# DAISIE_probdist: The joint distribution of endemics and non-endemics under the... In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

## Description

This function calculates the joint distribution of the number of endemics and non-endemics for a given set of parameter values, a given mainland species pool size and a given set of times

## Usage

 `1` ```DAISIE_probdist(pars1, pars2, tvec, initEI = c(0, 0), initprobs = NULL) ```

## Arguments

 `pars1` Vector of model parameters: `pars1[1]` corresponds to lambda^c (cladogenesis rate) `pars1[2]` corresponds to mu (extinction rate) `pars1[3]` corresponds to K (clade-level carrying capacity) `pars1[4]` corresponds to gamma (immigration rate) `pars1[5]` corresponds to lambda^a (anagenesis rate) `pars2` Vector of settings: `pars2[1]` corresponds to res, the maximum number of endemics or non-endemics for which the ODE system is solved; this must be much larger than the actual number for which the probability needs to be calculated.) `pars2[2]` corresponds to M, size of the mainland pool, i.e the number of species that can potentially colonize the island. `tvec` The times at which the probabilities need to be computed. `initEI` The initial values for the number of endemics and non-endemics; either this or initprobs must be NULL `initprobs` The initial probability distribution for the number of endemics and non-endemics; either this or initEI must be NULL

## Details

To obtain a matrix of probabilities with endemics in rows and non-endemics in columns for a certain time, one can run DAISIE_convertprobdist

## Value

A matrix of dimensions 1 + length(tvec) and pars[2]^2 + 1] where the first column contains the times at which the probabilities are evaluated and the other columns contain the joint probabilities.

## Author(s)

Rampal S. Etienne

## References

Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12``` ```### Compute the probability distribution at t = 4 and t = 8, for a mainland pool # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting # from an empty island prob_dists <- DAISIE_probdist( pars1 = c(0.3,0.35,Inf,0.75,0.012), pars2 = c(100,250), tvec = c(4,8), initEI = c(0,0), initprobs = NULL ) ```

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.