DAISIE_ExpEIN2: The expected number of endemics and non-endemics under the...

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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, where there can be diversity-dependence

Usage

DAISIE_ExpEIN2(
  tvec,
  pars,
  M,
  initEI = NULL,
  res = 1000,
  ddmodel = 11,
  methode = "ode45",
  reltolint = 1e-16,
  abstolint = 1e-16
)

Arguments

tvec	The times at which the probabilities 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.
res	Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade.
ddmodel	Sets the model of diversity-dependence: ddmodel = 0 : no diversity dependence ddmodel = 1 : linear dependence in speciation rate ddmodel = 11: linear dependence in speciation rate and in immigration rate ddmodel = 2 : exponential dependence in speciation rate ddmodel = 21: exponential dependence in speciation rate and in immigration rate
methode	Method of the ODE-solver. Supported Boost ODEINT solvers (steppers) are: "odeint::runge_kutta_cash_karp54" "odeint::runge_kutta_fehlberg78" "odeint::runge_kutta_dopri5" "odeint::bulirsch_stoer" without odeint::-prefix, ode method is assumed. The default method overall is "lsodes" for DAISIE_ML_CS() and "ode45" from ode() for DAISIE_ML_IW().
reltolint	Numeric relative tolerance of the integration
abstolint	Numeric absolute tolerance of the integration

Value

tot_expEIN

The output is a list with three elements: ExpE The number of endemic species at the times in tvec ExpI The number of non-endemic species at the times in tvec ExpN The sum of the number of endemics and non-endemics at the times in tvec

Author(s)

Rampal S. Etienne

Examples

DAISIE_ExpEIN2(tvec = c(0.000001,0.5,0.75,1),
                         pars = c(0.3,0.1,10,1,0.1),
                         M = 1000,
                         initEI = rbind(c(1,0),c(2,0),c(0,1)))

DAISIE documentation built on June 8, 2025, 11:28 a.m.