Phylogenies in entropart • entropart

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.

Formats used

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.

Conversion between classes

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

hclust

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

phylo

Conversion to a phylo object is straightforward.

require("ape")

## Loading required package: ape

plot(phyloTree <- as.phylo(hTree))
axis(1)

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 phyloobjects can be identical to other phylogenies.

phyloTree$edge.length <- 2*phyloTree$edge.length
plot(phyloTree)
axis(1)

phylog

The last conversion is from phylo to phylog.

require("ade4")

## 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

Newick dendrograms

A Newick description of a dendrogram can be read into a phylo object.

NewickABC <- "(C:2,(A:1,B:1):1);"
plot(phyloABC <- ape::read.tree(text=NewickABC))
axis(1)