Drop tip from multiPhylo object in R
I have 100s of phylogenetic trees in a multiPhylo object. There is one tip I need to drop from all of these trees. How can I do this in R?
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Brice Sarver
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written
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phylofun
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written
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phylofun
1 answer
A multiPhylo object is basically just a list of phylo objects. These can be operated on using the standard approaches for working with lists, so we use lapply to return a list for coercion back to the starting data type.
library(ape)
one <- rlineage(1, 1)
two <- rlineage(1, 1)
combined <- c(one, two)
# check: returns "multiPhylo"
class(combined)
results <- lapply(combined, drop.tip, "t2")
# explicitly convert back to an object of class multiPhylo
final <- do.call(c, results)
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Provide an example input data. Make a dummy multiPhylo object with 2 or 3 trees, and post output of
dput(myDummyTrees).