similarity_to_dissimilarity {bioregion} | R Documentation |
This function converts a data.frame of similarity metrics between sites to dissimilarity metrics (= beta diversity).
similarity_to_dissimilarity(similarity)
similarity |
the output object from |
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.
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:
\(dissimilarity = 1 - similarity\)
Boris Leroy (leroy.boris@gmail.com), Maxime Lenormand (maxime.lenormand@inrae.fr) and Pierre Denelle (pierre.denelle@gmail.com)
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