supportRegionHiSSE: Adaptive Sampling of the Likelihood Surface under the new...

In hisse: Hidden State Speciation and Extinction

Adaptive Sampling of the Likelihood Surface under the new version of HiSSE

Description

Adaptively samples points for each parameter to obtain an estimate of the confidence intervals.

Usage

SupportRegionHiSSE(hisse.obj, n.points=1000, scale.int=0.1, desired.delta=2, 
min.number.points=10, verbose=TRUE)

Arguments

hisse.obj	an object of class hisse.fit that contains the MLE from a model run.
n.points	indicates the number of points to sample.
scale.int	the scaling multiplier that defines interval to randomly sample. By default the value is set to 0.1, meaning that values are drawn at random along an interval that encompasses 10 percent above and below the MLE.
desired.delta	defines the number lnL units away from the MLE to include. By default the value is set to 2.
min.number.points	sets the minimum number of points that can be returned. By default the value is set to 10.
verbose	a logical indicating whether progress should be printed to the screen. The default is TRUE.

Details

This is the support region estimator for the new version of hisse.

Note the scale.int option. This roughly sets the variance for sampling points. If this seems to take a long while to find enough points within the desired likelihood region consider reducing scale.int to either 0.05 or, in some cases, 0.01.

Value

SupportRegionHiSSE returns an object of class hisse.support. This is a list with elements:

$ci	the sampled confidence interval.
$points.within.region	the sampled points that within 2lnL units from the MLE.
$all.points	all points sampled by the adaptive sampler.

Author(s)

Jeremy M. Beaulieu

References

Beaulieu, J.M, and B.C. O'Meara. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65:583-601.

FitzJohn R.G., Maddison W.P., and Otto S.P. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58:595-611.

Maddison W.P., Midford P.E., and Otto S.P. 2007. Estimating a binary characters effect on speciation and extinction. Syst. Biol. 56:701-710.

Nee S., May R.M., and Harvey P.H. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344:305-311.

hisse documentation built on Feb. 16, 2023, 10:26 p.m.