylogenies

Finding distance between nodes and tips

Comparing average absolute rates between clades

Ontogenetic shape vectors analysis

Draw colorbar on a plot

Checking species names for misspelling and synonyms

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

Move tips or clades

Get sister clade

Tracing nodes along paths

Taxonomic inspection of the tree at the genus level

Make fossil species on a phylogeny

Matrix of branch lengths along root-to-tip paths

Testing search.trend overfit

Lollipop charts

Plot the RRphylo output onto the phylogenetic tree

Graphical representation of search.conv results

Upward tip or node to root path

Testing search.conv overfit

Graphical representation of search.shift results

Plot RRphylo rates at a specified node

Testing search.shift overfit

Testing PGLS_fossil overfit

Testing RRphylo overfit

random.evolvability.test

Randomization test for phylogenetic structuring in evolvability

Graphical representation of search.trend results

Phylogenetic tree calibration

retrieve.angles

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

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

Brownian Motion rate computation

Cross-reference tree and data

Find a node subtending to a clade of desired size

Locating shifts in phenotypic evolutionary rates

Producing simulated phenotypes with trends

Searching for evolutionary trends in phenotypes and rates

Searching for morphological convergence among species and clades

Create alternative phylogenies from a given tree

Get descending tips

Test for phylogenetic clustering

Rescaling phylogenetic trees

Altering phylogenetic trees

Fast construction of phylogenetic trees

Computing historical rates

Visualize the difference between phylogenetic trees

Example dataset

RRphylo-package

Phylogenetic Ridge Regression Methods for Comparative Studies

RRphylo-deprecated

Deprecated functions in Package RRphylo

Phylogenetic Generalized Least Square with phylogenies including fossils

RRphylo-defunct

Defunct functions in Package RRphylo

DataOrnithodirans

Example dataset

Example dataset

Example dataset

Example dataset

Example dataset