This package is devoted to exploratory analysis of phylogenetic comparative
data. It re-implements and extends phylogenetic procedures from the
ade4 package (which are now deprecated).
Comparative data (phylogeny+traits) are handled as phylo4d
objects, a canonical class implemented by the
Trees are handled as
phylo objects (from the
ape package) or as phylo4 objects (
Main functionalities of
adephylo are summarized below.
=== TOPOLOGICAL INFORMATION ===
Several functions allow one to retrieve topological information from a tree; such information can be used, for instance, as a basis to compute distances or proximities between tips.
listDD: lists the direct descendants from each node of a
listTips: lists the tips descending from each node of a
.tipToRoot: finds the set of nodes between a tip and the
root of a tree.
sp.tips: finds the shortest path between tips of a tree.
treePart: defines partitions of tips reflecting the topology
of a tree. This function can output non-independent dummy vectors, or
alternatively an orthonormal basis used by the orthogram procedure.
=== PHYLOGENETIC PROXIMITIES/DISTANCES ===
Several phylogenetic proximities and distances are implemented. Auxiliary function easing the computation of other distances/proximities are also provided:
distRoot: computes different distances of a set of tips to
distTips: computes different pairwise distances in a set of
proxTips: computes different proximities between a set of
=== MEASURES/TESTS OF PHYLOGENETIC AUTOCORRELATION ===
Several procedures allow one to measure, and/or test phylogenetic signal in biological traits:
abouheif.moran: performs Abouheif's test, designed to detect
phylogenetic autocorrelation in a quantitative trait. This implementation is
not based on original heuristic procedure, but on the exact formulation
proposed by Pavoine et al. (2008), showing that the test is in fact a
Moran's index test. This implementation further extends the procedure by
allowing any measure of phylogenetic proximity (5 are proposed).
orthogram: performs the orthonormal decomposition of
variance of a quantitative variable on an orthonormal basis as in Ollier et
al. (2005). It also returns the results of five non parametric tests
associated to the variance decomposition.
moran.idx: computes Moran's index of autocorrelation given a
variable and a matrix of proximities among observations (no test).
=== MODELLING/INVESTIGATION OF PHYLOGENETIC SIGNAL ===
Rather than testing or measuring phylogenetic autocorrelation, these procedures can be used for further investigation of phylogenetic signal. Some, like
me.phylo, can be used to remove phylogenetic autocorrelation.
Others can be used to understand the nature of this autocorrelation (i.e.,
to ascertain which traits and tips are concerned by phylogenetic
orthobasis.phylo: these synonymous
functions compute Moran's eigenvectors (ME) associated to a tree. These
vectors model different observable phylogenetic signals. They can be used as
covariables to remove phylogenetic autocorrelation from data.
orthogram: the orthogram mentioned above also provides a
description of how biological variability is structured on a phylogeny.
ppca: performs a phylogenetic Principal Component Analysis
(pPCA, Jombart et al. 2010). This multivariate method investigates
phylogenetic patterns in a set of quantitative traits.
=== GRAPHICS ===
Some plotting functions are proposed, most of them being devoted to representing phylogeny and a quantitative information at the same time.
table.phylo4d: fairly customisable way of representing
traits onto the tips of a phylogeny. Several traits can be plotted in a
bullseye: an alternative to
based on fan-like representation, better for large trees.
plot.ppca: several plots associated to a phylogenetic
principal component analysis (see
=== DATASETS ===
Several datasets are also proposed. Some of these datasets replace former version from
ade4, which are now deprecated.
Here is a list of available datasets:
To cite adephylo, please use the reference given by
Thibaut Jombart <firstname.lastname@example.org>
with contributions Stephane Dray <email@example.com> and Anders Ellern Bilgrau <firstname.lastname@example.org>.
Parts of former code from
ade4 by Daniel
Chessel and Sebastien Ollier.
ade4 package for multivariate analysis.
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