regular_sampling_scheme {island}

c/e rates for a regular sampling scheme

Description

regular_sampling_scheme estimates colonization and extinction rates for a community or groups in a community.
NLL_rss returns the Negative Log-Likelihood of a pair of colonization and extinction rates for a regular sampling scheme.

Usage

regular_sampling_scheme(
  x,
  vector,
  level = NULL,
  n = NULL,
  step = NULL,
  CI = FALSE
)

NLL_rss(x, vector, c, e)

Arguments

x

A single dataset.

vector

A vector indicating the columns with presence-absence data.

level

The name of the column that contain groups used to subset them and calculate their colonization and extinction rates.

n

Minimal number of rows for each group.

step

Accuracy to calculate the c_e pairs with.

CI

Logical. Should confidence intervals be returned?

c

A colonization rate.

e

An extinction rate.

Details

The confidence intervals are calculated with a binary search seeded with the hessian of the estimated rates.

Value

regular_sampling_scheme returns a dataframe with colonization and extinction rates along with their lower and upper confidence intervals (optional), for each group if specified, and its number of rows and NLL. NLL_rss gives the NLL for a dataframe given a specific c and e.

See Also

irregular_single_dataset, irregular_multiple_datasets

Examples

regular_sampling_scheme(alonso15[[1]], 3:6)
regular_sampling_scheme(alonso15[[1]], 3:6, "Guild", n = 5)
regular_sampling_scheme(alonso15[[1]], 3:6, "Guild", n = 5, CI = TRUE)
NLL_rss(alonso15[[1]], 3:6, 0.52, 0.39)