dissRicotta: Plot-to-Plot Functional or Phylogenetic Dissimilarity

In adiv: Analysis of Diversity

Plot-to-Plot Functional or Phylogenetic Dissimilarity

Description

The function calculates plot-to-plot functional or phylogenetic dissimilarity based on index D_{AB} in Ricotta et al. (2015).

Usage

dissRicotta(comm, dis)

Arguments

comm

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

dis

a matrix of (functional or phylogenetic) dissimilarities rescaled in the range [0, 1] or an object of class dist [obtained by functions like dsimFun in this package adiv, vegdist in package vegan, gowdis in package FD, or dist.ktab in package ade4 for functional dissimilarities, or functions like dsimTree in this package adiv, cophenetic.phylo in package ape or distTips in package adephylo for phylogenetic dissimilarities; See also function dsimTaxo for taxonomic data].

Value

The function returns a semi-matrix of class dist with the values of the proposed dissimilarities for each pair of plots. Note that dissimilarities among species need first to be rescaled in the range [0, 1]. If the dissimilarities are outside the range 0-1 (as it is usually the case in phylogenetic studies for instance), a warning message is displayed and all dissimilarities are divided by the maximum observed dissimilarity.

Author(s)

Giovanni Bacaro and Sandrine Pavoine [e-mail]

References

Ricotta, C., Bacaro, G., Pavoine, S. (2015) A cautionary note on some phylogenetic dissimilarity measures. Journal of Plant Ecology, 8, 12–16.

Examples

## Not run: 
if(require(ape)){
# Phylogenetic tree
s<-"test(((v:20,w:20):10,(x:20,y:20):10):15,z:45):5;"
plot(test <- read.tree(text=s))

# Phylogenetic distances among species
tdist <- cophenetic(test)/100

# Matrix of abundances of the species in four communities; 
# communities A and C are identical;
# communities B and D are identical;
comm <- t(data.frame(A = rep(0.2, 5), 
B = c(0.1, 0.2, 0.2, 0, 0.5), C = rep(0.2, 5), 
D = c(0.1, 0.2, 0.2, 0, 0.5), row.names = letters[22:26]))

# Index DAB
dissRicotta(comm, tdist)
}

## End(Not run)

adiv documentation built on May 29, 2024, 7:11 a.m.