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 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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 |
In |
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. |
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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