Description Usage Arguments Value Author(s) References Examples
View source: R/addFossilToPhy.R
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.
1 2 3 4 5 6 7 | 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)
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