rangemapSim: Pairwise similarity between rangemaps

View source: R/rangemapSim.R

rangemapSimR Documentation

Pairwise similarity between rangemaps

Description

Calculate pairwise similarity among rangemaps from a matrix of their areas of intersection and union

Usage

rangemapSim(rangemap.matrix, total.area, 
method = c("Jaccard", "Sorensen", "Simpson", "Baroni"), 
diag = FALSE, upper = FALSE, verbosity = 2)

Arguments

rangemap.matrix

a matrix like the one produced by function pairwiseRangemaps, containing the areas of pairwise intersection among rangemaps in the lower triangle, individual rangemap areas in the diagonal, and pairwise union areas in the upper diagonal.

total.area

numeric value indicating the total size of the study area, in the same units as the areas in the rangemap.matrix. Used only if 'method' uses shared absences (as is the case of "Baroni")

method

character value indicating the similarity index to use. Currently implemented indices are "Jaccard", "Sorensen", "Simpson" and "Baroni". The default is the first one.

diag

logical value indicating if the diagonal of the resulting matrix should be filled

upper

logical value indicating if the upper triangle of the resulting matrix should be filled (symmetrical to the lower triangle)

verbosity

integer number indicating the amount of messages to display.

Details

Distributional relationships among species are commonly determined based on pair-wise (dis)similarities in species' occurrence patterns. Some of the most commonly employed similarity indices are those of Jaccard (1901), Sorensen (1948), Simpson (1960) and Baroni-Urbani & Buser (1976), which are here implemented for comparing rangemaps based on their areas of intersection and union (Barbosa & Estrada, in press).

Value

This function returns a square matrix of pairwise similarities between the rangemaps in 'rangemap.matrix', calculated with the (first) similarity index specified in 'method'.

Author(s)

A. Marcia Barbosa

References

Barbosa A.M. & Estrada A. (in press) Calcular corotipos sin dividir el territorio en OGUs: una adaptacion de los indices de similitud para su utilizacion directa sobre areas de distribucion. In: Areas de distribucion: entre puentes y barreras. Universidad de Granada, Spain.

Baroni-Urbani C. & Buser M.W. (1976) Similarity of Binary Data. Systematic Zoology, 25: 251-259

Jaccard P. (1901) Etude comparative de la distribution florale dans une portion des Alpes et des Jura. Memoires de la Societe Vaudoise des Sciences Naturelles, 37: 547-579

Simpson G.G. (1960) Notes on the measurement of faunal resemblance. Amer. J. Sci. 258A, 300-311

Sorensen T. (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskab, 5(4): 1-34

See Also

pairwiseRangemaps; simFromSetOps; simMat


fuzzySim documentation built on Oct. 31, 2022, 1:07 a.m.