dateNodes: Absolute Dates for Nodes of a Time-Scaled Phylogeny

Description

This function returns the ages of nodes (both internal and terminal tips) for a given phylogeny of class 'phylo'. Specialized for use with time-scaled trees from paleotree, see Details.

Usage

dateNodes(tree, rootAge = tree$root.time, labelDates = FALSE,
  tolerance = 0.001)

Arguments

tree

A phylogeny object of class 'phylo'. Must have edge.lengths!

rootAge

The root age of the tree, assumed by default to be equal to the element tree$root.time, which is a standard element for trees time-scaled by the paleotree package. If not given by the user and if the $root.time element does not exist, then the maximum

labelDates

If FALSE (the default), the dates returned are labeled with the tip/node numbers as in tree$edge. If TRUE, they are labeled with the tip labels of every descendant tip, which for terminal tips means a single taxon label, and for internal t

tolerance

The tolerance within which a node date has to be removed from time = 0 (i.e. the modern) to issue a warning that there are 'negative' node dates.

Value

Returns a vector of length Ntip(tree) + Nnode(tree) which contains the dates for all terminal tip nodes and internal nodes for the tree, in that order, as numbered in the tree$edge matrix. These dates are always on a descending scale (i.e. time before present); see rootAge for how the present time is determined. If rootAge is so defined that some nodes may occur later than time = 0 units before present, this function may (confusingly) return negative dates and a warning message will be issued.

Details

This function is specialized for phylo objects time-scaled or simulated with functions from paleotree, and thus have a $root.time element. This function will still work without such, but users should see the details for the rootAge argument.

Examples

Run this code

#let's simulate some example data
set.seed(444)
taxa <- simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,maxExtant=0)
#get the true time-sclaed tree
tree1 <- taxa2phylo(taxa)

#now let's try dateNodes
dateNodes(tree1)

#let's ignore $root.time
dateNodes(tree1,rootAge=NULL)

#with the lengthy tip-label based labels
   #some of these will be hideously long
dateNodes(tree1,labelDates=TRUE)