adiv (version 2.2.1)

DP: Plot-to-plot functional or phylogenetic dissimilarity

Description

The function DP calculates Ricotta et al. (2020) plot-to-plot functional or phylogenetic beta uniqueness (index named \(D_F\) for functional data and \(D_P\) for phylogenetic data, calculated with equation 2 in Ricotta et al. 2020).

Usage

DP(mtree, comm, height = NULL, diag = FALSE, upper = FALSE, tol = 0.001)

Value

The function returns a (semi-)matrix of class dist with the values of the proposed dissimilarities for each pair of plots.

Arguments

mtree

an object inheriting the class phylo (see package ape), phylo4 (see package phylobase), or hclust. The tree must be ultrametric: equal distance from any tip to the root.

comm

a matrix containing the relative or absolute abundance of all species in plots. Columns are species and plots are rows. Column labels (species names) should be assigned as in mtree.

height

either NULL or a numeric. See details.

diag

a logical value indicating whether the diagonal of the distance matrix should be printed by function print.dist.

upper

a logical value indicating whether the upper triangle of the distance matrix should be printed by function print.dist.

tol

a tolerance threshold. A value between -tol and tol is considered as zero. See details.

Author

Sandrine Pavoine

Details

Object mtree defines a tree with species as tips. If argument height is NULL, then the root of the tree will be placed at the most recent common ancestor of all species occurring in the set of plots (given in object comm). An alternative position for the root can be given by specifying the height of the tree (argument height). In that case, height must be higher than the distance between tips and the most recent common ancestor of all species.

The tolerance threshold tol is particularly important if your tree is not exactly ultrametric due to approximation problems. In that case, the distance from tip to root varies according to the tip considered, although it should not (variations are due to approximation problems). A difference smaller than tol in the distance to root for two species will thus be considered as null.

References

Ricotta, C., Laroche, F., Szeidl, L., Pavoine, S. (2020) From alpha to beta functional and phylogenetic redundancy. Methods in Ecology and Evolution. In press.

See Also

betaTreeUniqueness for beta uniqueness, treeUniqueness for alpha uniqueness

Examples

if (FALSE) {
if(require(ape) && require(ade4)){
data(RutorGlacier)
phy <- read.tree(text=RutorGlacier$TreeNW)
plot(phy)

ab <- RutorGlacier$Abund[, phy$tip.label]

# Phylogenetic dissimilarities between plots
# (Ricotta et al. 2020)
Dp <- DP(phy, ab, tol=0.00001)
# Principal Coordinate Analysis of the dissimilarities
pcoDp <- dudi.pco(sqrt(Dp), full=TRUE)
s.class(pcoDp$li, as.factor(RutorGlacier$Fac))
}
}