adephylo-package | R Documentation |

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
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.

The `ade4`

package for multivariate analysis.

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