convratsig: Tests the signifiance of convergent evolution by the ratio of...

Description Usage Arguments Details Value References Examples

View source: R/convratsig.R

Description

convratsig tests the significance of convergence (as quantified by convrat) using evolutionary simulations.

Usage

1
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

1
2
3
4
phyl<-rtree(10)
phendata<-fastBM(phyl,nsim=2)
convtips<-c("t1","t2","t3")
answer<-convratsig(phyl,phendata,convtips,10)

convevol documentation built on May 2, 2019, 6:53 a.m.