calcCsCt: Computes Ct values for a pair of tips. Internal, called in...
In convevol: Analysis of Convergent Evolution

calcCsCt

R Documentation

Computes Ct values for a pair of tips. Internal, called in calcConv.

Description

calcCsCt Computes Ct values for a pair of tips. Internal, called in calcConv.

Usage

calcCsCt(
  tips,
  ancList,
  allDists,
  phy,
  VERBOSE = FALSE,
  allVals,
  edge,
  lim.height = NULL
)

Arguments

`tips`	vector of two tips
`ancList`	list of node paths for all tips in the user provided phylogeny
`allDists`	matrix of phenotypic distances between all exterior and interior node pairs
`phy`	The time calibrated phylogeny of interest in phylo format
`VERBOSE`	logical value indicating whether model information should be printed during computation
`allVals`	a matrix of observed and reconstructed phenotypes for all user supplied traits at interior and exterior nodes
`edge`	a list of data frames, each including the edge matrix of user supplied phylogeny, along with node heights and reconstructed phenotype for each of the user supplied traits
`lim.height`	an optional tree height used to limit Dmax.t, passed only if groups are defined and a conservative test is run (see calcConv)

Details

Function incorporates the optimizations introduced by Zelditch et al. (2017), which significantly improve runtimes

Reconstructions part way along branches are obtained using equation [2] of Felsenstein (1985), following code modified from the phytools (Revell, 2012) function contMap

Value

A list of the Ct values

References

Grossnickle DM, Brightly WH, Weaver LN, Stanchak KE, Roston RA, Pevsner SK, Stayton CT, Polly PD, Law CJ. 2022. A cautionary note on quantitative measures of phenotypic convergence. in revision Zelditch ML, Ye J, Mitchell JS, Swiderski DL. 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 Stayton CT. 2015. The definition, recognition, and interpretation of convergent evolution and two new measures for quantifying and assessing the significance of convergence. Evolution 69(8): 2140-2153. Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223. Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125, 1-15.

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