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

This function computes the maximum likelihood estimates of the parameters of the relationships between parameters of the DAISIE model with clade-specific diversity-dependence and island area and distance of the island to the mainlandor nearest landmass, for data from lineages colonizing several islands/archipelagos. It also outputs the corresponding loglikelihood that can be used in model comparisons.

A note on the sigmoidal functions used in distance_dep: For anagenesis and cladogenesis, the functional relationship is k * (d/d0)^x/(1 + (d/d0)^x); for colonization the relationship is: k - k * (d/d0)^x/(1 + (d/d0)^x). The d0 parameter is the 11th parameter entered. In the of 'sigmoidal_col_ana', the 11th parameter is the d0 for colonization and the 12th is the d0 for anagenesis.

1 2 3 4 5 6 7 | ```
DAISIE_MW_ML(datalist, initparsopt, idparsopt, parsfix, idparsfix,
res = 100, ddmodel = 11, cond = 0, island_ontogeny = NA,
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), distance_type = "continent",
distance_dep = "power", parallel = "local", cpus = 3)
``` |

`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. |

`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 |

`island_ontogeny` |
type of island ontonogeny. If NA, then constant ontogeny is assumed |

`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` |
sets whether parameters and likelihood should be printed (1) or not (0) |

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

`distance_type` |
Use 'continent' if the distance to the continent should be used, use 'nearest_big' if the distance to the nearest big landmass should be used, and use 'biologically_realistic' if the distance should take into account some biologically realism, e.g. an average of the previous two if both are thought to contribute. |

`distance_dep` |
Sets what type of distance dependence should be used. Default is a power law, denoted as 'power'. Alternatives are an exponantial relationship denoted by 'exp' or sigmoids, either 'sigmoidal_col' for a sigmoid in the colonization, 'sigmoidal_ana' for sigmoidal anagenesis, 'sigmoidal_clado' for sigmoidal cladogenesis, and 'sigmoidal_col_ana' for signoids in both colonization and anagenesis. |

`parallel` |
Sets whether parallel computation should be used. Use 'no' if no parallel computing should be used, 'cluster' for parallel computing on a unix/linux cluster, and 'local' for parallel computation on a local machine. |

`cpus` |
Number of cpus used in parallel computing. Default is 3. Will not have an effect if parallel = 'no'. |

The output is a dataframe containing estimated parameters and maximum loglikelihood.

`lambda_c0` |
gives the maximum likelihood estimate of lambda^c, the rate of cladogenesis for unit area |

`y` |
gives the maximum likelihood estimate of y, the exponent of area for the rate of cladogenesis |

`mu0` |
gives the maximum likelihood estimate of mu0, the extinction rate |

`x` |
gives the maximum likelihood estimate of x, the exponent of 1/area for the extinction rate |

`K0` |
gives the maximum likelihood estimate of K0, the carrying-capacity for unit area |

`z` |
gives the maximum likelihood estimate of z, the exponent of area for the carrying capacity |

`gamma0` |
gives the maximum likelihood estimate of gamma0, the immigration rate for unit distance |

`y` |
gives the maximum likelihood estimate of alpha, the exponent of 1/distance for the rate of colonization |

`lambda_a0` |
gives the maximum likelihood estimate of lambda^a0, the rate of anagenesis for unit distance |

`beta` |
gives the maximum likelihood estimate of beta, the exponent of 1/distance for 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>.

1 | ```
cat('No examples')
``` |

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