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utilities.R
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utilities.R
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## some utility functions
## written by Liam J. Revell 2011, 2012, 2013, 2014, 2015, 2016, 2017
## function to expand clades in a plot by a given factor
## written by Liam J. Revell 2017
expand.clade<-function(tree,node,factor=5){
cw<-reorder(tree)
tips<-setNames(rep(1,Ntip(tree)),cw$tip.label)
get.tips<-function(node,tree){
dd<-getDescendants(tree,node)
tree$tip.label[dd[dd<=Ntip(tree)]]
}
desc<-unlist(lapply(node,get.tips,tree=cw))
for(i in 2:Ntip(cw)){
tips[i]<-tips[i-1]+
if(names(tips)[i]%in%desc){
1
} else if(names(tips)[i-1]%in%desc){
1
} else 1/factor
}
obj<-list(tree=tree,tips=tips)
class(obj)<-"expand.clade"
obj
}
## S3 print method for the object class "expand.clade"
print.expand.clade<-function(x,...){
cat("An object of class \"expand.clade\" consisting of:\n")
cat(paste("(1) A phylogenetic tree (x$tree) with",Ntip(x$tree),
"tips and\n ",x$tree$Nnode,"internal nodes.\n"))
cat("(2) A vector (x$tips) containing the desired tip-spacing.\n\n")
}
## S3 plot method for the object class "expand.clade"
plot.expand.clade<-function(x,...){
args<-list(...)
args$tree<-x$tree
args$tips<-x$tips
if(inherits(args$tree,"simmap")) do.call(plotSimmap,args)
else do.call(plotTree,args)
}
## function to add a geological or other temporal legend to a plotted tree
## written by Liam J. Revell 2017
geo.legend<-function(leg=NULL,colors=NULL,alpha=0.2,...){
if(hasArg(cex)) cex<-list(...)$cex
else cex<-par()$cex
if(hasArg(plot)) plot<-list(...)$plot
else plot<-TRUE
if(hasArg(show.lines)) show.lines<-list(...)$show.lines
else show.lines<-TRUE
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(is.null(colors)){
colors<-setNames(c(
rgb(255,242,127,255,maxColorValue=255),
rgb(255,230,25,255,maxColorValue=255),
rgb(253,154,82,255,maxColorValue=255),
rgb(127,198,78,255,maxColorValue=255),
rgb(52,178,201,255,maxColorValue=255),
rgb(129,43,146,255,maxColorValue=255),
rgb(240,64,40,255,maxColorValue=255),
rgb(103,165,153,255,maxColorValue=255),
rgb(203,140,55,255,maxColorValue=255),
rgb(179,225,182,255,maxColorValue=255),
rgb(0,146,112,255,maxColorValue=255),
rgb(127,160,86,255,maxColorValue=255),
rgb(247,67,112,255,maxColorValue=255)),
c("Quaternary","Neogene","Paleogene",
"Cretaceous","Jurassic","Triassic",
"Permian","Carboniferous","Devonian",
"Silurian","Ordovician","Cambrian",
"Precambrian"))
}
if(is.null(leg)){
leg<-rbind(c(2.588,0),
c(23.03,2.588),
c(66.0,23.03),
c(145.0,66.0),
c(201.3,145.0),
c(252.17,201.3),
c(298.9,252.17),
c(358.9,298.9),
c(419.2,358.9),
c(443.8,419.2),
c(485.4,443.8),
c(541.0,485.4),
c(4600,541.0))
rownames(leg)<-c("Quaternary","Neogene","Paleogene",
"Cretaceous","Jurassic","Triassic",
"Permian","Carboniferous","Devonian",
"Silurian","Ordovician","Cambrian",
"Precambrian")
t.max<-max(obj$xx)
ii<-which(leg[,2]<=t.max)
leg<-leg[ii,]
leg[max(ii),1]<-t.max
}
colors<-sapply(colors,make.transparent,alpha=alpha)
if(plot){
y<-c(rep(0,2),rep(par()$usr[4],2))
ylabel<--1/25*obj$Ntip
for(i in 1:nrow(leg)){
strh<-strheight(rownames(leg)[i])
polygon(c(leg[i,1:2],leg[i,2:1]),y,
col=colors[rownames(leg)[i]],border=NA)
if(show.lines){
lines(x=rep(leg[i,1],2),y=c(0,par()$usr[4]),
lty="dotted",col="grey")
lines(x=c(leg[i,1],mean(leg[i,])-0.8*cex*
get.asp()*strheight(rownames(leg)[i])),
y=c(0,ylabel),lty="dotted",col="grey")
lines(x=c(leg[i,2],mean(leg[i,])+0.8*cex*
get.asp()*strheight(rownames(leg)[i])),
y=c(0,ylabel),lty="dotted",col="grey")
lines(x=rep(mean(leg[i,])-0.8*cex*
get.asp()*strheight(rownames(leg)[i]),2),
y=c(ylabel,par()$usr[3]),lty="dotted",col="grey")
lines(x=rep(mean(leg[i,])+0.8*cex*
get.asp()*strheight(rownames(leg)[i]),2),
y=c(ylabel,par()$usr[3]),lty="dotted",col="grey")
}
polygon(x=c(leg[i,1],
mean(leg[i,])-0.8*cex*get.asp()*strh,
mean(leg[i,])-0.8*cex*get.asp()*strh,
mean(leg[i,])+0.8*cex*get.asp()*strh,
mean(leg[i,])+0.8*cex*get.asp()*strh,
leg[i,2]),y=c(0,ylabel,par()$usr[3],
par()$usr[3],ylabel,0),
col=colors[rownames(leg)[i]],border=NA)
text(x=mean(leg[i,])+
if(obj$direction=="leftwards") 0.12*strh else -0.12*strh,
y=ylabel,labels=rownames(leg)[i],
srt=90,adj=c(1,0.5),cex=cex)
}
}
invisible(list(leg=leg,colors=colors))
}
## borrowed from mapplots
get.asp<-function(){
pin<-par("pin")
usr<-par("usr")
asp<-(pin[2]/(usr[4]-usr[3]))/(pin[1]/(usr[2]-usr[1]))
asp
}
round.polygon<-function(x,y,col="transparent"){
## just space holding for now
}
## draw a box around a clade
## written by Liam J. Revell 2017
cladebox<-function(tree,node,color=NULL,...){
if(is.null(color)) color<-make.transparent("yellow",0.2)
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
h<-max(nodeHeights(tree))
parent<-tree$edge[which(tree$edge[,2]==node),1]
x0<-max(c(obj$xx[node]+obj$xx[parent])/2,obj$xx[node]-0.05*h)
x1<-obj$x.lim[2]
dd<-getDescendants(tree,node)
y0<-min(range(obj$yy[dd]))-0.5
y1<-max(range(obj$yy[dd]))+0.5
polygon(c(x0,x1,x1,x0),c(y0,y0,y1,y1),col=color,
border=0)
}
## draw tip labels as linking lines to text
## written by Liam J. Revell 2017
linklabels<-function(text,tips,link.type=c("bent","curved","straight"),
...){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(!(lastPP$direction%in%c("leftwards","rightwards")))
stop("direction should be \"rightwards\" or \"leftwards\".")
if(hasArg(cex)) cex<-list(...)$cex
else cex<-1
if(hasArg(col)) col<-list(...)$col
else col<-"black"
if(hasArg(lty)) lty<-list(...)$lty
else lty<-"dashed"
if(hasArg(lwd)) lwd<-list(...)$lwd
else lwd<-1
if(hasArg(link.offset)) link.offset<-list(...)$link.offset
else link.offset<-0.1*max(lastPP$xx)
if(hasArg(font)) font<-list(...)$font
else font<-3
link.type<-link.type[1]
xpos<-lastPP$xx[tips]+strwidth("i")
ypos<-lastPP$yy[tips]
xmax<-rep(max(lastPP$xx),length(tips))+link.offset
ylab<-seq(min(lastPP$yy),max(lastPP$yy),
by=(max(lastPP$yy)-min(lastPP$yy))/(length(tips)-1))
ylab<-ylab[rank(ypos)]
text(xmax,ylab,gsub("_"," ",text),pos=4,font=font,cex=cex,
offset=0)
if(link.type=="curved"){
for(i in 1:length(tips))
drawCurve(c(xpos[i],xmax[i]),c(ypos[i],ylab[i]),
scale=0.05,lty=lty,col=col,lwd=lwd)
} else if(link.type=="bent"){
tipmax<-max(lastPP$xx)
for(i in 1:length(tips)){
ff<-strwidth("W")
segments(xpos[i],ypos[i],tipmax+link.offset/2,ypos[i],
lty=lty,col=col,lwd=lwd)
segments(tipmax+link.offset/2,ypos[i],tipmax+
link.offset/2+ff,ylab[i],lty=lty,col=col,lwd=lwd)
segments(tipmax+link.offset/2+ff,ylab[i],xmax[i],ylab[i],
lty=lty,col=col,lwd=lwd)
}
} else if(link.type=="straight")
segments(xpos,ypos,xmax,ylab,lty=lty,col=col)
}
## function forces a tree to be ultrametric using two different methods
## written by Liam J. Revell 2017
force.ultrametric<-function(tree,method=c("nnls","extend")){
method<-method[1]
if(method=="nnls") tree<-nnls.tree(cophenetic(tree),tree,
rooted=TRUE,trace=0)
else if(method=="extend"){
h<-diag(vcv(tree))
d<-max(h)-h
ii<-sapply(1:Ntip(tree),function(x,y) which(y==x),
y=tree$edge[,2])
tree$edge.length[ii]<-tree$edge.length[ii]+d
} else
cat("method not recognized: returning input tree\n\n")
tree
}
## function to create curved clade labels for a fan tree
## written by Liam J. Revell 2017
arc.cladelabels<-function(tree=NULL,text,node=NULL,ln.offset=1.02,
lab.offset=1.06,cex=1,orientation="curved",...){
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(obj$type!="fan") stop("method works only for type=\"fan\"")
h<-max(sqrt(obj$xx^2+obj$yy^2))
if(hasArg(mark.node)) mark.node<-list(...)$mark.node
else mark.node<-TRUE
if(hasArg(interactive)) interactive<-list(...)$interactive
else {
if(is.null(node)) interactive<-TRUE
else interactive<-TRUE
}
if(interactive) node<-getnode()
if(hasArg(lwd)) lwd<-list(...)$lwd
else lwd<-par()$lwd
if(hasArg(col)) col<-list(...)$col
else col<-par()$col
if(mark.node) points(obj$xx[node],obj$yy[node],pch=21,
bg="red")
if(is.null(tree)){
tree<-list(edge=obj$edge,tip.label=1:obj$Ntip,
Nnode=obj$Nnode)
class(tree)<-"phylo"
}
d<-getDescendants(tree,node)
d<-sort(d[d<=Ntip(tree)])
deg<-atan(obj$yy[d]/obj$xx[d])*180/pi
ii<-intersect(which(obj$yy[d]>=0),which(obj$xx[d]<0))
deg[ii]<-180+deg[ii]
ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]<0))
deg[ii]<-180+deg[ii]
ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]>=0))
deg[ii]<-360+deg[ii]
draw.arc(x=0,y=0,radius=ln.offset*h,deg1=min(deg),
deg2=max(deg),lwd=lwd,col=col)
if(orientation=="curved")
arctext(text,radius=lab.offset*h,
middle=mean(range(deg*pi/180)),cex=cex)
else if(orientation=="horizontal"){
x0<-lab.offset*cos(median(deg)*pi/180)*h
y0<-lab.offset*sin(median(deg)*pi/180)*h
text(x=x0,y=y0,label=text,
adj=c(if(x0>=0) 0 else 1,if(y0>=0) 0 else 1),
offset=0)
}
}
## function to return a node index interactively from a plotted tree
## written by Liam J. Revell 2017
getnode<-function(...){
if(hasArg(env)) env<-list(...)$env
else env<-get("last_plot.phylo",envir=.PlotPhyloEnv)
xy<-unlist(locator(n=1))
points(xy[1],xy[2])
d<-sqrt((xy[1]-env$xx)^2+(xy[2]-env$yy)^2)
ii<-which(d==min(d))[1]
ii
}
## function mostly to interactively label nodes by clicking
## written by Liam J. Revell 2017
labelnodes<-function(text,node=NULL,interactive=TRUE,
shape=c("circle","ellipse","rect"),...){
shape<-shape[1]
if(hasArg(circle.exp)) circle.exp<-list(...)$circle.exp
else circle.exp<-1.3
if(hasArg(rect.exp)) rect.exp<-list(...)$rect.exp
else rect.exp<-1.6
if(hasArg(cex)) cex<-list(...)$cex
else cex<-1
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
h<-cex*strheight("A")
w<-cex*strwidth(text)
rad<-circle.exp*h*diff(par()$usr[1:2])/diff(par()$usr[3:4])
if(is.null(node)){
if(!interactive){
cat("No nodes provided. Setting interactive mode to TRUE.\n")
interactive<-TRUE
}
node<-vector(length=length(text))
}
for(i in 1:length(text)){
if(interactive){
cat(paste("Click on the node you would like to label ",
text[i],".\n",sep=""))
flush.console()
ii<-getnode(env=obj)
node[i]<-ii
} else ii<-node[i]
if(shape=="circle")
draw.circle(obj$xx[ii],obj$yy[ii],rad,col="white")
else if(shape=="ellipse")
draw.ellipse(obj$xx[ii],obj$yy[ii],0.8*w[i],h,
col="white")
else if(shape=="rect")
rect(xleft=obj$xx[ii]-0.5*rect.exp*w[i],
ybottom=obj$yy[ii]-0.5*rect.exp*h,
xright=obj$xx[ii]+0.5*rect.exp*w[i],
ytop=obj$yy[ii]+0.5*rect.exp*h,col="white",
ljoin=1)
text(obj$xx[ii],obj$yy[ii],label=text[i],cex=cex)
}
invisible(node)
}
## convert object of class "birthdeath" into birth & death rates
bd<-function(x){
if(class(x)!="birthdeath") stop("x should be an object of class 'birthdeath'")
b<-x$para[2]/(1-x$para[1])
d<-b-x$para[2]
setNames(c(b,d),c("b","d"))
}
## compute AIC weights
aic.w<-function(aic){
d.aic<-aic-min(aic)
x<-exp(-1/2*d.aic)/sum(exp(-1/2*d.aic))
class(x)<-"aic.w"
x
}
print.aic.w<-function(x,...){
if(hasArg(signif)) signif<-list(...)$signif
else signif<-8
print(round(unclass(x),signif))
}
## function to compute all paths towards the tips from a node
## written by Liam J. Revell
node.paths<-function(tree,node){
d<-Descendants(tree,node,"children")
paths<-as.list(d)
while(any(d>Ntip(tree))){
jj<-1
new.paths<-list()
for(i in 1:length(paths)){
if(paths[[i]][length(paths[[i]])]<=Ntip(tree)){
new.paths[[jj]]<-paths[[i]]
jj<-jj+1
} else {
ch<-Descendants(tree,paths[[i]][length(paths[[i]])],
"children")
for(j in 1:length(ch)){
new.paths[[jj]]<-c(paths[[i]],ch[j])
jj<-jj+1
}
}
}
paths<-new.paths
d<-sapply(paths,function(x) x[length(x)])
}
paths
}
## function to compute a modification of Grafen's edge lengths
## written by Liam J. Revell 2016
modified.Grafen<-function(tree,power=2){
max.np<-function(tree,node){
np<-node.paths(tree,node)
if(length(np)>0) max(sapply(np,length)) else 0
}
nn<-1:(Ntip(tree)+tree$Nnode)
h<-sapply(nn,max.np,tree=tree)+1
h<-(h/max(h))^power
edge.length<-vector()
for(i in 1:nrow(tree$edge))
edge.length[i]<-diff(h[tree$edge[i,2:1]])
tree$edge.length<-edge.length
tree
}
## function to compute all rotations
## written by Liam J. Revell 2016
allRotations<-function(tree){
if(!is.binary.tree(tree)){
was.binary<-FALSE
if(is.null(tree$edge.length)){
tree<-compute.brlen(tree)
had.edge.lengths<-FALSE
} else had.edge.lengths<-TRUE
tree<-multi2di(tree)
} else was.binary<-TRUE
nodes<-1:tree$Nnode+Ntip(tree)
trees<-vector(mode="list",length=2^length(nodes))
ii<-2
trees[[1]]<-tree
for(i in 1:length(nodes)){
N<-ii-1
for(j in 1:N){
trees[[ii]]<-rotate(trees[[j]],nodes[i])
ii<-ii+1
}
}
trees<-lapply(trees,untangle,"read.tree")
if(!was.binary){
trees<-lapply(trees,di2multi)
if(!had.edge.lengths) trees<-lapply(trees,
function(x){
x$edge.length<-NULL
x
})
}
class(trees)<-"multiPhylo"
trees
}
## function to rotate a multifurcation in all possible ways
## written by Liam J. Revell 2016
rotate.multi<-function(tree,node){
kids<-Children(tree,node)
if(length(kids)>2){
ii<-sapply(kids,function(x,y) which(y==x),y=tree$edge[,2])
jj<-permn(ii)
foo<-function(j,i,t){
t$edge[i,]<-t$edge[j,]
if(!is.null(t$edge.length))
t$edge.length[i]<-t$edge.length[j]
untangle(t,"read.tree")
}
obj<-lapply(jj[2:length(jj)],foo,i=ii,t=tree)
class(obj)<-"multiPhylo"
} else obj<-untangle(rotate(tree,node),"read.tree")
obj
}
## wrapper for bind.tree that takes objects of class "simmap"
## written by Liam J. Revell 2016
bind.tree.simmap<-function(x,y,where="root"){
x<-reorder(x)
y<-reorder(y)
rootx<-x$edge[1,1]
rooty<-y$edge[1,1]
xy<-read.tree(text=write.tree(bind.tree(x,y,where)))
Mx<-rbind(matchLabels(x,xy),matchNodes(x,xy,"distances"))
My<-rbind(matchLabels(y,xy),matchNodes(y,xy,"distances"))
if(where!="root"&&where<=Ntip(x))
Mx[which(is.na(Mx[,2])),2]<-findMRCA(xy,y$tip.label)
xy$maps<-vector(mode="list",length=nrow(xy$edge))
ix<-sapply(Mx[-which(Mx[,1]==rootx),1],
function(x,y) which(y==x),y=x$edge[,2])
ixy<-sapply(Mx[-which(Mx[,1]==rootx),2],
function(x,y) which(y==x),y=xy$edge[,2])
xy$maps[ixy]<-x$maps[ix]
iy<-sapply(My[-which(My[,1]==rooty),1],
function(x,y) which(y==x),y=y$edge[,2])
ixy<-sapply(My[-which(My[,1]==rooty),2],
function(x,y) which(y==x),y=xy$edge[,2])
xy$maps[ixy]<-y$maps[iy]
xy$mapped.edge<-makeMappedEdge(xy$edge,xy$maps)
ns<-c(setNames(getStates(xy,"tips"),1:Ntip(xy)),
getStates(xy,"nodes"))
xy$node.states<-cbind(ns[as.character(xy$edge[,1])],
ns[as.character(xy$edge[,2])])
xy$states<-getStates(xy,"tips")
attr(xy,"class")<-c("simmap",class(xy))
xy
}
## generic function to convert an object of class "simmap" to "phylo"
## written by Liam J. Revell 2016
as.phylo.simmap<-function(x,...){
x$maps<-NULL
x$mapped.edge<-NULL
if(!is.null(x$node.states)) x$node.states<-NULL
if(!is.null(x$states)) x$states<-NULL
if(!is.null(x$Q)) x$Q<-NULL
if(!is.null(x$logL)) x$logL<-NULL
if(!is.null(attr(x,"map.order"))) attr(x,"map.order")<-NULL
class(x)<-setdiff(class(x),"simmap")
x
}
## generic function to convert an object of class "multiSimmap" to "multiPhylo"
## written by Liam J. Revell 2016
as.multiPhylo.multiSimmap<-function(x,...){
obj<-lapply(x,as.phylo)
class(obj)<-setdiff(class(x),"multiSimmap")
obj
}
## generic function to convert object of class "phylo" to "multiPhylo"
## written by Liam J. Revell 2016
as.multiPhylo.phylo<-function(x,...){
obj<-list(x)
class(obj)<-"multiPhylo"
obj
}
as.multiPhylo<-function(x,...){
if (identical(class(x),"multiPhylo")) return(x)
UseMethod("as.multiPhylo")
}
## get mapped states
## written by Liam J. Revell 2016
mapped.states<-function(tree,...){
if(!(inherits(tree,"simmap")||inherits(tree,"multiSimmap")))
stop("tree should be an object of class \"simmap\" or \"multiSimmap\".")
else {
if(inherits(tree,"simmap")){
if(!is.null(tree$mapped.edge))
obj<-sort(colnames(tree$mapped.edge))
else
obj<-sort(unique(unlist(lapply(tree$maps,function(x) names(x)))))
} else if(inherits(tree,"multiSimmap")) {
obj<-sapply(tree,mapped.states,...)
}
}
obj
}
## match labels between trees (equivalent to matchNodes)
## written by Liam J. Revell 2016
matchLabels<-function(tr1,tr2){
foo<-function(x,y) if(length(obj<-which(y==x))>0) obj else NA
M<-cbind(1:Ntip(tr1),sapply(tr1$tip.label,foo,y=tr2$tip.label))
colnames(M)<-c("tr1","tr2")
M
}
## compute the probability of states changes along edges of the tree
## written by Liam J. Revell 2015
edgeProbs<-function(trees){
if(!inherits(trees,"multiSimmap")) stop("trees should be an object of class \"multiSimmap\".")
SS<-sapply(trees,getStates,"tips")
states<-sort(unique(as.vector(SS)))
m<-length(states)
TT<-sapply(states,function(x,y) sapply(y,paste,x,sep="->"),
y=states)
nn<-c(TT[upper.tri(TT)],TT[lower.tri(TT)])
## this function computes for a given edge
fn<-function(edge,trees,states){
obj<-sapply(trees,function(x,e,s)
if(names(x$maps[[e]])[1]==
s[1]&&names(x$maps[[e]])[length(x$maps[[e]])]==s[2]) TRUE
else FALSE,e=edge,s=states)
sum(obj)/length(obj)
}
edge.probs<-matrix(0,nrow(trees[[1]]$edge),m,
dimnames=list(apply(trees[[1]]$edge,1,paste,collapse=","),nn))
k<-1
for(i in 1:m) for(j in 1:m){
if(i!=j){
edge.probs[,k]<-sapply(1:nrow(trees[[1]]$edge),fn,
trees=trees,states=states[c(i,j)])
k<-k+1
}
}
edge.probs<-cbind(edge.probs,1-rowSums(edge.probs))
colnames(edge.probs)[ncol(edge.probs)]<-"no change"
edge.probs
}
## get a position in the tree interactively
## written by Liam J. Revell 2015, 2016
get.treepos<-function(message=TRUE,...){
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(obj$type=="phylogram"&&obj$direction=="rightwards"){
if(message){
cat("Click on the tree position you want to capture...\n")
flush.console()
}
if(hasArg(x)) x<-list(...)$x
else x<-NULL
if(hasArg(y)) y<-list(...)$y
else y<-NULL
if(is.null(x)||is.null(y)){
x<-unlist(locator(1))
y<-x[2]
x<-x[1]
}
d<-pos<-c()
for(i in 1:nrow(obj$edge)){
x0<-obj$xx[obj$edge[i,]]
y0<-obj$yy[obj$edge[i,2]]
if(x<x0[1]||x>x0[2]){
d[i]<-min(dist(rbind(c(x,y),c(x0[1],y0))),
dist(rbind(c(x,y),c(x0[2],y0))))
pos[i]<-if(x>x0[2]) 0 else diff(obj$xx[obj$edge[i,]])
} else {
d[i]<-abs(y0-y)
pos[i]<-obj$xx[obj$edge[i,2]]-x
}
}
ii<-which(d==min(d))
list(where=obj$edge[ii,2],pos=pos[ii])
} else stop("Does not work for the plotted tree type.")
}
## fastDist: uses fastHeight to compute patristic distance between a pair of species
fastDist<-function(tree,sp1,sp2){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(is.null(tree$edge.length)) stop("tree should have edge lengths.")
if(sp1==sp2) 0
else fastHeight(tree,sp1,sp1)+fastHeight(tree,sp2,sp2)-
2*fastHeight(tree,sp1,sp2)
}
# function reorders simmap tree
# written Liam Revell 2011, 2013, 2015
reorderSimmap<-function(tree,order="cladewise",index.only=FALSE,...){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
ii<-reorder.phylo(tree,order,index.only=TRUE,...)
if(!index.only){
if(inherits(ii,"phylo")) ii<-whichorder(ii$edge[,2],tree$edge[,2]) ## bug workaround
tree$edge<-tree$edge[ii,]
tree$edge.length<-tree$edge.length[ii]
if(!is.null(tree$maps)){
tree$maps<-tree$maps[ii]
tree$mapped.edge<-tree$mapped.edge[ii,]
}
attr(tree,"order")<-order
return(tree)
} else return(ii)
}
## S3 reorder method for objects of class "simmap"
reorder.simmap<-function(x,...) reorderSimmap(x,...)
# function whichorder
# written by Liam Revell 2011, 2013, 2015
whichorder<-function(x,y) sapply(x,function(x,y) which(x==y),y=y)
# function returns random state with probability given by y
# written by Liam J. Revell 2013, 2015
rstate<-function(y){
if(length(y)==1) return(names(y)[1])
else {
p<-y/sum(y)
if(any(p<0)){
warning("Some probabilities (slightly?) < 0. Setting p < 0 to zero.")
p[p<0]<-0
}
return(names(which(rmultinom(1,1,p)[,1]==1)))
}
}
## mark the changes on a plotted "simmap" object
## written by Liam J. Revell 2015
markChanges<-function(tree,colors=NULL,cex=1,lwd=2,plot=TRUE){
states<-sort(unique(getStates(tree)))
if(is.null(colors)) colors<-setNames(palette()[1:length(states)],
states)
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
nc<-sapply(tree$maps,length)-1
ii<-which(nc>0)
nc<-nc[ii]
xx<-yy<-vector()
for(i in 1:length(ii)){
for(j in 1:nc[i]){
ss<-names(tree$maps[[ii[i]]])[j+1]
mm<-tree$edge[ii[i],1]
dd<-tree$edge[ii[i],2]
x<-rep(obj$xx[mm]+cumsum(tree$maps[[ii[i]]])[j],2)
y<-c(obj$yy[dd]-0.5*mean(strheight(LETTERS)*cex),
obj$yy[dd]+0.5*mean(strheight(LETTERS)*cex))
if(plot) lines(x,y,lwd=lwd,col=colors[ss],lend=2)
xx<-c(xx,setNames(x[1],
paste(names(tree$maps[[ii[i]]])[j:(j+1)],
collapse="->")))
yy<-c(yy,mean(y))
}
}
XY<-cbind(xx,yy)
colnames(XY)<-c("x","y")
invisible(XY)
}
## function to label clades
## written by Liam J. Revell 2014, 2015
cladelabels<-function(tree=NULL,text,node,offset=NULL,wing.length=NULL,cex=1,
orientation="vertical"){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(is.null(tree)){
wing.length<-1
if(is.null(offset)) offset<-8
tree<-list(edge=lastPP$edge,
tip.label=1:lastPP$Ntip,
Nnode=lastPP$Nnode)
H<-matrix(lastPP$xx[tree$edge],nrow(tree$edge),2)
tree$edge.length<-H[,2]-H[,1]
class(tree)<-"phylo"
}
if(is.null(offset)) offset<-0.5
xx<-mapply(labelSubTree,node,text,
MoreArgs=list(tree=tree,pp=lastPP,offset=offset,wl=wing.length,cex=cex,
orientation=orientation))
}
## internal function used by cladelabels
## written by Liam J. Revell 2014, 2015
labelSubTree<-function(tree,nn,label,pp,offset,wl,cex,orientation){
if(is.null(wl)) wl<-1
tree<-reorder(tree)
tips<-getDescendants(tree,nn)
tips<-tips[tips<=length(tree$tip.label)]
ec<-0.7 ## expansion constant
sw<-pp$cex*max(strwidth(tree$tip.label[tips]))
sh<-pp$cex*max(strheight(tree$tip.label))
cw<-mean(strwidth(LETTERS)*cex)
h<-max(sapply(tips,function(x,tree)
nodeHeights(tree)[which(tree$edge[,2]==x),2],
tree=tree))+sw+offset*cw
y<-range(pp$yy[tips])
lines(c(h,h),y+ec*c(-sh,sh))
lines(c(h-wl*cw,h),
c(y[1]-ec*sh,y[1]-ec*sh))
lines(c(h-wl*cw,h),
c(y[2]+ec*sh,y[2]+ec*sh))
text(h+cw,mean(y),
label,srt=if(orientation=="horizontal") 0 else 90,
adj=if(orientation=="horizontal") 0 else 0.5,cex=cex)
}
## get all the extant/extinct tip names
## written by Liam J. Revell 2012, 2015
getExtant<-function(tree,tol=1e-8){
if(!inherits(tree,"phylo")) stop("tree should be object of class \"phylo\".")
H<-nodeHeights(tree)
tl<-max(H)
x<-which(H[,2]>=(tl-tol))
y<-tree$edge[x,2]
y<-y[y<=length(tree$tip)]
z<-tree$tip.label[y]
return(z)
}
getExtinct<-function(tree,tol=1e-8) setdiff(tree$tip.label,getExtant(tree,tol))
# function splits tree at split
# written by Liam Revell 2011, 2014, 2015
splitTree<-function(tree,split){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(split$node>length(tree$tip.label)){
# first extract the clade given by shift$node
tr2<-extract.clade(tree,node=split$node)
tr2$root.edge<-tree$edge.length[which(tree$edge[,2]==split$node)]-split$bp
#now remove tips in tr2 from tree
tr1<-drop.clade(tree,tr2$tip.label)
nn<-if(!is.null(tree$node.label)) c(tree$node.label,"NA") else "NA"
tr1$tip.label[which(tr1$tip.label%in%nn)]<-"NA"
tr1$edge.length[match(which(tr1$tip.label=="NA"),tr1$edge[,2])]<-split$bp
} else {
# first extract the clade given by shift$node
tr2<-list(edge=matrix(c(2L,1L),1,2),tip.label=tree$tip.label[split$node],edge.length=tree$edge.length[which(tree$edge[,2]==split$node)]-split$bp,Nnode=1L)
class(tr2)<-"phylo"
# now remove tip in tr2 from tree
tr1<-tree
tr1$edge.length[match(which(tr1$tip.label==tr2$tip.label[1]),tr1$edge[,2])]<-split$bp
tr1$tip.label[which(tr1$tip.label==tr2$tip.label[1])]<-"NA"
}
trees<-list(tr1,tr2)
class(trees)<-"multiPhylo"
trees
}
# function drops entire clade
# written by Liam Revell 2011, 2015
drop.clade<-function(tree,tip){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
nn<-if(!is.null(tree$node.label)) c(tree$node.label,"NA") else "NA"
tree<-drop.tip(tree,tip,trim.internal=FALSE)
while(sum(tree$tip.label%in%nn)>1)
tree<-drop.tip(tree,tree$tip.label[tree$tip.label%in%nn],
trim.internal=FALSE)
tree
}
## function to re-root a phylogeny along an edge
## written by Liam J. Revell 2011-2016
reroot<-function(tree,node.number,position=NULL,interactive=FALSE,...){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(interactive){
plotTree(tree,...)
cat("Click where you would like re-root the plotted tree\n")
flush.console()
obj<-get.treepos(message=FALSE)
node.number<-obj$where
position<-tree$edge.length[which(tree$edge[,2]==node.number)]-obj$pos
}
if(is.null(position)) position<-tree$edge.length[which(tree$edge[,2]==node.number)]
tt<-splitTree(tree,list(node=node.number,bp=position))
p<-tt[[1]]
d<-tt[[2]]
tip<-if(length(which(p$tip.label=="NA"))>0) "NA" else p$tip.label[which(p$tip.label%in%tree$node.label)]
p<-root(p,outgroup=tip,resolve.root=T)
bb<-which(p$tip.label==tip)
p$tip.label[bb]<-"NA"
ee<-p$edge.length[which(p$edge[,2]==bb)]
p$edge.length[which(p$edge[,2]==bb)]<-0
cc<-p$edge[which(p$edge[,2]==bb),1]
dd<-setdiff(p$edge[which(p$edge[,1]==cc),2],bb)
p$edge.length[which(p$edge[,2]==dd)]<-p$edge.length[which(p$edge[,2]==dd)]+ee
obj<-paste.tree(p,d)
if(interactive) plotTree(obj,...)
obj
}
## function to add an arrow pointing to a tip or node in the tree
## written by Liam J. Revell 2014, 2017
add.arrow<-function(tree=NULL,tip,...){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(!is.null(tree)){
if(inherits(tree,"contMap")) tree<-tree$tree
else if(inherits(tree,"densityMap")) tree<-tree$tree
}
if(is.numeric(tip)){
ii<-tip
if(!is.null(tree)&&ii<=length(tree$tip.label)) tip<-tree$tip.label[ii]
else tip<-""
} else if(is.character(tip)&&!is.null(tree)) ii<-which(tree$tip.label==tip)
if(hasArg(offset)) offset<-list(...)$offset
else offset<-1
strw<-lastPP$cex*(strwidth(tip)+offset*mean(strwidth(c(LETTERS,letters))))
if(hasArg(arrl)) arrl<-list(...)$arrl
else {
if(lastPP$type=="fan") arrl<-0.3*max(lastPP$xx)
else if(lastPP$type=="phylogram") arrl<-0.15*max(lastPP$xx)
}
if(hasArg(hedl)) hedl<-list(...)$hedl
else hedl<-arrl/3
if(hasArg(angle)) angle<-list(...)$angle
else angle<-45
arra<-angle*pi/180
asp<-if(lastPP$type=="fan") 1 else (par()$usr[4]-par()$usr[3])/(par()$usr[2]-par()$usr[1])
if(hasArg(col)) col<-list(...)$col
else col<-"black"
if(hasArg(lwd)) lwd<-list(...)$lwd
else lwd<-2
if(lastPP$type=="fan") theta<-atan2(lastPP$yy[ii],lastPP$xx[ii])
else if(lastPP$type=="phylogram") theta<-0
segments(x0=lastPP$xx[ii]+cos(theta)*(strw+arrl),
y0=lastPP$yy[ii]+sin(theta)*(strw+arrl),
x1=lastPP$xx[ii]+cos(theta)*strw,
y1=lastPP$yy[ii]+sin(theta)*strw,
col=col,lwd=lwd,lend="round")
segments(x0=lastPP$xx[ii]+cos(theta)*strw+cos(theta+arra/2)*hedl,
y0=lastPP$yy[ii]+sin(theta)*strw+sin(theta+arra/2)*hedl*asp,
x1=lastPP$xx[ii]+cos(theta)*strw,
y1=lastPP$yy[ii]+sin(theta)*strw,
col=col,lwd=lwd,lend="round")
segments(x0=lastPP$xx[ii]+cos(theta)*strw+cos(theta-arra/2)*hedl,
y0=lastPP$yy[ii]+sin(theta)*strw+sin(theta-arra/2)*hedl*asp,
x1=lastPP$xx[ii]+cos(theta)*strw,
y1=lastPP$yy[ii]+sin(theta)*strw,
col=col,lwd=lwd,lend="round")
invisible(list(x0=lastPP$xx[ii]+cos(theta)*(strw+arrl),
y0=lastPP$yy[ii]+sin(theta)*(strw+arrl),
x1=lastPP$xx[ii]+cos(theta)*strw,
y1=lastPP$yy[ii]+sin(theta)*strw))
}
## function to ladderize phylogeny with mapped discrete character
## written by Liam J. Revell 2014, 2015
ladderize.simmap<-function(tree,right=TRUE){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
obj<-read.tree(text=write.tree(ladderize(tree,right=right)))
rN<-Ntip(obj)+1
T<-cbind(1:Ntip(obj),sapply(obj$tip.label,function(x,y) which(y==x),y=tree$tip.label))
N<-matchNodes(obj,tree)
M<-rbind(T,N[N[,1]!=rN,])
ii<-sapply(M[,1],function(x,y) which(y==x),y=obj$edge[,2])
jj<-sapply(M[,2],function(x,y) which(y==x),y=tree$edge[,2])
obj$maps<-vector(length=nrow(tree$edge),mode="list")
obj$mapped.edge<-matrix(NA,nrow(tree$edge),ncol(tree$mapped.edge),
dimnames=list(apply(tree$edge,1,paste,collapse=","),
colnames(tree$mapped.edge)))
if(!is.null(tree$states))
obj$states<-tree$states[sapply(obj$tip.label,function(x,y) which(y==x),y=tree$tip.label)]
if(!is.null(tree$node.states)) obj$node.states<-matrix(NA,nrow(tree$edge),2)
for(i in 1:length(ii)){
obj$maps[[ii[i]]]<-tree$maps[[jj[i]]]
obj$mapped.edge[ii[i],]<-tree$mapped.edge[jj[i],]
if(!is.null(tree$node.states)) obj$node.states[ii[i],]<-tree$node.states[jj[i],]
}
obj
}
## for backward compatibility
repPhylo<-function(tree,times) rep(tree,times)
## S3 method rep for objects of class "phylo" and "multiPhylo"
## written by Liam J. Revell 2014
rep.phylo<-function(x,...){
if(hasArg(times)) times<-list(...)$times
else times<-(...)[[1]]
for(i in 1:times) obj<-if(i==1) x else if(i==2) c(obj,x) else c(obj,list(x))
class(obj)<-"multiPhylo"
obj
}
rep.multiPhylo<-function(x,...){
if(hasArg(times)) times<-list(...)$times
else times<-(...)[[1]]
for(i in 1:times) obj<-if(i==1) x else if(i>=2) c(obj,x)
class(obj)<-"multiPhylo"
obj
}
## function to rescale simmap style trees
## written by Liam J. Revell 2012, 2013, 2014, 2015, 2017
rescaleSimmap<-function(tree,...){
if(inherits(tree,"multiPhylo")){
cls<-class(tree)
trees<-unclass(tree)
trees<-lapply(trees,rescaleSimmap,...)
class(trees)<-cls
return(trees)
} else if(inherits(tree,"phylo")){
if(hasArg(lambda)) lambda<-list(...)$lambda
else lambda<-1
if(hasArg(totalDepth)) depth<-totalDepth<-list(...)$totalDepth
else if(hasArg(depth)) depth<-totalDepth<-list(...)$depth
else depth<-totalDepth<-max(nodeHeights(tree))
if(lambda!=1){
e<-lambdaTree(tree,lambda)$edge.length/tree$edge.length
tree$edge.length<-tree$edge.length*e
tree$maps<-mapply(function(x,y) x*y,tree$maps,e)
tree$mapped.edge<-tree$mapped.edge*matrix(rep(e,ncol(tree$mapped.edge)),length(e),ncol(tree$mapped.edge))
}
if(depth!=max(nodeHeights(tree))){
h<-max(nodeHeights(tree))
s<-depth/h
tree$edge.length<-tree$edge.length*s
tree$maps<-lapply(tree$maps,"*",s)
tree$mapped.edge<-tree$mapped.edge*s
}
return(tree)
} else message("tree should be an object of class \"phylo\" or \"multiPhylo\"")
}
## function to drop one or more tips from a tree but retain all ancestral nodes as singletons
## written by Liam J. Revell 2014, 2015
drop.tip.singleton<-function(tree,tip){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
N<-Ntip(tree)
m<-length(tip)
ii<-sapply(tip,function(x,y) which(y==x),y=tree$tip.label)
tree$tip.label<-tree$tip.label[-ii]
ii<-sapply(ii,function(x,y) which(y==x),y=tree$edge[,2])
tree$edge<-tree$edge[-ii,]
tree$edge.length<-tree$edge.length[-ii]
tree$edge[tree$edge<=N]<-as.integer(rank(tree$edge[tree$edge<=N]))
tree$edge[tree$edge>N]<-tree$edge[tree$edge>N]-m
N<-N-m
if(any(sapply(tree$edge[tree$edge[,2]>N,2],"%in%",tree$edge[,1])==FALSE)) internal<-TRUE
else internal<-FALSE
while(internal){
ii<-which(sapply(tree$edge[,2],"%in%",c(1:N,tree$edge[,1]))==FALSE)[1]
nn<-tree$edge[ii,2]
tree$edge<-tree$edge[-ii,]
tree$edge.length<-tree$edge.length[-ii]
tree$edge[tree$edge>nn]<-tree$edge[tree$edge>nn]-1