Wednesday, December 6, 2017

Pybus & Harvey's γ through time

A phytools user today contacted me to ask about an evident discrepancy between an LTT plot (which on average seemed to be curved upward), and a calculated value of Pybus & Harvey's (2000) γ statistic (which was nonsignificant but negative). Visually, to me it seemed that this was most likely explained by a notable slightly negative curvature of the LTT plot towards the present day where there are many more internode distances. However, it also occurred to me that we can easily plot γ through time as well, and this might help us to see what parts of our plot are influencial in the measured value of γ.

Note that this assumes a pure-birth process of lineage accumulation through time. If we have extinction (which, in general, should result in positive γ), we need the 'pull of the present' to detect it, and by slicing of the end of our tree in computing γ we might find a value close to zero rather than positive!

Here are our functions:

gtt<-function(tree,n=100,...){
    if(hasArg(plot)) plot<-list(...)$plot
    else plot<-FALSE
    obj<-ltt(tree,plot=FALSE)
    t<-obj$times[which(obj$ltt==3)[1]]
    h<-max(nodeHeights(tree))
    x<-seq(t,h,by=(h-t)/(n-1))
    trees<-lapply(x,treeSlice,tree=tree,orientation="rootwards")
    gamma<-sapply(trees,function(x,plot){ 
        obj<-unlist(gammatest(ltt<-ltt(x,plot=FALSE)));
        if(plot) plot(ltt,xlim=c(0,h),ylim=c(1,Ntip(tree)),
            log.lineages=FALSE,log="y");
        Sys.sleep(0.01);
        obj},plot=plot)
    object<-list(t=x,gamma=gamma[1,],p=gamma[2,],tree=tree)
    class(object)<-"gtt"
    object
}
## plot method
plot.gtt<-function(x,...){
    args<-list(...)
    args$x<-x$t
    args$y<-x$gamma
    if(!is.null(args$show.tree)){ 
        show.tree<-args$show.tree
        args$show.tree<-NULL
    } else show.tree<-TRUE
    if(is.null(args$xlim)) args$xlim<-c(0,max(x$t))
    if(is.null(args$xlab)) args$xlab<-"time"
    if(is.null(args$ylab)) args$ylab<-expression(gamma)
    if(is.null(args$lwd)) args$lwd<-3
    if(is.null(args$type)) args$type<-"s"
    do.call(plot,args)
    if(show.tree) plotTree(x$tree,add=TRUE,ftype="off",mar=par()$mar,
        xlim=args$xlim,color=make.transparent("blue",0.1))
}
print.gtt<-function(x,...)
    cat("Object of class \"gtt\".\n\n")

Let's try it with a simulated tree:

library(phytools)
tree
## 
## Phylogenetic tree with 500 tips and 499 internal nodes.
## 
## Tip labels:
##  t106, t107, t97, t451, t452, t75, ...
## 
## Rooted; includes branch lengths.
object<-gtt(tree)
object
## Object of class "gtt".
plot(object)

plot of chunk unnamed-chunk-2

Note that since our intervals are evenly spaced, rather than linked to events on the tree, the choice of a 'step' line plot is purely cosmetic and I could've also used straight lines:

plot(object,type="l")

plot of chunk unnamed-chunk-3

The function gtt has an option plot=TRUE that will create an animation of the LTT plot for the tree. Something like this:

object<-gtt(tree,plot=TRUE)

The .gif was generated in R using ImageMagick as follows:

png(file="gtt-%03d.png",width=600,height=600)
object<-gtt(tree,plot=TRUE)
dev.off()
system("ImageMagick convert -delay 10 -loop 0 *.png gtt-anim.gif")
file.remove(list.files(pattern=".png"))

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