Description Usage Arguments Value
Computes MLE for single type species under a clade specific scenario
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | DAISIE_ML1(
datalist,
initparsopt,
idparsopt,
parsfix,
idparsfix,
idparsnoshift = 6:10,
res = 100,
ddmodel = 0,
cond = 0,
eqmodel = 0,
x_E = 0.95,
x_I = 0.98,
tol = c(1e-04, 1e-05, 1e-07),
maxiter = 1000 * round((1.25)^length(idparsopt)),
methode = "lsodes",
optimmethod = "subplex",
CS_version = 1,
verbose = 0,
tolint = c(1e-16, 1e-10),
island_ontogeny = NA
)
|
datalist |
Data object containing information on colonisation and
branching times. This object can be generated using the DAISIE_dataprep
function, which converts a user-specified data table into a data object, but
the object can of course also be entered directly. It is an R list object
with the following elements. |
initparsopt |
The initial values of the parameters that must be optimized, they are all positive. |
idparsopt |
The ids of the parameters that must be optimized. The ids
are defined as follows: |
parsfix |
The values of the parameters that should not be optimized. |
idparsfix |
The ids of the parameters that should not be optimized, e.g. c(1,3) if lambda^c and K should not be optimized. |
idparsnoshift |
For datatype = 'single' only: The ids of the parameters that should not be different between two groups of species; This can only apply to ids 6:10, e.g. idparsnoshift = c(6,7) means that lambda^c and mu have the same values for both groups. |
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: |
cond |
cond = 0 : conditioning on island age |
eqmodel |
Sets the equilibrium constraint that can be used during the
likelihood optimization. Only available for datatype = 'single'. |
x_E |
Sets the fraction of the equlibrium endemic diversity above which the endemics are assumed to be in equilibrium; only active for eqmodel = 13 or 15. |
x_I |
Sets the fraction of the equlibrium non-endemic diversity above which the system is assumed to be in equilibrium; only active for eqmodel = 15. |
tol |
Sets the tolerances in the optimization. Consists of: |
maxiter |
Sets the maximum number of iterations in the optimization. |
methode |
Method of the ODE-solver. See package deSolve for details. Default is "lsodes". |
optimmethod |
Method used in likelihood optimization. Default is "subplex" (see subplex package). Alternative is 'simplex' which was the method in previous versions. |
CS_version |
For internal testing purposes only. Default is 1, the original DAISIE code. |
verbose |
In simulation and dataprep functions a logical,
|
tolint |
Vector of two elements containing the absolute and relative tolerance of the integration. |
island_ontogeny |
In |
The output is a dataframe containing estimated parameters and maximum loglikelihood.
lambda_c |
gives the maximum likelihood estimate of lambda^c, the rate of cladogenesis |
mu |
gives the maximum likelihood estimate of mu, the extinction rate |
K |
gives the maximum likelihood estimate of K, the carrying-capacity |
gamma |
gives the maximum likelihood estimate of gamma, the immigration rate |
lambda_a |
gives the maximum likelihood estimate of lambda^a, the rate of anagenesis |
loglik |
gives the maximum loglikelihood |
df |
gives the number of estimated parameters, i.e. degrees of feedom |
conv |
gives a message on convergence of optimization; conv = 0 means convergence |
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