calcCsCt {convevol}

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.