calcConv: Quantifies convergent evolution by the ratio of the current...

In convevol: Analysis of Convergent Evolution

Quantifies convergent evolution by the ratio of the current to maximum past phenotypic distance between two or more lineages, as described in Stayton (2015). Code written by Jonathan S. Mitchell for Zelditch et al. (2017).

Description

calcConv prepares arguements for the CalcCs function

Usage

calcConv(phy, traits, focaltaxa, VERBOSE = FALSE)

Arguments

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
VERBOSE	Whether or not to print progress

Details

calcConv is a wrapper function which formats data, performs ancestral state reconstructions, obtains distance matrices, and determines pairwise combinations of focal taxa, which are then used as arguements for the CalcCs function, which calculates values for C1-C4 of Stayton (2015) for each pair of putatively convergent taxa.

Value

C1-C4 convergence measures for all pairs of putatively convergent taxa.

References

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.

Examples

phy<-rtree(100)
traits<-fastBM(phy,nsim=3)
focaltaxa<-c("t1","t50","t100")
answer<-calcConv(phy,traits,focaltaxa,VERBOSE=FALSE)

convevol documentation built on July 9, 2023, 5:07 p.m.