Absolute Dates for Nodes of a Time-Scaled Phylogeny
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.
A phylogeny object of class 'phylo'. Must have edge.lengths!
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 depth of the tree will be taken as the root age, which implicitly assumes the latest most terminal tip is an extant taxon at the modern day (time = 0). If rootAge is so defined that some nodes may occur later than time = 0, this function may return negative dates.
If FALSE (the default), the dates returned are labeled with the
tip/node numbers as in
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.
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
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
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.
David W. Bapst, based on a function originally written by Graeme Lloyd.
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#let's simulate some example data set.seed(444) record<-simFossilRecord(p=0.1, q=0.1, nruns=1, nTotalTaxa=c(30,40), nExtant=0) taxa<-fossilRecord2fossilTaxa(record) #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)
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