evodiss: Pair-wise Phylogenetic Dissimilarities between Communities

In adiv: Analysis of Diversity

Pair-wise Phylogenetic Dissimilarities between Communities

Description

The function calculates PD-dissimilarity indices described and/or discussed in Pavoine (2016). Part of them are parametric indices.

Usage

evodiss(phyl, comm, method = NULL, q = NULL, 
w = c("evoab", "even", "speciesab"), diag = FALSE, 
upper = FALSE, tol = 1e-08)

Arguments

phyl	an object inheriting the class phylo (see package ape), phylo4 (see package phylobase) or hclust.
comm	a data frame typically with communities as rows, species as columns and an index of abundance as entries. Species should be labeled as in the phylogenetic tree where they are the tips.
method	one of the following string codes: "Minkowski", "Euclidean", "Manhattan", "Chord", "ScaledCanberra", "Divergence", "BC", "MH", "LG", "Hellinger", "chi2", "Hill", "Renyi", "C", "U", "S". See Details.
q	a vector with nonnegative value(s) for parameter q only used with method="Minkowski", "Hill", "Renyi" (parametric indices). q controls the importance given to rare compared to abundant evolutionary units. See Details.
w	either a numeric vector giving weights for communities (same order as in comm), or a string among "even", "evoab", and "speciesab". If several strings are given, only the first one is used. w is used only if method="Hill", "Renyi", "C", "U", or "S" is chosen. See details.
diag	logical argument passed to function as.dist (R base).
upper	logical argument passed to function as.dist (R base).
tol	numeric tolerance threshold: values between -tol and tol are considered equal to zero.

Details

The indices available are (formulas can be found in Supplementary material Appendix 1 of Pavoine 2016):

"Minkowski":^qevoD_{Minkowski}

"Euclidean": evoD_{Euclidean}

"Manhattan": evoD_{Manhattan}

Chord: evoD_{Chord}

ScaledCanberra: evoD_{ScaledCanberra}

Divergence: evoD_{Divergence}

BC: evoD_{Bray-Curtis}

MH: evoD_{Morisita-Horn}

LG: evoD_{Profile}

Hellinger: evoD_{Hellinger}

chi2: evoD_{Chi2}

Hill: 1-\bar{V}_{q2}

Renyi: ^qevoD_{Renyi}

C: 1-\bar{C}_{q2}

U: 1-\bar{U}_{q2}

S: 1-\bar{S}_{q2}

The weights of the communities (argument w) can be "even" (even weights, i.e. relative abundances are considered for evolutionary units), "evoab" (proportional to the summed abundances of all evolutionary units, i.e. absolute abundances are considered for evolutionary units), or "speciesab" (proportional to the summed abundances of all species). Note that if the phylogenetic tree is ultrametric (the distance from any species to the root is constant), then options "evoab" and "speciesab" are equivalent.

Value

An object of class dist containing the PD-dissimilarities (phylogenetic dissimilarities) between communities.

Author(s)

Sandrine Pavoine [e-mail]

References

The methodologies are presented in

Pavoine, S. (2016) A guide through a family of phylogenetic dissimilarity measures among sites. Oikos, 125, 1719–1732.

They gather, in a common framework, indices introduced in

Chiu, C.-H., Jost, L., Chao, A. (2014) Phylogenetic beta diversity, similarity and differentiation measures based on Hill numbers. Ecological Monographs, 84, 21–44.

and earlier work extended here in a phylogenetic context and reviewed in

Legendre, P. and De Caceres, M. (2013) Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters, 16, 951–963.

See Also

evodiss_family

Examples

## Not run: 
if(require(ape)){

data(batcomm)
phy <- read.tree(text=batcomm$tre)
ab <- batcomm$ab[,phy$tip.label]

evodiss(phy, ab, "LG")
evodiss(phy, ab, "Hellinger")
evodiss(phy, ab, "Chord")

evodiss(phy, ab, "Hill", q=2)
evodiss(phy, ab, "Hill", q=2, w="even")

}

## End(Not run)

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