optimPaleo: Simplified Optimizer for 'paleotree' Likelihood Functions

In paleotree: Paleontological and Phylogenetic Analyses of Evolution

Simplified Optimizer for paleotree Likelihood Functions

Description

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.

Usage

optimPaleo(modelFun)

Arguments

modelFun

A likelihood function for a model, of class paleotreeFunc.

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.

Value

Returns the results from using optim.

See Also

constrainParPaleo and modelMethods

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))

paleotree documentation built on Aug. 22, 2022, 9:09 a.m.