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getRates_modified_Etka_Yapar.R
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getRates_modified_Etka_Yapar.R
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getrates_ey <- function(tree, bins, maps, type, log=F, uncert="confint") {
isNumberInRange <- function(number, rng){
if(number <= rng[2] & number > rng[1]){
return(TRUE)
}
return(FALSE)
}
if (type == "all"){
changes<-countchanges(tree, maps)
} else {
changes<-countchanges(tree, maps)
changes<-parsetypes(changes, type)
}
h<-max(nodeHeights(tree))
b<-bins
segs<-cbind(seq(0,h-h/b,h/b), seq(1/b*h,h,h/b))
#compute the mean number of sampled changes for each segment
subset_segments <- apply(segs, 1, function(rng){
changes_this_range_this_type <- sapply(changes, function(sm){
if(nrow(sm) == 0){
return(0)
}
inThisRange <- sapply(sm[,1], function(number){
isNumberInRange(number, rng)
})
result = sum(inThisRange)
return(result)
})
N <- length(maps)
avg <- sum(changes_this_range_this_type) / N
if(uncert == "confint"){
se <- sd(changes_this_range_this_type) / sqrt(N)
upper <- avg + 2*se
lower <- avg - 2*se
return(c(avg, lower, upper))
}
if(uncert == "quantile"){
return(c(avg, quantile(changes_this_range_this_type, c(0.25, 0.75))))
}
})
subset_segments <- t(subset_segments)
colnames(subset_segments) <- c("mean", "lwr", "upr")
nchanges <- subset_segments[,"mean"]
lchanges <- subset_segments[,"lwr"]
uchanges <- subset_segments[,"upr"]
#print("accounting for LTT")
#control for the total edge length present in a segment using LTT computation
LTT<-ltt(tree,plot=FALSE)
LTT<-cbind(LTT$ltt[2:(length(LTT$ltt)-1)],
LTT$times[2:(length(LTT$ltt)-1)],
LTT$times[3:length(LTT$ltt)])
ii<-1
edge.length<-rep(0,b)
#print(segs)
for(i in 1:nrow(segs)){
done.seg<-FALSE
while(LTT[ii,2]<=segs[i,2]&&done.seg==FALSE){
edge.length[i]<-edge.length[i]+
LTT[ii,1]*(min(segs[i,2],LTT[ii,3])-
max(segs[i,1],LTT[ii,2]))
if(LTT[ii,3]>=segs[i,2]) done.seg<-TRUE
if(LTT[ii,3]<=segs[i,2]) ii<-if(ii<nrow(LTT)) ii+1 else ii
}
}
#print bins thru time
timesegs<-h-as.vector(t(segs))
if(log==T) {
magnitude<-rbind(nchanges/log(edge.length),nchanges/log(edge.length))
lmagnitude<-rbind(lchanges/log(edge.length),lchanges/log(edge.length))
umagnitude<-rbind(uchanges/log(edge.length),uchanges/log(edge.length))
} else {
magnitude<-rbind(nchanges/edge.length,nchanges/edge.length)
lmagnitude<-rbind(lchanges/edge.length,lchanges/edge.length)
umagnitude<-rbind(uchanges/edge.length,uchanges/edge.length)
}
out<-list()
out[[1]]<-segs
out[[2]]<-timesegs
out[[3]]<-magnitude
out[[4]]<-type
out[[5]]<-lmagnitude
out[[6]]<-umagnitude
names(out)<-c("segs", "timesegs", "magnitude", "type", "mag.lwr", "mag.upr")
return(out)
}
rateplot_ey <- function(rates, tree, ylim, spline,color, width, lty, alpha, confint=F){
if (spline == T) {
smoothed <- smooth.spline(x=jitter(rates$timesegs, factor=0.1), y=rates$magnitude, cv=T)
newx<- seq(from = max(rates$timesegs), to=0, length.out = 100)
pred<-predict(smoothed, x = newx)
#print(c(max(rates$segs), min(rates$segs)))
plot(x=newx, y=pred$y,
lwd=width, type='l',
xlim=c(max(rates$segs), min(rates$segs)),
ylab="mean number of changes / total edge length",
xlab="time since the present",
#main=rates$type,
ylim,
col=color,
lty=lty)
if(confint ==T){
midtimepoints <- apply(rates$segs, 1, function(x){
return(x[1] + ((x[2] - x[1])/2) )
})
midtimepoints <- rev(midtimepoints)
midtimepoints <- jitter(midtimepoints, factor=0.2)
points(midtimepoints, rates$magnitude[1,], col=color)
segments(midtimepoints, rates$mag.lwr[1,], midtimepoints, rates$mag.upr[1,], col=color)
}
} else {
plot(rates$timesegs, rates$magnitude,
lwd=width, type="l",
xlim=c(max(rates$segs), min(rates$segs)),
lend=0,xlab="time since the present",
ylab="mean number of changes / total edge length",
#main=rates$type,
ylim)
}
plotTree(tree,add=TRUE,ftype="off",lwd=1,color=make.transparent("grey", alpha),
mar=par()$mar,direction="leftwards",xlim=c(max(rates$segs),min(rates$segs)))
#abline(v=66, col="red", lwd=2)
}
segplot_ey <-function(rates, ylim, color, spline, width, ax=T, lty,
y.lab="mean number of changes / total edge length", x.lab="time since the present", confint=F) {
if (spline == T) {
smoothed <- smooth.spline(x=jitter(rates$timesegs, factor=0.1), y=rates$magnitude, cv=T)
newx<- seq(from = max(rates$timesegs), to=0, length.out = 100)
pred<-predict(smoothed, x = newx)
plot(x=newx, y=pred$y,
lwd=width, type='l',
xlim=c(max(rates$segs), min(rates$segs)),
ylab=y.lab,
xlab=x.lab,
#main=rates$type,
ylim,
col=color,
axes=ax,
lty=lty)
if(confint == T){
midtimepoints <- apply(rates$segs, 1, function(x){
return(x[1] + ((x[2] - x[1])/2) )
})
midtimepoints <- rev(midtimepoints)
midtimepoints <- jitter(midtimepoints, factor=0.2)
points(midtimepoints, rates$magnitude[1,], col=color)
segments(midtimepoints, rates$mag.lwr[1,], midtimepoints, rates$mag.upr[1,], col=color)
}
} else {
plot(rates$timesegs, rates$magnitude,
lwd=width, type="l",
xlim=c(max(rates$segs), min(rates$segs)),
lend=0,xlab="time since the present",
ylab="mean number of changes / total edge length",
#main=rates$type,
ylim,
col=color,
axes=ax)
}
}