# Phylogenetic tree calibration The function is a wrapper around the functions "scalePhylo", "assign.ages", and "assign.brlen" written by Gene Hunt (http://paleobiology.si.edu/staff/individuals/hunt.cfm). It rescales tree branch lengths according to given calibration dates. ```r scaleTree(tree, tip.ages=NULL, node.ages=NULL) ``` ## Arguments - `tree`: a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous. - `tip.ages`: a named vector including the ages (i.e. distance from the youngest tip within the tree) of the tips to be changed. If unspecified, the function assumes all the tips are correctly placed with respect to the root. Names can be either tip labels or numbers. - `node.ages`: a named vector including the ages (i.e. distance from the youngest tip within the tree) of the nodes to be changed. If no calibration date for nodes is supplied, the tree root is fixed and the function shifts node position only where needed to fit tip ages. ## Returns Rescaled phylogentic tree with tip labels ordered according to their position in the tree. ## Examples ```r library(ape) library(phytools) data("DataFelids") DataFelids$treefel->treefel max(nodeHeights(treefel))->H #### Example 1 #### rep(0,4)->tipAges names(tipAges)<-tips(treefel,146) scaleTree(treefel,tipAges)->treeS1 edge.col<-rep("black",nrow(treefel$edge)) edge.col[which(treeS1$edge[,2]%in%getDescendants(treeS1,146))]<-"red" layout(2:1) plot(treefel,edge.color = edge.col,show.tip.label=FALSE) plot(treeS1,edge.color = edge.col,show.tip.label=FALSE) #### Example 2 #### nodeAges<-c(23.5,15.6) names(nodeAges)<-c(85,139) scaleTree(treefel,node.ages=nodeAges)->treeS2 edge.col<-rep("black",nrow(treefel$edge)) edge.col[which(treeS1$edge[,2]%in%c(getDescendants(treeS1,85), getDescendants(treeS1,139)))]<-"red" layout(2:1) plot(treefel,edge.color = edge.col,show.tip.label=FALSE) nodelabels(bg="w",frame="n",node=c(85,139),col="green") plot(treeS2,edge.color = edge.col,show.tip.label=FALSE) nodelabels(bg="w",frame="n",node=c(85,139),col="green") #### Example 3 #### 16->nodeAges names(nodeAges)<-"145" tipAges<-19 names(tipAges)<-treefel$tip.label[1] scaleTree(treefel,tip.ages = tipAges,node.ages=nodeAges)->treeS3 edge.col<-rep("black",nrow(treefel$edge)) edge.col[which(treeS3$edge[,2]%in%c(1,getMommy(treefel,1), getDescendants(treeS3,145)))]<-"red" layout(2:1) plot(treefel,edge.color = edge.col,show.tip.label=FALSE) nodelabels(bg="w",frame="n",node=145,col="green") plot(treeS3,edge.color = edge.col,show.tip.label=FALSE) nodelabels(bg="w",frame="n",node=145,col="green") ``` ## See Also c("[list(\"scaleTree\")](../doc/Tree-Manipulation.html#scaleTree)", "[\n](../doc/Tree-Manipulation.html#scaleTree)", "[ vignette](../doc/Tree-Manipulation.html#scaleTree)") ## Author(s) Silvia Castiglione, Pasquale Raia, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

scaleTree function