dissimilarity_to_similarity: Convert dissimilarity metrics to similarity metrics

In bioregion: Comparison of Bioregionalisation Methods

Convert dissimilarity metrics to similarity metrics

Description

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

Usage

dissimilarity_to_similarity(dissimilarity, include_formula = TRUE)

Arguments

dissimilarity	the output object from dissimilarity() or similarity_to_dissimilarity().
include_formula	a boolean indicating whether metrics based on custom formula(s) should also be converted (see Details). The default is TRUE.

Value

A data.frame with the additional class bioregion.pairwise.metric, providing similarity metrics for each pair of sites based on a dissimilarity object.

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 there are columns based on your own formula (argument formula in dissimilarity()) or not in the original list of dissimilarity metrics (argument metrics in dissimilarity()) and if the argument include_formula is set to FALSE, they will also be copied identically. Otherwise there are going to be converted like they other columns (default behavior).

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

Euclidean similarity = 1 / (1 - Euclidean distance)

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

similarity = 1 - dissimilarity

Author(s)

Maxime Lenormand ([e-mail])
Boris Leroy ([e-mail])
Pierre Denelle ([e-mail])

See Also

For more details illustrated with a practical example, see the vignette: https://biorgeo.github.io/bioregion/articles/a3_pairwise_metrics.html.

Associated functions: similarity 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)

dissimil <- dissimilarity(comat, metric = "all")
dissimil

similarity <- dissimilarity_to_similarity(dissimil)
similarity

bioregion documentation built on April 12, 2025, 9:13 a.m.