similarity_to_dissimilarity {bioregion}

R Documentation

Convert similarity indices to dissimilarity metrics

Description

This function converts a data.frame of similarity metrics between sites to dissimilarity metrics (= beta diversity).

Usage

similarity_to_dissimilarity(similarity)

Arguments

similarity

the output object from similarity() or a data.frame with the first columns called "Site1" and "Site2", and the other columns being the similarity metrics.

Value

A data.frame with additional class bioregion.pairwise.metric, providing one or several similarity metric(s) between each pair of sites. The two first columns represent each pair of sites, and the other column represent similarity metrics. Columns with names "a", "b", "c", "A", "B" and "C" are not altered.

Note

The behavior of this function changes depending on column names. Columns "Site1" and "Site2" are copied identically. If there are columns called "a", "b", "c", "A", "B", "C", they will also be copied identically.

If a column is called "Euclidean", its distance will be calculated based on the following formula:

\(Euclidean distance = (1 - Euclidean similarity) / Euclidean similarity\)

Otherwise, all other columns will be transformed into dissimilarity with the following formula:

\(dissimilarity = 1 - similarity\)

Author(s)

Boris Leroy (leroy.boris@gmail.com), Maxime Lenormand (maxime.lenormand@inrae.fr) and Pierre Denelle (pierre.denelle@gmail.com)

See Also

dissimilarity_to_similarity()

Examples

comat <- matrix(sample(0:1000, size = 50, replace = TRUE,
prob = 1 / 1:1001), 5, 10)
rownames(comat) <- paste0("Site", 1:5)
colnames(comat) <- paste0("Species", 1:10)

simil <- similarity(comat, metric = "all")
simil

dissimilarity <- similarity_to_dissimilarity(simil)
dissimilarity

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