Geographical Restrictedness for stacked data.frame

Compute the geographical restrictedness for each species present in the stacked data.frame. Geographical restrictedness is an index related to the extent of a species in a given dataset, it is close to 1 when the species is present in only a single site of the dataset (restricted) and close to 0 when the species is present at all sites. It estimates the geographical extent of a species in a dataset. See restrictedness() for details on restrictedness computation. You can either use _stack() or _tidy() functions as they are aliases of one another.

restrictedness_stack(com_df, sp_col, com, relative = FALSE)

restrictedness_tidy(com_df, sp_col, com, relative = FALSE)

Arguments

com_df

a stacked (= tidy) data.frame of communities

sp_col

a character vector indicating the name of the species column

com

a character vector indicating the name of the community column

relative

a logical (default = FALSE), indicating if restrictedness should be computed relative to restrictedness from a species occupying a single site

Value

A stacked data.frame containing species' names and their restrictedness value in the Ri column, similar to what uniqueness_stack() returns.

See also

restrictedness(), uniqueness_stack()

Examples

data("aravo", package = "ade4")

# Site-species matrix converted into data.frame
mat = as.matrix(aravo$spe)
dat = matrix_to_stack(mat, "value", "site", "species")
dat$site = as.character(dat$site)
dat$species = as.character(dat$species)
ri_df = restrictedness_stack(dat, "species", "site")
head(ri_df)
#>     species Ri
#> 1 Agro.rupe  0
#> 2 Alch.glau  0
#> 3 Alch.pent  0
#> 4 Alch.vulg  0
#> 5 Alop.alpi  0
#> 6 Andr.brig  0