DAISIE_ExpEIN2 {DAISIE} | 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, 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)))
[Package
DAISIE version 4.6.0
Index]