collapse_locus_subtree: Collapse a clade into a single tip
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Details Value Examples

Collapse a clade into a single tip

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collapse_locus_subtree(list_of_subtrees, locus_to_collapse)

collapse_clade(list_of_subtrees, locus_to_collapse)

`list_of_subtrees`	a list of type 'multiPhylo'
`locus_to_collapse`	a subtree found within a subst of 'list_of_subtrees'

Takes a clade as input and collapses that clade to one tip in all trees in 'list_of_subtrees'.

multiPhy (list of trees) with the subtree in question collapse

lambda <- 1.0
mu <- 0.2
nt <- 10
trees <- sim_stBD(sbr = lambda, sdr = mu, numbsim = 1, n_tips = nt)
subtrees_of_trees <- ape::subtrees(trees[[1]])
st_of_interest <- subtrees_of_trees[[1]]
collapse_st_of_interest <- collapse_locus_subtree(trees, st_of_interest)