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#' @title Fast construction of phylogenetic trees
#' @description The function can either attaches new tips and/or clades derived
#' from a source phylogeny to a pre-existing backbone tree, or build a new
#' phylogenetic tree from scratch.
#' @usage
#' tree.merger(backbone=NULL,data,source.tree=NULL,age.offset=NULL,tip.ages =
#' NULL, node.ages = NULL,plot=TRUE,filename=NULL)
#' @param backbone the backbone tree to attach tips/clades on. This is
#' \code{NULL} when constructing the tree from scratch.
#' @param data a dataset including as columns:\enumerate{\item bind = the
#' tips/clades to be attached; \item reference = the reference tip or clade
#' where 'bind' must be attached; \item poly = logical specifying if 'bind'
#' and 'reference' should form a polytomous clade.} See details for further
#' explanations.
#' @param source.tree the tree where 'bind' clades are to be extracted from. If
#' no clade has to be attached, it can be left unspecified.
#' @param age.offset if the most recent age (i.e. the maximum distance from the
#' tree root) differs between the source and the backbone trees, the
#' “age.offset” is the difference between them in this exact order (source
#' minus backbone). It is positive when the backbone tree attains younger age
#' than the source tree, and vice-versa.
#' @param tip.ages as in \code{\link{scaleTree}}, a named vector including the
#' ages (i.e. the time distance from the youngest tip within the tree) of the
#' tips. If unspecified when merging, the function assumes all the tips on the
#' backbone tree are correctly placed and places all the new tips at the
#' maximum distance from the tree root (i.e. the present if the tips are
#' extant). If unspecified when building a new tree, all the tips are placed
#' at the maximum distance from the tree root.
#' @param node.ages as in \code{\link{scaleTree}}, a named vector including the
#' ages (i.e. the time distance from the youngest tip within the tree) of the
#' nodes. The nodes must be defined by collating the names of the two
#' phylogenetically furthest tips it subtends to, separated by the "-" symbol
#' (see examples). If no calibration date for nodes is supplied when merging,
#' the function may shift the node position back in time as to place new
#' tips/clades and to fit tip ages. If no \code{node.ages} is supplied when
#' building a new tree, all the nodes, including the tree root, are arbitrarly
#' placed either to accommodate \code{tip.ages} or to have 1 unit time
#' distance with one another along a lineage (when \code{tip.ages = NULL}).
#' @param plot if \code{TRUE}, the function produces an interactive plotting
#' device to check the placing of each \code{bind}.
#' @param filename if \code{plot=TRUE} and provided a \code{filename} (with or
#' without the path), the function stores a pdf file showing the plot of the
#' entire phylogeny.
#' @importFrom ape bind.tree
#' @importFrom stats setNames
#' @return New/merged phylogenetic tree.
#' @author Silvia Castiglione, Carmela Serio, Giorgia Girardi, Pasquale Raia
#' @details The following description of the \code{data} argument applies both
#' when merging the tree and when building it from zero. In the latter case,
#' the first row of \code{data} must include as 'bind' and 'reference' the
#' first pair of tips to set the tree up (meaning, the 'reference' tip is not
#' also listed as 'bind'). The function attaches tips and/or clades from the
#' \code{source} tree to the \code{backbone} tree according to the \code{data}
#' object. Within the latter, a clade, either to be bound or to be the
#' reference, must be indicated by collating the names of the two
#' phylogenetically furthest tips belonging to it, separated by the "-"
#' symbol. Alternatively, if
#' \code{backbone$node.label}/\code{source.tree$node.label} is not
#' \code{NULL}, a bind/reference clade can be indicated as "Clade
#' NAMEOFTHECLADE" when appropriate. Similarly, an entire genus on the
#' \code{backbone} or the \code{source.tree} can be indicated as "Genus
#' NAMEOFTHEGENUS" (see examples below). If the "Genus NAMEOFTHEGENUS" mode is
#' used for a species/clade belonging to one or more different genera, the
#' function automatically sets as reference the clade including all the species
#' belonging to the reference genus, regardless of they are already on the
#' \code{backbone} or binded.
#'
#' Duplicated 'bind' produce error. Tips/clades set to be attached to the same
#' 'reference' with 'poly=FALSE' are considered to represent a polytomy. Tips
#' set as 'bind' which are already on the backbone tree are removed from the
#' latter and placed according to the 'reference'. See examples and
#' \href{../doc/Tree-Manipulation.html#tree.merger.html}{vignette} for
#' clarifications.
#' @export
#' @seealso
#' \href{../doc/Tree-Manipulation.html#tree.merger.html}{\code{tree.merger}
#' vignette}; \href{../doc/Tree-Manipulation.html#scaleTree}{\code{scaleTree}
#' vignette};
#' @references Castiglione, S., Serio, C., Mondanaro, A., Melchionna, M., &
#' Raia, P. (2022). Fast production of large, time-calibrated, informal
#' supertrees with tree.merger. \emph{Palaeontology}, 65:
#' e12588.https://doi.org/10.1111/pala.12588
#' @references Pandolfi, L., Martino, R., Rook, L., & Piras, P. (2020).
#' Investigating ecological and phylogenetic constraints in Hippopotaminae
#' skull shape. \emph{Rivista Italiana di Paleontologia e Stratigrafia}, 126:
#' 37-49.
#' @examples
#' \dontrun{
#'
#' ### Merging phylogenetic information ###
#' require(ape)
#' DataCetaceans$treecet->treecet
#' treecet$node.label[131-Ntip(treecet)]<-"Crown_Mysticeti"
#'
#' data.frame(bind=c("Clade Crown_Mysticeti",
#' "Aetiocetus_weltoni",
#' "Saghacetus_osiris",
#' "Zygorhiza_kochii",
#' "Ambulocetus_natans",
#' "Genus Kentriodon",
#' "Tursiops_truncatus-Delphinus_delphis",
#' "Kogia_sima",
#' "Eurhinodelphis_cristatus",
#' "Grampus_griseus",
#' "Eurhinodelphis_bossi"),
#' reference=c("Fucaia_buelli-Aetiocetus_weltoni",
#' "Aetiocetus_cotylalveus",
#' "Fucaia_buelli-Tursiops_truncatus",
#' "Saghacetus_osiris-Fucaia_buelli",
#' "Dalanistes_ahmedi-Fucaia_buelli",
#' "Clade Delphinida",
#' "Stenella_attenuata-Stenella_longirostris",
#' "Kogia_breviceps",
#' "Eurhinodelphis_longirostris",
#' "Globicephala_melas-Pseudorca_crassidens",
#' "Eurhinodelphis_longirostris"),
#' poly=c(FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE))->dato
#'
#' c("Aetiocetus_weltoni"=28.0,
#' "Saghacetus_osiris"=33.9,
#' "Zygorhiza_kochii"=34.0,
#' "Ambulocetus_natans"=40.4,
#' "Kentriodon_pernix"=15.9,
#' "Kentriodon_schneideri"=11.61,
#' "Kentriodon_obscurus"=13.65,
#' "Eurhinodelphis_bossi"=13.65,
#' "Eurhinodelphis_cristatus"=5.33)->tip.ages
#' c("Ambulocetus_natans-Fucaia_buelli"=52.6,
#' "Balaena_mysticetus-Caperea_marginata"=21.5)->node.ages
#'
#' # remove some tips from the original tree and create a source tree
#' drop.tip(treecet,c(names(tip.ages),
#' tips(treecet,131)[-which(tips(treecet,131)%in%
#' c("Caperea_marginata","Eubalaena_australis"))],
#' tips(treecet,195)[-which(tips(treecet,195)=="Tursiops_aduncus")]))->backtree
#' drop.tip(treecet,which(!treecet$tip.label%in%c(names(tip.ages),
#' tips(treecet,131),
#' tips(treecet,195))))->sourcetree
#'
#' plot(backtree,cex=.6)
#' plot(sourcetree,cex=.6)
#'
#' tree.merger(backbone=backtree,data=dato,source.tree=sourcetree,
#' tip.ages=tip.ages,node.ages = node.ages, plot=TRUE)->treeM
#'
#'
#' ### Building a new phylogenetic tree ###
#' # Build the phylogenetic tree shown in
#' # Pandolfi et al. 2020 - Figure 2 (see reference)
#' data.frame(bind=c("Hippopotamus_lemerlei",
#' "Hippopotamus_pentlandi",
#' "Hippopotamus_amphibius",
#' "Hippopotamus_antiquus",
#' "Hippopotamus_gorgops",
#' "Hippopotamus_afarensis",
#' "Hexaprotodon_sivalensis",
#' "Hexaprotodon_palaeindicus",
#' "Archaeopotamus_harvardi",
#' "Saotherium_mingoz",
#' "Choeropsis_liberiensis"),
#' reference=c("Hippopotamus_madagascariensis",
#' "Hippopotamus_madagascariensis-Hippopotamus_lemerlei",
#' "Hippopotamus_pentlandi-Hippopotamus_madagascariensis",
#' "Hippopotamus_amphibius-Hippopotamus_madagascariensis",
#' "Hippopotamus_antiquus-Hippopotamus_madagascariensis",
#' "Hippopotamus_gorgops-Hippopotamus_madagascariensis",
#' "Genus Hippopotamus",
#' "Hexaprotodon_sivalensis",
#' "Hexaprotodon_sivalensis-Hippopotamus_madagascariensis",
#' "Archaeopotamus_harvardi-Hippopotamus_madagascariensis",
#' "Saotherium_mingoz-Hippopotamus_madagascariensis"),
#' poly=c(FALSE,
#' TRUE,
#' FALSE,
#' FALSE,
#' TRUE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE,
#' FALSE))->dato.new
#'
#' tree.merger(data=dato.new)->tree.new # uncalibrated tree
#'
#'
#' # Please note: the following ages are only used to show how to use the function
#' # they are not assumed to be correct.
#' c("Hippopotamus_lemerlei"=0.001,
#' "Hippopotamus_pentlandi"=0.45,
#' "Hippopotamus_amphibius"=0,
#' "Hippopotamus_antiquus"=0.5,
#' "Hippopotamus_gorgops"=0.4,
#' "Hippopotamus_afarensis"=0.75,
#' "Hexaprotodon_sivalensis"=1,
#' "Hexaprotodon_palaeindicus"=0.4,
#' "Archaeopotamus_harvardi"=5.2,
#' "Saotherium_mingoz"=4,
#' "Choeropsis_liberiensis"=0)->tip.ages1
#' c("Choeropsis_liberiensis-Hippopotamus_amphibius"=13,
#' "Archaeopotamus_harvardi-Hippopotamus_amphibius"=8.5,
#' "Hexaprotodon_sivalensis-Hexaprotodon_palaeindicus"=6)->node.ages1
#'
#' tree.merger(data=dato.new,tip.ages=tip.ages1)->tree.new1 # calibrating tips only
#'
#' # calibrating tips and nodes
#' tree.merger(data=dato.new,tip.ages=tip.ages1,node.ages=node.ages1)->tree.new2
#'
#' }
tree.merger<-function(backbone=NULL,data,source.tree=NULL,age.offset=NULL,
tip.ages = NULL, node.ages = NULL,plot=TRUE,filename=NULL){
# require(ape)
# require(phytools)
# require(manipulate)
misspacks<-sapply(c("manipulate","scales"),requireNamespace,quietly=TRUE)
if(any(!misspacks)){
stop("The following package/s are needed for this function to work, please install it/them:\n ",
paste(names(misspacks)[which(!misspacks)],collapse=", "),
call. = FALSE)
}
data->dat
if(is.null(backbone)){
if(dat[1,]$reference%in%dat$bind)
stop("Please indicate as first row of data the first pair of tips to build the tree on.")
startsp<-unlist(dat[1,1:2])
dat<-dat[-1,]
if(any(dat$reference==startsp[2])){
dat$poly[which(dat$reference==startsp[2])]<-TRUE
dat$reference[which(dat$reference==startsp[2])]<-paste(startsp,collapse="-")
}
tree<-list()
tree$edge<-matrix(c(3,1,3,2),ncol=2,byrow=TRUE)
tree$tip.label<-startsp
tree$Nnode<-1
tree$edge.length<-rep(1,2)
class(tree)<-"phylo"
} else backbone->tree
source.tree->tree2
max(diag(vcv(tree)))->H
H-diag(vcv(tree))->ages
if(!is.null(age.offset)&&age.offset<0){
ages+abs(age.offset)->ages
H+abs(age.offset)->Hset
}else H->Hset
# if(is.null(min.branch)) min(tree$edge.length)->min.branch
#### DATA CHECK ####
if(!all(colnames(dat)%in%c("bind","reference","poly"))) {
if(any(is.na(as.logical(dat[,3])))) stop("Check columns order: it should be 'bind', 'reference', 'poly'")
warning("Colnames not matching: columns assumed to be ordered as 'bind','reference','poly\n'",immediate. = TRUE)
colnames(dat)<-c("bind","reference","poly")
}
if(!is.logical(dat$poly)) as.logical(dat$poly)->dat$poly
### Check for wrong poly assignment ###
if(any(apply(dat,1,function(k) (!grepl("-",k[2]))&!grepl("Genus",k[2])&!grepl("Clade",k[2])&as.logical(k[3])))){
warning("Found poly=TRUE at binding two tips, automatically changed to FALSE\n",immediate.=TRUE)
lapply(1:nrow(dat),function(k){
if((!grepl("-",dat[k,2]))&!grepl("Genus",k[k,2])&!grepl("Clade",k[k,2])&dat[k,3]){
dat[k,3]<<-FALSE
message(paste(" Please check",dat[k,1],"&",dat[k,2],"in your dataset",sep=" "))
}
})
}
### Check for genera and clades as bind ###
if(any(grepl("Genus",dat$bind))){
if(is.null(tree2)) stop("Please provide the source.tree")
sapply(1:nrow(dat),function(k){
if(grepl("Genus",dat[k,]$bind)){
trimws(gsub("Genus ","",dat[k,]$bind))->genref
getGenus(tree2,genref)->getgenref
if(getgenref[2]==1) dat[k,]$bind<<-grep(genref,tree2$tip.label,value=TRUE) else
dat[k,]$bind<<-paste(tips(tree2,getgenref[,3])[c(1,length(tips(tree2,getgenref[,3])))],collapse="-")
}
})
}
if(any(grepl("Clade",dat$bind))){
sapply(1:nrow(dat),function(k){
if(grepl("Clade",dat[k,]$bind)){
if(!gsub("Clade ","",dat[k,]$bind)%in%tree2$node.label) stop("Required node.label not indicated on the source.tree")
tips(tree2,Ntip(tree2)+which(tree2$node.label==gsub("Clade ","",dat[k,]$bind)))->claref
dat[k,]$bind<<-paste(claref[c(1,length(claref))],collapse="-")
}
})
}
data.frame(dat,bind.type=sapply(strsplit(dat[,1],"-"),length))->dat
if(any(dat$bind.type==2)&is.null(tree2)) stop("Please provide the source.tree")
bind.all<-unlist(sapply(1:nrow(dat),function(x) {
ifelse(dat[x,4]==2,des<-tips(tree2,getMRCA(tree2,strsplit(dat[x,1],"-")[[1]])),des<-dat[x,1])
des
}))
if(any(duplicated(bind.all))) stop(paste(paste(bind.all[duplicated(bind.all)],collapse = ", "),"names duplicated in supplied tips"))
if(all(dat$bind.type==1)&(!is.null(tree2))) tree2<-NULL
# if(any(dat$bind%in%tree2$tip.label)) drop.tip(tree2,dat[which(dat$bind%in%tree2$tip.label),1])->tree2
# dat$bind.tips<-NA
# if(all(dat$bind.type==1)) dat$bind.tips<-dat$bind else{
# dat[which(dat$bind.type==2),]$bind.tips<-lapply(dat$bind[which(dat$bind.type==2)],function(x) tips(tree2,getMRCA(tree2,strsplit(x,"-")[[1]])))
# if(any(is.na(dat$bind.tips))) dat[which(is.na(dat$bind.tips)),]$bind.tips<-dat[which(is.na(dat$bind.tips)),]$bind
# }
dat$bind.tips<-dat$bind
if(any(dat$bind.type==2))
dat[which(dat$bind.type==2),]$bind.tips<-lapply(dat$bind[which(dat$bind.type==2)],function(x) tips(tree2,getMRCA(tree2,strsplit(x,"-")[[1]])))
### bind missing from tree2 ###
if(!all(unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)){
stop(paste(paste(unlist(dat[which(dat$bind.type==2),]$bind.tips)[which(
unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)],
collapse=", "),"not in source.tree"))
}
### reference missing ###
# if(!all(unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))){
# stop(paste(paste(unlist(strsplit(dat$reference,"-"))[which(!unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))],
# collapse=","),"missing from the backbone, the source and the tips to be attached"))
# }
### bind already on the backbone ###
if(any(dat$bind%in%tree$tip.label)){
warning(paste(paste(dat[which(dat$bind%in%tree$tip.label),1],collapse=", "),"removed from the backbone tree\n"),immediate. = TRUE)
drop.tip(tree,dat[which(dat$bind%in%tree$tip.label),1])->tree
}
### Check for genera and clades as references ###
if(any(grepl("Genus",dat$reference))){
dat$bindgen<-sapply(dat$bind.tips,function(j) unique(sapply(j,function(x) strsplit(x,"_")[[1]][1])))
sapply(1:nrow(dat),function(k){
if(grepl("Genus",dat[k,]$reference)){
trimws(gsub("Genus ","",dat[k,]$reference))->genref
try(getGenus(tree,genref),silent = TRUE)->getgenref
if(!inherits(getgenref,"try-error")){
if(getgenref[2]==1) gentree<-grep(genref,tree$tip.label,value=TRUE) else
gentree<-paste(tips(tree,getgenref[,3])[c(1,length(tips(tree,getgenref[,3])))],collapse="-")
genbind<-dat$bindgen[[k]]
dat[k,]$reference<<-gentree
if(genref%in%genbind){
if(length(genbind)>1&any(sapply(dat$bindgen,function(w) all(w%in%genref))))
dat[k,]$reference<<-paste(c(gentree,sapply(dat[which(sapply(dat$bindgen,function(w) all(w%in%genref))),]$bind.tips,"[[",1)),collapse="-")
}else{
if(any(sapply(dat$bindgen,function(w) any(w%in%genref))))
dat[k,]$reference<<-paste(c(gentree,
sapply(dat[which(sapply(dat$bindgen,function(w) any(w%in%genref))),]$bind.tips,"[[",1)),collapse="-")
}
}else stop(paste("Genus",genref,"missing from the backbone tree"))
}
})
dat$bindgen<-NULL
}
if(any(grepl("Clade",dat$reference))){
sapply(1:nrow(dat),function(k){
if(grepl("Clade",dat[k,]$reference)){
if(!gsub("Clade ","",dat[k,]$reference)%in%tree$node.label) stop("Required node.label not indicated on the tree")
tips(tree,Ntip(tree)+which(tree$node.label==gsub("Clade ","",dat[k,]$reference)))->claref
dat[k,]$reference<<-paste(claref[c(1,length(claref))],collapse="-")
}
})
}
### duplicated reference ###
table(dat$reference)->tab.ref
if(any(tab.ref>1)){
for(j in 1:length(which(tab.ref>1))){
dat[which(dat$reference==names(which(tab.ref>1)[j])),]->ref.mult
# if(any(isTRUE(ref.mult$poly))) ref.mult[-which(isTRUE(ref.mult$poly)),]->ref.mult
if(any(ref.mult$poly)) ref.mult[which(!ref.mult$poly),]->ref.mult
paste(strsplit(ref.mult$reference[1],"-")[[1]][1],strsplit(ref.mult$bind[1],"-")[[1]][1],sep="-")->ref.mult$reference[-1]
# ref.mult[-1,]$poly<-TRUE
ref.mult$poly[-1]<-TRUE
dat[match(ref.mult$bind,dat$bind),]<-ref.mult
}
}
if(!is.null(tree2)){
dat$MRCAbind<-NA
sapply(dat[which(dat$bind.type==2),]$bind.tips,function(x) getMRCA(tree2,x))->dat$MRCAbind[which(dat$bind.type==2)]
if(any(dat$bind.type==2)){
unlist(sapply(dat[which(dat$bind.type==2),]$MRCAbind,function(x) tree$tip.label[which(tree$tip.label%in%tips(tree2,x))]))->remt
if(length(remt)>0){
drop.tip(tree,remt)->tree
ages[-match(remt,names(ages))]->ages
warning(paste(paste(remt,collapse=", "),"already on the source tree: removed from the backbone tree\n"),immediate. = TRUE)
}
}
}
### ordering ###
strsplit(dat$reference,"-")->refs
dat$ref.tree1<-NA
lapply(refs,function(x){
if(all(x%in%tree$tip.label)) NA else x[which(!x%in%tree$tip.label)]
})->ref.tree
dat[which(is.na(ref.tree)),][order(dat[which(is.na(ref.tree)),]$bind.type),]$ref.tree1<-seq(1,length(which(is.na(ref.tree))))
if(any(!is.na(ref.tree))){
dat[which(!is.na(ref.tree)),]->dat.new
dat.new$ref.tree1<-ref.tree[-which(is.na(ref.tree))]
if(any(unlist(dat.new$ref.tree1)%in%unlist(dat.new$bind.tips))){
while(nrow(dat.new)>0){
which(!sapply(dat.new$ref.tree1,function(w) any(w%in%unlist(dat.new$bind.tips))))->outs
# which(!(dat.new[,7]%in%unlist(dat.new$bind.tips)|dat.new[,8]%in%unlist(dat.new$bind.tips)))
if(length(outs)<1) stop("Recursive species attachment: check rows ",paste(rownames(dat.new),collapse = ", ")," in data")
dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<-max(dat$ref.tree1,na.rm=TRUE)+1:length(outs)
dat.new[-outs,]->dat.new
}
}else{
# which(!(dat.new[,7]%in%unlist(dat.new$bind.tips)|dat.new[,8]%in%unlist(dat.new$bind.tips)))->outs
which(!sapply(dat.new$ref.tree1,function(w) any(w%in%unlist(dat.new$bind.tips))))->outs
dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<-
max(dat$ref.tree1,na.rm=TRUE)+1:length(which(!dat.new$ref.tree1%in%dat.new[,1]))
}
}
dat[order(dat$ref.tree1),]->dat
### binding ###
pb <- txtProgressBar(min = 0, max = nrow(dat), style = 3)
for(k in 1:nrow(dat)){
setTxtProgressBar(pb,k)
if(length(strsplit(dat$reference,"-")[[k]])>1)
getMRCA(tree,strsplit(dat$reference,"-")[[k]])->where.ref else
which(tree$tip.label==strsplit(dat$reference,"-")[[k]])->where.ref
if(where.ref!=(Ntip(tree)+1))
tree$edge.length[which(tree$edge[,2]==where.ref)]->br.len else{
if(is.null(tree$root.edge)||tree$root.edge==0) tree$root.edge<-mean(tree$edge.length)
tree$root.edge->br.len
}
if(dat$bind.type[k]==1){
if(dat$poly[k]){
0->pos.ref
max(tree$edge.length[which(tree$edge[,1]%in%where.ref)])->br.len
} else br.len/2->pos.ref
bind.tip(tree,dat$bind[k],where.ref,position = pos.ref,edge.length =br.len/2)->tree
}else{
extract.clade(tree2,dat$MRCAbind[k])->cla
if(dat$poly[k]){
0->pos.ref
if(where.ref==(Ntip(tree)+1)&&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>H)
# rescale(cla,"depth",(H+max(diag(vcv(cla)))/10))->cla else
rescaleRR(cla,height=(H+max(diag(vcv(cla)))/10))->cla else
if(where.ref!=(Ntip(tree)+1)&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))
# rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla
rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla
cla$root.edge<-max(diag(vcv(cla)))/10
}else{
if(where.ref==(Ntip(tree)+1)) br.len/2+(max(diag(vcv(cla)))-max(diag(vcv(tree))))->pos.ref else {
max(diag(vcv(cla)))+br.len/2->Hcla
if((H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])<H/1000){
# rescale(cla,"depth",br.len/4)->cla
rescaleRR(cla,height=br.len/4)->cla
pos.ref<-br.len-br.len/4
}else{
if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),1])){
# rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla
rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla
pos.ref<-br.len/2
}else if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))
(max(diag(vcv(cla)))+br.len/2)-(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])->pos.ref else br.len/2->pos.ref
}
}
cla$root.edge<-br.len/2
}
bind.tree(tree,cla,where=where.ref,position = pos.ref)->tree
}
}
close(pb)
message("Binding done!")
if(is.null(backbone)){
tree$edge.length<-rep(1,length(tree$edge.length))
if(!is.null(tip.ages)) tree<-rescaleRR(tree,height=tip.ages[which.max(tip.ages)]+tip.ages[which.max(tip.ages)]/10)
}
trycal<-try({
### tips calibration ages ###
if(is.null(tip.ages)){
rep(0,length(tree$tip.label))->tip.ages
names(tip.ages)<-tree$tip.label
tip.ages[match(names(ages),names(tip.ages))]<-ages
}else{
if(any(!names(tip.ages)%in%tree$tip.label)){
warning(paste(paste(names(tip.ages)[which(!names(tip.ages)%in%tree$tip.label)],collapse=", "),
"not on the final tree: removed from the vector of tip.ages\n"),immediate. = TRUE)
tip.ages<-tip.ages[which(names(tip.ages)%in%tree$tip.label)]
}
if(!all(names(ages)%in%names(tip.ages))) c(ages[which(!names(ages)%in%names(tip.ages))],tip.ages)->tip.ages
if(!all(tree$tip.label%in%names(tip.ages))){
rep(0,length(which(!tree$tip.label%in%names(tip.ages))))->tip.add
names(tip.add)<-tree$tip.label[which(!tree$tip.label%in%names(tip.ages))]
c(tip.ages,tip.add)->tip.ages
}
}
### nodes calibration ages ###
if(!is.null(node.ages)){
sapply(names(node.ages),function(x){
getMRCA(tree,unlist(strsplit(x,"-")))
})->names(node.ages)
}else node.ages<-c()
### age original root ###
if(!is.null(backbone)&!getMRCA(tree,names(ages))%in%names(node.ages))
node.ages<-setNames(c(node.ages,Hset),c(names(node.ages),getMRCA(tree,names(ages))))
# {
# node.ages<-c(node.ages,Hset)
# names(node.ages)[length(node.ages)]<-getMRCA(tree,names(ages))
# }
### time distances inside attached clades ###
if(any(dat$bind.type==2)){
unlist(lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x){
c(x,getDescendants(tree2,x)[which(getDescendants(tree2,x)>Ntip(tree2))])->des
dist.nodes(tree2)->dn
max(diag(vcv(tree2)))-dn[which(rownames(dn)==(Ntip(tree2)+1)),match(des,rownames(dn))]->dndes
names(dndes)<-des
dndes
}))->ages.fix
if(!is.null(age.offset)&&age.offset>0) ages.fix+age.offset->ages.fix
# sapply(names(ages.fix),function(x) getMRCA(tree,tips(tree2,as.numeric(x))))->names(ages.fix)
sapply(1:length(ages.fix),function(x){
getMRCA(tree,tips(tree2,as.numeric(names(ages.fix)[x])))->nodex
tip.ages[match(tips(tree,nodex),names(tip.ages))]->tipx.ages
if(any(tipx.ages>ages.fix[x])) NA else nodex
})->names(ages.fix)
ages.fix<-ages.fix[which(!is.na(names(ages.fix)))]
if(any(!names(ages.fix)%in%names(node.ages)))
c(ages.fix[which(!names(ages.fix)%in%names(node.ages))],node.ages)->node.ages
}
if(max(diag(vcv(tree)))>H&&(!(Ntip(tree)+1)%in%names(node.ages)))
warning(paste("Root age not indicated: the tree root arbitrarily set at\n",round(max(diag(vcv(tree))),2)),immediate.=TRUE)
scaleTree(tree,node.ages=node.ages,tip.ages =tip.ages)->tree.final->tree.plot
message("Age Calibration done!")
},silent=TRUE)
if(inherits(trycal,"try-error")){
warning("Age Calibration failed with the error: \n",trycal[1],
"\n Returning the uncalibrated version of the tree",call.=FALSE)
tree->tree.final->tree.plot
}
if(plot){
if(any(dat$bind.type==2)) lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x)
c(getMRCA(tree.plot,tips(tree2,x)),getDescendants(tree.plot,getMRCA(tree.plot,tips(tree2,x)))))->cla.plot else cla.plot<-c()
c(which(tree.plot$tip.label%in%dat$bind[which(dat$bind.type==1)]),unlist(cla.plot))->all.plot
colo<-rep(scales::hue_pal()(2)[2],nrow(tree.plot$edge))
colo[match(all.plot,tree.plot$edge[,2])]<-scales::hue_pal()(2)[1]
names(colo)<-tree.plot$edge[,2]
colo[which(as.numeric(names(colo))<=Ntip(tree.plot))]->colo.tips
tree.plot$tip.label[which(!tree.plot$tip.label%in%unique(c(unlist(strsplit(dat$bind,"-")),unlist(strsplit(dat$reference,"-")))))]<-" "
names(colo.tips)<-tree.plot$tip.label[as.numeric(names(colo.tips))]
if(!is.null(filename)){
pdf(file=paste(filename,".pdf",sep=""))
if(Ntip(tree.plot)<100)
plot(tree.plot,edge.color=colo,cex=.6,tip.color=colo.tips[match(tree.plot$tip.label,names(colo.tips))]) else
plot(tree.plot,edge.color=colo,type="fan",cex=.6,tip.color=colo[which(tree.plot$edge[,2]<=Ntip(tree.plot))])
dev.off()
}
lapply(1:nrow(dat),function(x){
getMRCA(tree.final,c(unlist(dat$bind.tips[x]),unlist(strsplit(dat$reference[x],"-"))))->MRCAplot
extract.clade(tree.final,getMRCA(tree.final,c(unlist(dat$bind.tips[x]),unlist(strsplit(dat$reference[x],"-")))))->cla
colo[which(names(colo)%in%getDescendants(tree.final,MRCAplot))]->colo.cla
as.numeric(names(colo.cla))->nam.colo
which(cla$tip.label%in%tree.final$tip.label[nam.colo[which(nam.colo<=Ntip(tree.final))]])->nam.colo[which(nam.colo<=Ntip(tree.final))]
if(any(nam.colo>Ntip(tree.final))) sapply(nam.colo[which(nam.colo>Ntip(tree.final))],function(r) getMRCA(cla,tips(tree.final,r)))->nam.colo[which(nam.colo>Ntip(tree.final))]
names(colo.cla)<-nam.colo
colo.cla<-colo.cla[match(cla$edge[,2],names(colo.cla))]
list(cla,colo.cla)
})->clades.plot
names(clades.plot)<-dat[,1]
taxon<-manipulate::picker(as.list(dat[,1]))
manipulate::manipulate(plot(clades.plot[[which(names(clades.plot)==taxon)]][[1]],edge.color=clades.plot[[which(names(clades.plot)==taxon)]][[2]],cex=.6),
taxon=taxon)
}
return(tree.final)
}
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