Description Details Author(s) See Also
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
phylobase
package. Trees are handled as phylo
objects (from the ape
package) or as phylo4
objects (phylobase
's extension of phylo
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 tree.
- listTips
: lists the tips descending from each node
of a tree.
- .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 the
root.
- distTips
: computes different pairwise distances in a set of tips.
- proxTips
: computes different proximities between a
set of tips.
=== 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 non-independence).
- me.phylo
/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 single graphic.
- bullseye
: an alternative to
table.phylo4d
based on fan-like representation, better
for large trees.
- scatter.ppca
, screeplot.ppca
,
plot.ppca
: several plots associated to a phylogenetic
principal component analysis (see ppca
).
=== 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: carni19
,
carni70
, lizards
, maples
,
mjrochet
, palm
, procella
,
tithonia
, and ungulates
.
To cite adephylo, please use the reference given by
citation("adephylo")
.
Package: | adephylo |
Type: | Package |
Version: | 1.1-7 |
Date: | 2014-11-10 |
License: | GPL (>=2) |
Thibaut Jombart <tjombart@imperial.ac.uk>
with contributions Stéphane Dray <dray@biomserv.univ-lyon1.fr> and Anders Ellern Bilgrau <abilgrau@math.aau.dk>.
Parts of former code from ade4
by Daniel Chessel and Sébastien
Ollier.
The ade4
package for multivariate analysis.
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