calc_loglike_for_optim_stratified: Take model parameters and the data and calculate the...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_stratified_v1.R

This is the stratified version of calc_loglike_for_optim. This function is an input to optim or optimx, the ML estimation routines.

  calc_loglike_for_optim_stratified(params,
    BioGeoBEARS_run_object, phy,
    tip_condlikes_of_data_on_each_state,
    print_optim = TRUE, areas_list, states_list,
    force_sparse = FALSE, cluster_already_open = FALSE)

`params`	A vector of parameters for optimization.
`BioGeoBEARS_run_object`	Object containing the run parameters, and the model.
`phy`	An ape tree object
`tip_condlikes_of_data_on_each_state`	Conditional likelihoods at tips. A numeric matrix with rows representing tips, and columns representing states/geographic ranges. The cells give the likelihood of the observation data under the assumption that the tip has that state; typically this means that the known geographic range gets a '1' and all other states get a 0.
`print_optim`	If TRUE (default), print the optimization steps as ML estimation progresses.
`areas_list`	A list of the desired area names/abbreviations/letters (?).
`states_list`	A list of the possible states/geographic ranges, in 0-based index form.
`force_sparse`	Should sparse matrix exponentiation be used? Default `FALSE`.
`cluster_already_open`	The cluster object, if it has already been started.

ttl_loglike The log-likelihood of the data under the input model and parameters.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

convolve chainsaw_result

test=1

Loading required package: rexpokit
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Rcpp
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges