| convratsig {convevol} | R Documentation |
Tests the signifiance of convergent evolution by the ratio of the current to maximum past phenotypic distance
Description
convratsig tests the significance of convergence (as quantified by convrat) using evolutionary simulations.
Usage
convratsig(phyl, phendata, convtips, nsim)
Arguments
phyl |
The phylogeny of interest in phylo format |
phendata |
Phenotypic data for all tips |
convtips |
A list consisting of the names of all convergent taxa |
nsim |
The number of simulations to conduct |
Details
The function simulates evolution via Brownian motion using the input tree and parameters derived from the observed data. It calculates a convergence metric for each simulation and calculates statistics from the number of times the simulated value exceeds the observed value.
Value
The convergence metric of interest (C1, C2, etc...), a cutoff value (the value that the observed measure would have to exceed in order to be considered significant), a P-value for the statistic, and all simulated values.
References
Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R langauge. Bioinformatics, 20, 289-290.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3 217-223.
Examples
phyl<-rtree(10)
phendata<-fastBM(phyl,nsim=2)
convtips<-c("t1","t2","t3")
answer<-convratsig(phyl,phendata,convtips,10)