optimPaleo

This function is a deliberately simplistic automation wrapper for the function
<code><a href="/link/optim?package=paleotree&version=3.4.7" data-mini-rdoc="paleotree::optim">optim</a></code> and the use of the <code>"L-BFGS-B"</code> optimizing method,
with initial parameter values and bounds provided with <code>parInit</code>,
<code>parLower</code> and <code>parUpper</code>. 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.

Provides tools for transforming, a posteriori time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of
fossil taxa using stratigraphic data. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.

David Bapst

paleotree

Paleontological and Phylogenetic Analyses of Evolution

optimPaleo function

<dl><dt>modelFun</dt>
<dd>A likelihood function for a model, of class <code>paleotreeFunc</code>.</dd></dl>

Arguments

This function is a deliberately simplistic automation wrapper for the function
<code><a href='https://rdrr.io/r/stats/optim.html'>optim</a></code> and the use of the <code>"L-BFGS-B"</code> optimizing method,
with initial parameter values and bounds provided with <code>parInit</code>,
<code>parLower</code> and <code>parUpper</code>. 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.

Simplified Optimizer for paleotree Likelihood Functions — optimPaleo

<dl>

<dt>modelFun</dt>
<dd>A likelihood function for a model, of class <code>paleotreeFunc</code>.</dd>

</dl>

optimPaleo: Simplified Optimizer for `paleotree` Likelihood Functions

Description

Usage

Value

Arguments

Details

See Also

Examples