addFossilToPhy: add a fossil to an interior branch of a time-scaled phylogeny
In motmot.2.0: Models of Trait Macroevolution on Trees

Description Usage Arguments Value Author(s) References Examples

the function takes a time-scaled phylogeny and adds a fossil at a branch in the past

1 2	addFossilToPhy(phy, inGroup, fossil, fossilAge, minLength = 0.1, maxLength = NULL)

`phy`	An object of class "phylo" (see ape package).
`inGroup`	vector of tip labels defined as the ingroup - the fossil(s) will be placed on the stem branch leading to the 'inGroups' most recent common ancestor
`fossil`	tip labels for the new fossil
`fossilAge`	age of the fossil
`minLength`	minimum length leading to the fossil
`maxLength`	maximum length leading to the fossil. If NULL (default) then the maximum bound is half the length of the branch leading to the crown node

the the time-scaled phylogeny with the fossil attached

Mark Puttick

Puttick, M. N., Kriwet, J., Wen, W., Hu, S., Thomas, G. H., & Benton, M. J. (2017). Body length of bony fishes was not a selective factor during the biggest mass extinction of all time. Palaeontology, 60, 727-741.

data(anolis.tree)
plot(anolis.tree)
nodelabels(214, 214)
# add fossil to node 214
in.groups <- node.descendents(x=214, phy=anolis.tree, tip.labels=TRUE)[[2]]
fossilPhy <- addFossilToPhy(anolis.tree, in.groups, fossil="fakeFossil", fossilAge=60)
plot(fossilPhy)