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Returns a tree with added clade


addClade(tree, id, clade)



TreeMan object


tip/node ID in tree to which the clade will be added


TreeMan object


Add a TreeMan object to an existing TreeMan object by specifying an ID at which to attach. If the id specified is an internal node, then the original clade descending from that node will be replaced. Before running, ensure no IDs are shared between the tree and the clade, except for the IDs in the clade of that tree that will be replaced. Note, returned tree will not have a node matrix.


t1 <- randTree(100)
# extract a clade
cld <- getSubtree(t1, "n2")
# remove the same clade
t2 <- rmClade(t1, "n2")
# add the clade again
t3 <- addClade(t2, "n2", cld)
# t1 and t3 should be the same
# note there is no need to remove a clade before adding
t3 <- addClade(t1, "n2", cld) # same tree