# DAISIE_ExpEIN: The expected number of endemics and non-endemics under the... In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

 DAISIE_ExpEIN R Documentation

## The expected number of endemics and non-endemics under the DAISIE model

### Description

This function calculates the expected number of endemics, non-endemics and the sum of these for a given set of parameter values, a given mainland species pool size and a given time

### Usage

``````DAISIE_ExpEIN(t, pars, M, initEI = c(0, 0))
``````

### Arguments

 `t` The time at which the expectations need to be computed. `pars` A numeric vector containing the model parameters: `pars[1]`: lambda^c (cladogenesis rate) `pars[2]`: mu (extinction rate) `pars[3]`: K (carrying capacity), set K=Inf for diversity independence. `pars[4]`: gamma (immigration rate) `pars[5]`: lambda^a (anagenesis rate) `pars[6]`: lambda^c (cladogenesis rate) for either type 2 species or rate set 2 in rate shift model `pars[7]`: mu (extinction rate) for either type 2 species or rate set 2 in rate shift model `pars[8]`: K (carrying capacity) for either type 2 species or rate set 2 in rate shift model, set K=Inf for diversity independence. `pars[9]`: gamma (immigration rate) for either type 2 species or rate set 2 in rate shift model `pars[10]`: lambda^a (anagenesis rate) for either type 2 species or rate set 2 in rate shift model Elements 6:10 are required only when type 2 species are included or in the rate shift model. For `DAISIE_sim_relaxed_rate()` `pars[6]` is the standard deviation of the gamma distribution for the relaxed parameter and the parameter chosen by the `relaxed_par` argument is the mean of the gamma distribution for the relaxed parameter. `M` Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island. `initEI` The initial values for the number of endemics and non-endemics. In `DAISIE_probdist()` or `DAISIE_margprobdist()` either this or initprobs must be NULL. In `DAISIE_numcol()` when it is NULL, it is assumed that the island is empty.

### Value

 `out` The output is a list with three elements: `ExpE` The number of endemic species `ExpI` The number of non-endemic species `ExpN` The sum of the number of endemics and non-endemics

### 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

``````
### Compute the expected values at t = 4, for a mainland pool size of 1000 potential
# colonists and a vector of 5 parameters (cladogenesis, extinction, clade-level carrying
# capacity, immigration, anagenesis)

DAISIE_ExpEIN(
t = 4,
pars = c(0.5,0.1,Inf,0.01,0.4),
M = 1000
)

``````

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.