| scarcity_stack {funrar} | R Documentation |
Scarcity on a stacked data.frame
Description
Compute scarcity values for several communities. Scarcity computation
requires relative abundances. Scarcity is close to 1 when a species is rare
in a community and close to 0 when it is abundant. See scarcity() function
or the functional rarity indices vignette included in the package (type
vignette("rarity_indices", package = "funrar")) for details about the
index. You can either use _stack() or _tidy() functions as they are
aliases of one another.
Usage
scarcity_stack(com_df, sp_col, com, abund)
scarcity_tidy(com_df, sp_col, com, abund)
Arguments
com_df |
a stacked (= tidy) data.frame from a single community with each row representing a species in a community |
sp_col |
a character vector, the name of the species column in |
com |
a character vector indicating the column name of communities ID in
|
abund |
a character vector, the name of the column containing relative abundances values |
Value
The same table as com_df with an added S_i column
for Scarcity values.
See Also
scarcity() and vignette("rarity_indices", package = "funrar")
for details on the scarcity metric; distinctiveness_stack(),
restrictedness_stack(), uniqueness_stack()
Examples
data("aravo", package = "ade4")
# Site-species matrix converted into data.frame
mat = as.matrix(aravo$spe)
mat = make_relative(mat)
dat = matrix_to_stack(mat, "value", "site", "species")
dat$site = as.character(dat$site)
dat$species = as.character(dat$species)
si_df = scarcity_stack(dat, "species", "site", "value")
head(si_df)