gmyc.support {splits} | R Documentation |
This function calculates support values of species clusters delmited by the GMYC function using information-theoretic multimodel inference.
gmyc.support(object, p=0.95) confset.gmyc(object, p=0.95)
object |
a gmyc object obtained by gmyc |
p |
level of confidence. models within p% confidence set are used to calculate support values |
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.
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.
Tomochika Fujisawa t.fujisawa05@gmail.com
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.
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)