nichetools (version 0.3.2)

extract_niche_size: extract niche size

Description

Extract niche size based on elliptical niche region of Bayesian estimates of sigma created by function niw.post() or siberEllipses() in the package nicheROVER or SIBER, respectfully. For nicheROVER this function is a wrapper around nicheROVER::niche.size.

Usage

extract_niche_size(
  data,
  pkg = NULL,
  name = NULL,
  prob = NULL,
  community_df = NULL
)

Value

if pkg is set to "nicheROVER" then a tibble containing three rows, sample_name, id, and niche_size is returned.

Arguments

data

a list or matrix created by the function niw.post() or siberEllipses() in the package nicheROVER or SIBER, respectfully.

pkg

a character string that is the name of the package that you're using. Defaults to "nicheROVER". Alternatively the user can supply the argument with "SIBER".

name

a character string that will be assigned as the column name for groups. Default is sample_name. Only to be used when pkg is set to "nicheROVER".

prob

a numeric bound by 0 and 1 indicating the probabilistic niche size. Default is 0.95. Only to be used when pkg is set to "nicheROVER".

community_df

a four column data frame. One of the columns has to be named community and the data in the column will be numeric as a character string(e.g., "1", "2", "3"). This is the order of the community names and will be used to join the actual community names to the correct data. These are the same class and values required by the function, createSiberObject() from SIBER. The second column will be the names of the groups that are needed to supply required by the function, createSiberObject() from SIBER. The third and fourth columns contains the actual names of the communities and groups the user is working with (e.g., "region", "common_name").

See Also

nicheROVER::niche.size(), nicheROVER::niw.post(), SIBER::siberEllipses(), and SIBER::createSiberObject()

Examples

extract_niche_size(data = niw_fish_post)