dislptransport {adiv}R Documentation

Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity

Description

The function dislptransport calculates the DKG measure of dissimilarity (Kosman 1996; Gregorius et al. 2003) applied here to functional differences between plots (eq. 3 in Ricotta et al. 2021).

Usage

dislptransport(comm, dis, diag = FALSE, upper = FALSE, Nind = 10000)

Arguments

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 dis.

dis

a matrix or an object of class dist providing the functional dissimilarities between species (dissimilarities are nonnegative, symmetric, and the dissimilarity between a species and itself is zero). Species here must be in the same order as in the columns of comm.

diag

logical value indicating whether the diagonal of the dissimilarity matrix should be printed by print.dist.

upper

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

Nind

an integer. The algorithmic index will be applied by assuming that each plot contains Nind individuals. The highest Nind, the most precise the index value will be (see Gregorius et al. 2003, for more details).

Value

The function dislptransport returns an object of class dist matrix with the values of the dissimilarity index DKG (Ricotta et al. 2021) for each pair of plots.

Author(s)

Sandrine Pavoine sandrine.pavoine@mnhn.fr

References

Ricotta, C., Kosman, E., Laroche, F., Pavoine, S. (2021) Beta redundancy for functional ecology. Methods in Ecology and Evolution, 12, 1062–1069. doi: 10.1111/2041-210X.13587

Gregorius, H.-R., Gillet, E.M., Ziehe, M. (2003) Measuring differences of trait distributions between populations. Biometrical Journal, 8, 959–973. doi: 10.1002/bimj.200390063

Kosman, E. (1996) Difference and diversity of plant pathogen populations: a new approach for measuring. Phytopathology, 86, 1152–1155.

See Also

betaUniqueness for plot-to-plot functional (or phylogenetic) uniqueness indices.

Examples

## Not run: 
data(RutorGlacier)
fundis <- dist(scale(RutorGlacier$Traits2[1:6]))
fundis <- fundis/max(fundis)
DKG <- dislptransport(RutorGlacier$Abund, fundis)

## End(Not run)

[Package adiv version 2.1.1 Index]