convevol (version 2.2.1)

plot2D: Plots calcConv or convSig output as a two-dimensional time series.

Description

plot2D Plots calcConv or convSig output as a two-dimensional time series.

Usage

plot2D(
  Ct,
  phy,
  tip,
  foc.trt,
  trait,
  pca = FALSE,
  save = FALSE,
  filename = "frame",
  dir = NULL,
  leg = FALSE,
  leg.pos = "topleft",
  width = 480,
  height = 480,
  ...
)

Value

Plots tracking putatively convergent taxa in two-dimensional morphospace through time

A table with trait values, morphospace distance, and nodeheights conincident with Dmax.t. See meas.path output from calcConvCt and convSigCt

Arguments

Ct

object containing calcConvCt or convSigCt output

phy

The time calibrated phylogeny of interest in phylo format

tip

vector of two tip labels indicating the putatively convergent taxa to be plotted in morphospace

foc.trt

vector of two traits to be used in plotting. If pca == TRUE this should indicate which PC axes should be plotted in format "PC1"

trait

the matrix of trait values used to compute Ct

pca

logical value indicating whether to conduct principal component analysis and plot PC scores instead of raw trait values

save

logical value indicating whether an animated time series (along with individual time slices) should be saved to a user specified folder

filename

character indicating the desired prefix for filenames to be saved

dir

optional character indicating the folderpath of the desired save location

leg

logical value indicating whether a legend should be added to plots

leg.pos

character indicating the position of the legend

width

pixel width of saved png files

height

pixel height of saved png files

...

optional arguments to be passed to plot

Details

None

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.

Examples

if (FALSE) {
library(phytools)
library(geiger)

# create time calibrated tree
mytree<-rtree(100)
mycalibration <- makeChronosCalib(mytree, node="root", age.max=50)
phy <- chronos(mytree, lambda = 1, model = "correlated", 
calibration = mycalibration, control = chronos.control() )
class(phy)<-"phylo"

# create three normally distributed phenotypic traits
traits <- cbind(rnorm(Ntip(phy)),rnorm(Ntip(phy)),rnorm(Ntip(phy)))
colnames(traits) <- c("V1","V2","V3")
rownames(traits) <- phy$tip.label

#	select two random tips, excluding sister taxa
pairs <- apply(combn(phy$tip.label,2),2,function(x) nodepath(phy,
which(phy$tip.label == x[1]),which(phy$tip.label == x[2])))
nosis <- combn(phy$tip.label,2)[,unlist(lapply(pairs, function(x) length(x) > 3))]
focaltaxa <- nosis[,sample(1:ncol(nosis),1)]

system.time(run <- calcConvCt(phy, traits, focaltaxa))
system.time(run2 <- convSigCt(phy, traits, focaltaxa, nsim=100))

plot2D(run, phy, focaltaxa[1:2], colnames(traits)[1:2], traits)
}