distinctDis: Dissimilarity-based Species' Originality

In adiv: Analysis of Diversity

Dissimilarity-based Species' Originality

Description

The function calculates five indices of species' originality.

Usage

distinctDis(dis, method = c("Rb", "AV", "FV", "NN", "Dstar", "full"), 
    palpha = 0, standardized = FALSE)

Arguments

dis	an object of class dist containing pair-wise (functional or phylogenetic) dissimilarities between species.
method	a vector of strings. Possible values are "Rb", "AV", "FV", "NN", "Dstar" and "full". "Rb" is for Pavoine et al. (2017) index Rb; "AV" is for AV, the average dissimilarity between a species and all others in a set (Eiswerth and Haney 1992; Ricotta 2004); "FV" is for FV, the average dissimilarity between a species and any other (including the focal species itself) (Schmera et al. 2009); "NN" is for the minimum dissimilarity between a species and any other (the dissimilarity to its Nearest Neighbor) (Pavoine et al. 2017); Dstar is the parametric indices ^{\alpha}D* developed by Pavoine and Ricotta (2021, Appendix B); "full" returns all indices.
palpha	a numeric which provides the value of parameter \alpha in index ^{\alpha}D* developed by Pavoine and Ricotta (2021, Appendix B).
standardized	a logical. If TRUE, the vector of originalities is divided by its sum (transforming absolute originalities into relative originalities).

Value

A data frame with species as rows and originality indices as columns.

Author(s)

Sandrine Pavoine [e-mail]

References

Eiswerth, M.E. and Haney, J.C. (1992) Allocating conservation expenditures: accounting for inter-species genetic distinctiveness. Ecological Economics, 5, 235–249.

Pavoine, S., Bonsall, M.B., Dupaix, A., Jacob, U., Ricotta, C. (2017) From phylogenetic to functional originality: guide through indices and new developments. Ecological Indicators, 82, 196–205.

Pavoine, S., Ricotta, C. (2021) On the relationships between rarity, uniqueness, distinctiveness, originality and functional/phylogenetic diversity. BiorXiv. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2021.08.09.455640")}

Ricotta, C. (2004) A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species. Diversity and Distributions, 10, 143–146.

Schmera, D., Podani, J., Eros, T. (2009) Measuring the contribution of community members to functional diversity. Oikos, 118, 961–971.

See Also

distinctTopo, distinctTree, distinctUltra

Examples

e <- rlnorm(10)
e <- sort(e)
names(e) <- paste("s", 1:10, sep="")
d <- dist(e)
barplot(e)

D <- distinctDis(d, standardized = TRUE)

par(mfrow=c(4,2))
plot(e, D[,1], xlab="trait", ylab="Rb")
plot(e, D[,2], xlab="trait", ylab="AV")
plot(e, D[,3], xlab="trait", ylab="FV")
plot(e, D[,4], xlab="trait", ylab="NN")

plot(D[,1], D[,2], xlab="Rb", ylab="AV")
plot(D[,1], D[,3], xlab="Rb", ylab="FV")
plot(D[,2], D[,3], xlab="AV", ylab="FV")
plot(D[,2], D[,4], xlab="AV", ylab="NN")
par(mfrow=c(1,1))

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