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).
Thibaut Jombart <tjombart@imperial.ac.uk>
with contributions
Stephane Dray <stephane.dray@univ-lyon1.fr> and Anders Ellern Bilgrau
<abilgrau@math.aau.dk>.
Parts of former code from ade4 by Daniel
Chessel and Sebastien Ollier.
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 |
| License: | GPL (>=2) |
The ade4 package for multivariate analysis.