regular_sampling_scheme: c/e rates for a regular sampling scheme

In island: Stochastic Island Biogeography Theory Made Easy

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)

island documentation built on June 22, 2024, 7:34 p.m.