regular_sampling_scheme: 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 = F)
NLL_rss(x, vector, c, e)

Arguments

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.

Minimal number of rows for each group.

step

Accuracy to calculate the c_e pairs with.

Logical. Should confidence intervals be returned?

A colonization rate.

An extinction rate.

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.

Details

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

Examples

Run this code

# NOT RUN {
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)
# }