dissimilarity_to_similarity {bioregion}

Convert dissimilarity metrics to similarity metrics

Description

This function converts a data.frame of dissimilarity metrics (beta diversity) between sites to 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 if the metrics based on your own formula should be converted (see Details). This argument is set to TRUE by default.

Value

A data.frame with additional class bioregion.pairwise.metric, providing similarity metric(s) between 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]) and Pierre Denelle ([e-mail])

See Also

similarity_to_dissimilarity() similarity() dissimilarity()

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