*entropart* is a package for *R* designed to estimate
diversity based on HCDT entropy or similarity-based entropy.

Several object classes can be used in *entropart* to represent
phylogenies and calculate phylogenetic diversity. They are detailed
here.

Supported phylogenies are classes `phylo`

from package
*ape*, `phylog`

from package *ade4* and
`hclust`

from package *base*.

To optimize performance, a specific class `PPtree`

, for
“preprocessed trees”, is introduced by the package: it is basically a
list containing a `phylo`

and an `hclust`

representation of the phylogeny and preprocessed useful statistics.

The arguments `Tree`

or `PhyloTree`

used in
phylogenetic diversity estimation functions of the package may be any of
those formats.

Let’s start from an ultrametric distance matrix. Three species are defined, with distance 1 between the first 2 and distance 2 between both and the last one.

```
dSp <- matrix(c(0, 1, 2, 1, 0, 2, 2, 2, 0), nrow=3, byrow=TRUE)
row.names(dSp) <- colnames(dSp) <- c("A", "B", "C")
dSp
```

```
## A B C
## A 0 1 2
## B 1 0 2
## C 2 2 0
```

An `hclust`

object is created by UPGMA hierarchical
clustering.

```
require("stats")
plot(hTree <- hclust(as.dist(dSp), method="average"), hang=-0.01, axes = F)
axis(2)
```

Node heights are stored in `$height`

.

`hTree$height`

`## [1] 1 2`

Conversion to a `phylo`

object is straightforward.

`## Loading required package: ape`

Edge lengths have been divided by 2 during the conversion, as
documented in `?as.phylo.hclust`

.

`phyloTree$edge.length`

`## [1] 1.0 0.5 0.5 0.5`

That does not suit our needs. In *entropart*, edge lengths are
multiplied by 2 after conversion, so that `phylo`

objects can
be identical to other phylogenies.

The last conversion is from `phylo`

to
`phylog`

.

`## Loading required package: ade4`

```
plot(phylogTree <- hclust2phylog(hTree))
axis(1)
```

Edge lengths are not stored directly in `phylog`

objects.
The `$droot`

component keeps distances from tips to root. The
`$Wdist`

component is a `dist`

(half a distance
matrix without the zero-diagonal) whose values are \(d_{s,t}=\sqrt{2 \delta_{s,t}^2}\), where
\(\delta_{s,t}\) is the distance
between species \(s\) ant \(t\).

`phylogTree$droot`

```
## C A B Int1 Root
## 2 2 2 1 0
```

`phylogTree$Wdist^2/2`

```
## C A
## A 2
## B 2 1
```