Functional diversity is defined as the total branch length in a trait dendrogram connecting all species, but excluding the unnecessary root segments of the tree (Petchey and Gaston 2006). Tree distance is the increase in total branch length when combining two sites.
treedive(comm, tree, match.force = TRUE, verbose = TRUE)
treeheight(tree)
treedist(x, tree, relative = TRUE, match.force = TRUE, ...)A vector of diversity values or a single tree height, or a
dissimilarity structure that inherits from dist and
can be used similarly.
Community data frame or matrix.
A dendrogram which for treedive must be for species
(columns).
Force matching of column names in data
(comm, x) and labels in tree. If FALSE,
matching only happens when dimensions differ (with a warning or
message). The order of data must match to the order in tree
if matching by names is not done.
Print diagnostic messages and warnings.
Use distances relative to the height of combined tree.
Other arguments passed to functions (ignored).
Jari Oksanen
Function treeheight finds the sum of lengths of connecting
segments in a dendrogram produced by hclust, or other
dendrogram that can be coerced to a correct type using
as.hclust. When applied to a clustering of species
traits, this is a measure of functional diversity (Petchey and Gaston
2002, 2006), and when applied to phylogenetic trees this is
phylogenetic diversity.
Function treedive finds the treeheight for each site
(row) of a community matrix. The function uses a subset of
dendrogram for those species that occur in each site, and excludes
the tree root if that is not needed to connect the species (Petchey
and Gaston 2006). The subset of the dendrogram is found by first
calculating cophenetic distances from the input
dendrogram, then reconstructing the dendrogram for the subset of the
cophenetic distance matrix for species occurring in each
site. Diversity is 0 for one species, and NA for empty
communities.
Function treedist finds the dissimilarities among
trees. Pairwise dissimilarity of two trees is found by combining
species in a common tree and seeing how much of the tree height is
shared and how much is unique. With relative = FALSE the
dissimilarity is defined as \(2 (A \cup B) - A - B\), where
\(A\) and \(B\) are heights of component trees and
\(A \cup B\) is the height of the combined tree. With relative = TRUE
the dissimilarity is \((2(A \cup B)-A-B)/(A \cup B)\).
Although the latter formula is similar to
Jaccard dissimilarity (see vegdist,
designdist), it is not in the range \(0 \ldots 1\), since combined tree can add a new root. When two zero-height
trees are combined into a tree of above zero height, the relative
index attains its maximum value \(2\). The dissimilarity is zero
from a combined zero-height tree.
The functions need a dendrogram of species traits or phylogenies as an
input. If species traits contain factor or
ordered factor variables, it is recommended to use Gower
distances for mixed data (function daisy in
package cluster), and usually the recommended clustering method
is UPGMA (method = "average" in function hclust)
(Podani and Schmera 2006). Phylogenetic trees can be changed into
dendrograms using function as.hclust.phylo in the
ape package.
It is possible to analyse the non-randomness of tree diversity
using oecosimu. This needs specifying an adequate Null
model, and the results will change with this choice.
Lozupone, C. and Knight, R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71, 8228--8235.
Petchey, O.L. and Gaston, K.J. 2002. Functional diversity (FD), species richness and community composition. Ecology Letters 5, 402--411.
Petchey, O.L. and Gaston, K.J. 2006. Functional diversity: back to basics and looking forward. Ecology Letters 9, 741--758.
Podani J. and Schmera, D. 2006. On dendrogram-based methods of functional diversity. Oikos 115, 179--185.
Function treedive is similar to the phylogenetic
diversity function pd in the package picante, but
excludes tree root if that is not needed to connect species. Function
treedist is similar to the phylogenetic similarity
phylosor in the package picante, but excludes
unneeded tree root and returns distances instead of similarities.
taxondive is something very similar from another bubble.
## There is no data set on species properties yet, and we demonstrate
## the methods using phylogenetic trees
data(dune)
data(dune.phylodis)
cl <- hclust(dune.phylodis)
treedive(dune, cl)
## Significance test using Null model communities.
## The current choice fixes numbers of species and picks species
## proportionally to their overall frequency
oecosimu(dune, treedive, "r1", tree = cl, verbose = FALSE)
## Phylogenetically ordered community table
dtree <- treedist(dune, cl)
tabasco(dune, hclust(dtree), cl)
## Use tree distances in capscale
capscale(dtree ~ 1, comm=dune)
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