lrttest: Calculate Likelihood Ratio Test (LRT)
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_generics_v1.R

The Likelihood Ratio Test (LRT) is a standard method for testing whether or not the data likelihood conferred by a more complex is significantly better than the data likelihood conferred by the simpler model, given a certain number of extra free parameters for the complex model. The null hypothesis is that there is no difference; rejection means that there is a statistically significant improvement in the more complex model.

1 2	lrttest(LnL_1, LnL_2, numparams1, numparams2, returnwhat = "pval")

`LnL_1`	Log-likelihood of more complex model.
`LnL_2`	Log-likelihood of simpler complex model.
`numparams1`	Number of free parameters of the more complex model.
`numparams2`	Number of free parameters of the less complex model.
`returnwhat`	If "pval", just return the p-value. If "all", return all of the intermediate outputs.

The LRT only works for situations in which the simpler model is nested within the more complex model (i.e., by taking some parameters of the more complex model and forcing them to be fixed to a specific value). In addition, the LRT may be unreliable in data-poor situations, and inherits whatever difficulties there may be in ML searches. See Burnham et al. (2002) for discussion.

This function assumes that LnL_1 and numparams1 refer to the more complex model, and that LnL_2 and numparams2 refer to the simpler model nested within the more complex one.

pval or LRT_result2. Depends on returnwhat.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Burnham_Anderson_2002

Matzke_2012_IBS

lrttest_on_summary_table

test=1

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