# Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies) Modifying a dated tree with `$root.time` elements often changes the actual timing of the root relative to the tips, such as when dropping tips, extending branches, or shift node ages backwards. When such modifications occur, the function `fixRootTime` can be used to find the correct root age. This function is mainly used as a utility function called by other tree-modifying functions discussed in the manual page for `modifyTerminalBranches`. This is typically performed via the function `fixRootTime`. ```r fixRootTime( treeOrig, treeNew, testConsistentDepth = TRUE, fixingMethod = "matchCladeTransferNodeAge" ) ``` ## Arguments - `treeOrig`: A `phylo` object of a time-scaled phylogeny with a `$root.time` element. - `treeNew`: A `phylo` object containing a modified form of `treeOrig` (with no extra tip taxa added, but possibly with some tip taxa removed). - `testConsistentDepth`: A logical, either `TRUE` or `FALSE`. If `TRUE` (the default) the tree's root-to-furthest-tip depth is tested to make sure this depth is not greater than the new `$root.time` appended to the output tree. - `fixingMethod`: must be an character value, with a length of 1. The default option `fixingMethod = "matchCladeTransferNodeAge"`, will determine the `$root.time` of the new tree by comparing the clades of taxa between the two input trees. The new root age assigned is the age of (**1**) the `treeOrig` clade that contains **all** taxa present in `treeNew` and, if the set of (1) contains multiple clades, (**2**) the clade in the first set that contains the fewest taxa not in `treeNew`. If `fixingMethod = "rescaleUsingTipToRootDist"`, the `root.time` assigned to `treeNew` is the `$root.time` of `treeOrig`, adjusted based on the change in total tree depth between `treeOrig` and `treeNew`, as measured between the root and the first matching taxon in both trees. The `"rescaleUsingTipToRootDist"` option was the default for `fixRootTime` prior to paleotree v2.3, and is the option used by function `minBranchLength` when applied to a tree with pre-existing root age element. ## Returns Gives back a modified phylogeny as a `phylo` object, with a modified `$root.time` element. ## Examples ```r #testing dropPaleoTip... and fixRootTime by extension #simple example tree <- read.tree(text = "(A:3,(B:2,(C:5,D:3):2):3);") tree$root.time <- 10 plot(tree,no.margin = FALSE) axisPhylo() # now a series of tests, dropping various tips (test <- dropPaleoTip(tree,"A")$root.time) # = 7 (test[2] <- dropPaleoTip(tree,"B")$root.time) # = 10 (test[3] <- dropPaleoTip(tree,"C")$root.time) # = 10 (test[4] <- dropPaleoTip(tree,"D")$root.time) # = 10 (test[5] <- dropPaleoTip(tree,c("A","B"))$root.time) # = 5 (test[6] <- dropPaleoTip(tree,c("B","C"))$root.time) # = 10 (test[7] <- dropPaleoTip(tree,c("A","C"))$root.time) # = 7 (test[8] <- dropPaleoTip(tree,c("A","D"))$root.time) # = 7 # is it all good? if not, fail so paleotree fails... if(!identical(test,c(7,10,10,10,5,10,7,7))){stop("fixRootTime fails!")} ``` ## See Also `modifyTerminalBranches`, `minBranchLength` ## Author(s) David W. Bapst

fixRootTime function