adiv (version 2.2.1)

distinctDis: 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)

Value

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

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).

Author

Sandrine Pavoine

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. 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))