gmyc.support: Calculating AIC-based support values for the GMYC clusters

Description Usage Arguments Details Value Author(s) References Examples

Description

This function calculates support values of species clusters delmited by the GMYC function using information-theoretic multimodel inference.

Usage

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gmyc.support(object, p=0.95)
confset.gmyc(object, p=0.95)

Arguments

object

a gmyc object obtained by gmyc

p

level of confidence. models within p% confidence set are used to calculate support values

Details

The function gmyc.support calculates support values of the GMYC-delimited species by using the multimodel comparison approach described by Burnham & Anderson (2002). The support value of a node is defined as the sum of Akaike weights of candidate delimitation models in which the node is included. Only models included in the p% confidence set obtained by confset.gmyc are used for calculation. See reference papers for further details.

Value

gmyc.support returns a vector containing GMYC support values for tree nodes. Support values are ordered following the node order of input tree. confset.gmyc returns a gmyc object which contains models within p%confidence set.

Author(s)

Tomochika Fujisawa [email protected]

References

Fujisawa, T. & Barraclough, TG. in press. Delimiting species using single-locus data and the generalized mixed Yule coalescent (GMYC) approach: A revised method and evaluation on simulated datasets. Systematic Biology.

Model selection and multimodel inference: A practical information-theoritic approach. 2nd ed. 2002. Springer Science. New York, USA.

Examples

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data(test.tr)
test <- gmyc(test.tr, method="single")
nsup <- gmyc.support(test)

#plot support values on tree
plot(test)
nsup[nsup==0] <- NA
nodelabels(round(nsup, 2), cex=0.6, frame="n", adj=1)

#how many models within the confidence set?
cs <- confset.gmyc(test)
length(cs$MRCA)

splits documentation built on May 31, 2017, 1:45 a.m.