modifyTerminalBranches: Modify or Drop Terminal Branches of Various Types

Description

These functions modify terminal branches or drop certain terminal branches based on various criteria.

Usage

dropZLB(tree)
dropExtant(tree, tol = 0.01)
dropExtinct(tree, tol = 0.01, ignore.root.time = FALSE)
addTermBranchLength(tree, addtime = 0.001)

Arguments

tree

A phylogeny as a phylo object

tol

Tolerance of determining modern age for distinguishing extinct from extant taxa

ignore.root.time

Ignore root.time in calculating which tips are extinct? root.time will still be adjusted

addtime

Extra amount of time to add to all terminal branch lengths.

Value

Gives back a modified phylogeny as a phylo object

Details

DropZLB drops tip-taxa that are attached to the tree via zero-length branches ("ZLBs"). This is sometimes useful for paleo-trees, as various time-scaling methods often produce these 'ZLBs'. This is advised for analyses of diversification/diversity, as these will appear as instanteous speciation+extinction events, when in reality they probably represent ancestor-descendant relationships.Note this function only drops terminal tips that are on a ZLB. If you want to collapse internal zero-length branches, see di2multi DropExtinct drops all terminal branches which end before the modern (i.e. extinct taxa). DropExtant drops all terminal branches which end at the modern (i.e. extant/still-living taxa). In both cases, the modern is defined based on tree$root.time if available, or the modern is inferred to be the point in time when the tip furthest from the root (the latest tip) terminates. If the input tree has a $root.time element, as expected for most paleo-tree objects handled by this library, that root.time is adjusted if the relative time of the root divergence changes when terminal branches are dropped. Adjusted root.times are only given if the input tree has root.times. addTermBranchLength adds 'addtime' to the terminal branch lengths of the tree. If there is a $root.time element, this is increased by an amount equal to addtime. A negative amount can be input to reduce the length of terminal branches. However, if negative branch lengths are produced, the function fails and a warning is produced.

Examples

Run this code

set.seed(444)
#Simulate some fossil ranges with simFossilTaxa
taxa <- simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,maxExtant=0)
#simulate a fossil record with imperfect sampling with sampleRanges
rangesCont<-sampleRanges(taxa,r=0.5)
#Now let's make a tree using taxa2phylo
tree <- taxa2phylo(taxa,obs_time=rangesCont[,2])
#compare the two trees
layout(1:2)
plot(ladderize(tree))
plot(ladderize(dropZLB(tree)))
layout(1)

#example using dropExtinct and dropExtant
set.seed(444)
taxa <- simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=40,maxtime=1000,maxExtant=20)
tree<-taxa2phylo(taxa)
phyloDiv(tree)
tree1 <- dropExtinct(tree)
phyloDiv(tree1)
tree2 <- dropExtant(tree)
phyloDiv(tree2)

#example using addTermBranchLength
set.seed(444)
treeA <- rtree(10)
treeB <- addTermBranchLength(treeA,1)
compareTermBranches(treeA,treeB)

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