data_generation {island}

Data simulation of colonization-extinction dynamics

Description

data_generation simulates species richness data according to the stochastic model of island biogeography
PA_simulation simulates presence-absence data according to the stochastic model of island biogeography

Usage

data_generation(x, column, transitions, iter, times)

PA_simulation(x, column, transitions, times = 1)

Arguments

x

A dataframe with the vector of initial absences and presences.

column

A number indicating the column with the initial presence-absence data.

transitions

A matrix with the transition probabilities of the simulation, in the form (T01, T10), that can contain one single pair or multiple pairs.

iter

Number of times that the specified dynamics should be repeated.

times

Number of temporal steps to simulate.

Details

To simulate community assembly, we need an initial vector of presence-absence, from which the subsequent assembly process will be simulated. This initial vector is considered as x[, column].

Value

A matrix with species richness representing each row consecutive samples and each column a replica of the specified dynamics or a matrix with presence-absence data for the specified dynamics, each row representing a species and each column consecutive samplings.

Note

You can simulate not only with a colonization and extinction pair, but with the pairs obtained from the environmental fit. In this case, you still have to indicate exactly the number of temporal steps that you are going to simulate.

See Also

cetotrans to obtain the transition probabilities associated with a colonization-extinction pair.

Examples

data_generation(as.data.frame(rep(0, 100)), 1,
matrix(c(0.5, 0.5), ncol = 2), 5, 25)
data_generation(alonso15[[1]], 3, matrix(c(0.5, 0.5), ncol = 2), 5, 25)
PA_simulation(as.data.frame(c(rep(0, 163), rep(1, 57))), 1, c(0.13, 0.19),
20)