DAISIE_margprobdist: The marginal distribution of endemics and non-endemics under...

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

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

Usage

DAISIE_margprobdist(pars1, pars2, tvec, initEI = c(0, 0),
  initprobs = NULL, pb = 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
pb	Rather than computing the joint distribution from given parameter values, one can also specify a precomputed probability distribution in the matrix format of DAISIE_probdist.

Value

out	A list of three vectors: pE The probability distribution of the number of endemic species pI The probability distribution of the number of non-endemic species pN The probability distribution of 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 marginal probability distributions 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

marg_prob_dists <- DAISIE_margprobdist(
   pars1 = c(0.3,0.35,Inf,0.75,0.012),
   pars2 = c(100,250),
   tvec = c(4,8),
   initEI = c(5,1),
   initprobs = NULL
   )

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