irregular_multiple_datasets {island}

c/e rates for irregular samplings in multiple datasets

Description

irregular_multiple_datasets estimates colonization and extinction rates for data in several datasets.
NLL_imd returns the Negative Log-Likelihood of a pair of colonization and extinction rates for irregular sampling schemes in several single dataset.

Usage

irregular_multiple_datasets(
  list,
  vectorlist,
  c,
  e,
  column = NULL,
  n = NULL,
  step = NULL,
  assembly = FALSE,
  jacobian = FALSE,
  verbose = FALSE,
  CI = FALSE
)

NLL_imd(list, vectorlist, c, e, assembly = FALSE)

Arguments

list

A list of dataframes.

vectorlist

A list of vectors indicating the columns with presence-absence data.

c

Tentative colonization rate.

e

Tentative extinction rate.

column

The name of the column with groups to calculate their c_e pair.

n

Minimal number of rows for each group.

step

Accuracy to calculate the c_e pairs with.

assembly

Logical indicating if the assembly starts from zero species or not.

jacobian

Logical. Use the semianalytical method to estimate colonization and extinction rates?

verbose

Logical. If TRUE, gives the output of the optimizer or the numerical solver that finds the values of c and e.

CI

Logical. If TRUE, gives the confidence interval of the colonization and extinction rates.

Value

irregular_multiple_datasets returns a dataframe with colonization and extinction rates and their upper and lower confidence interval, and if needed, the names of the groups to which colonization and extinction rates have been calculated. NLL_imd gives the NLL for a multiple datasets with irregular sampling schemes given a specific c and e.

Note

The columns with the presence-absence data should have the day of that sampling on the name of the column in order to calculate colonization and extinction.

See Also

regular_sampling_scheme, irregular_single_dataset

Examples

irregular_multiple_datasets(simberloff, list(3:17, 3:18, 3:17,
3:19, 3:17, 3:16), 0.001, 0.001)

irregular_multiple_datasets(simberloff, list(3:17, 3:18, 3:17, 3:19, 3:17,
 3:16), 0.001, 0.001, "Tax. Unit 1", n = 13)
irregular_multiple_datasets(simberloff, list(3:17, 3:18, 3:17, 3:19, 3:17,
 3:16), 0.001, 0.001, "Tax. Unit 1", n = 13, CI = TRUE)
 
 NLL_imd(simberloff, list(3:17, 3:18, 3:17, 3:19, 3:17, 3:16), 0.0051, 0.0117)