optimPaleo function

Simplified Optimizer for paleotree Likelihood Functions

This function is a deliberately simplistic automation wrapper for the function optim and the use of the "L-BFGS-B" optimizing method, with initial parameter values and bounds provided with parInit, parLower and parUpper. It is mainly provided here as a shorthand to be used in educational demonstrations where model-fitting is not the primary focus, and use in actual analyses should be avoided.

optimPaleo(modelFun)

Arguments

• modelFun: A likelihood function for a model, of class paleotreeFunc.

Returns

Returns the results from using optim.

Details

This is mainly provided in this publicly released package for pedagogical reasons. Users seeking an optimizer for their own analytical purposes should write their own optim function.

Examples

# This function simply replicates optim() as shown below
    # where modelFun is the likelihood function

#optim(parInit(modelFun),modelFun,
#               lower = parLower(modelFun),upper = parUpper(modelFun), 
#               method = "L-BFGS-B",control = list(maxit = 1000000))

See Also

constrainParPaleo and modelMethods