Description Usage Arguments Details Value Author(s) References See Also

This function computes the maximum likelihood estimates of the parameters of the DAISIE model with island-wide diversity-dependence for data from lineages colonizing an island. It also outputs the corresponding loglikelihood that can be used in model comparisons.

1 2 3 4 | ```
DAISIE_ML_IW(datalist, initparsopt, idparsopt, parsfix, idparsfix,
res = 100, ddmodel = 11, cond = 0, tol = c(1e-04, 1e-05, 1e-07),
maxiter = 1000 * round((1.25)^length(idparsopt)), methode = "ode45",
optimmethod = "subplex", verbose = 0, tolint = c(1e-16, 1e-14))
``` |

`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 |

`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. |

`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 |

`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. |

`verbose` |
Specifies whether intermediate output should be provided, because optimizationmay take long. Default is 0, no output. A value of 1 means the parameters and loglikelihood are printed. A value of 2 means also intermediate progress during loglikelihood computation is shown. |

`tolint` |
Vector of two elements containing the absolute and relative tolerance of the integration |

The result of sort(c(idparsopt, idparsfix)) should be identical to c(1:5).
If not, an error is reported that the input is incoherent. The same happens
when the length of initparsopt is different from the length of idparsopt,
and the length of parsfix is different from the length of idparsfix.

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 |

Rampal S. Etienne

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. <DOI:10.1111/ele.12461>.

`DAISIE_loglik_IW`

, `DAISIE_ML_CS`

`DAISIE_sim`

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