calcCsCt Computes Ct values for a pair of tips. Internal, called in calcConv.
calcCsCt(
tips,
ancList,
allDists,
phy,
VERBOSE = FALSE,
allVals,
edge,
lim.height = NULL
)A list of the Ct values
vector of two tips
list of node paths for all tips in the user provided phylogeny
matrix of phenotypic distances between all exterior and interior node pairs
The time calibrated phylogeny of interest in phylo format
logical value indicating whether model information should be printed during computation
a matrix of observed and reconstructed phenotypes for all user supplied traits at interior and exterior nodes
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
an optional tree height used to limit Dmax.t, passed only if groups are defined and a conservative test is run (see calcConv)
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
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.