addFossilToPhy: add a fossil to an interior branch of a time-scaled phylogeny

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

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

Usage

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

Arguments

phy	Input phylogeny an object of class phylo (see ape)
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

Value

the the time-scaled phylogeny with the fossil attached

Author(s)

Mark Puttick

References

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.

Examples

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)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.