BiodiversityR: disttransform – R documentation

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disttransform

Community Matrix Transformation

Description

Transforms a community matrix. Some transformation methods are described by distances for the original community matrix that result in the same distance matrix as calculated with the euclidean distance from the transformed community matrix. In several cases (methods of "hellinger", "chord", "profiles" and "chi.square), the method makes use of function decostand. In several other cases ("Braun.Blanquet", "Domin", "Hult", "Hill", "fix" and "coverscale.log"), the method makes use of function coverscale. For method "dispweight" a call is made to function dispweight.

Usage

disttransform(x, method="hellinger")

Arguments

`x`	Community data frame with sites as rows, species as columns and species abundance as cell values.
`method`	Distance measure for the original community matrix that the euclidean distance will calculate for the transformed community matrix: partial match to "hellinger", "chord", "profiles", "chi.square", "log", "square", "pa", "Braun.Blanquet", "Domin", "Hult", "Hill", "fix", "coverscale.log" and "dispweight".

Details

This functions transforms a community matrix.

Some transformation methods ("hellinger", "chord", "profiles" and "chi.square") have the behaviour that the euclidean distance from the transformed matrix will equal a distance of choice for the original matrix. For example, using method "hellinger" and calculating the euclidean distance will result in the same distance matrix as by calculating the Hellinger distance from the original community matrix.

Transformation methods ("Braun.Blanquet", "Domin", "Hult", "Hill", "fix" and "coverscale.log") call function coverscale.

Method "dispweight" uses function dispweight without specifying a grouping structure.

Value

The function returns a transformed community matrix.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Legendre, P. & Gallagher, E.D. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

Examples

library(vegan)
data(dune)
Community.1 <- disttransform(dune, method='hellinger')
Distmatrix.1 <- vegdist(Community.1,method='euclidean')
Distmatrix.1

BiodiversityR

Package for Community Ecology and Suitability Analysis

v2.13-1

GPL-3

Authors

Roeland Kindt [cre, aut] (<https://orcid.org/0000-0002-7672-0712>)

Initial release

2021-4-15