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