convSig | R Documentation |
convSig calculates the significance of measures of convergent evolution.
convSig(phy, traits, focaltaxa, nsim = 1000)
phy |
The phylogeny of interest in phylo format |
traits |
Phenotypic data for all tips |
focaltaxa |
A list consisting of the names of all putatively convergent taxa |
nsim |
The number of simulations to use to assess significance |
This script simulates data according to a Brownian motion model of evolution, and then assesses convergene on that simulated data. The number of times that the simulated data produces greater convergence than that observed in the empirical data is used to calculate a P-value.
C1-C4 convergence measures for all pairs of putatively convergent taxa and their associated p-values.
Stayton, C.T. 2015. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence. Evolution 69:2140-2453.
Zelditch, M.L., J. Ye, J.S. Mitchell, and D.L. Swiderski. 2017. Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae). Evolution 71:633-649.
phy<-rtree(100)
traits<-fastBM(phy,nsim=3)
focaltaxa<-c("t1","t50","t100")
answer<-convSig(phy,traits,focaltaxa,nsim=10)
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