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Collapses monophyletic tips of a phylogenetic tree prior to codiv()

collapse_monophyletic.Rd

Collapses monophyletic tips of a phylogenetic tree prior to codiv()

Usage

collapse_monophyletic(symbiont_subtree, Host_to_Symbiont_df)

Arguments

symbiont_subtree

A sub-node of the complete Symbiont_tree

Host_to_Symbiont_df

A data.frame() that pairs all of the tips in the Symbiont_tree with the tip in the Host_tree it was isolated from.

Value

A phylogenetic tree with monophyletic nodes (i.e. all tips from the same host) are collapsed into 1 tip.

Examples

collapse_monophyletic(Symbiont_tree, Host_to_Symbiont_df)
#> Error in collapse_monophyletic(Symbiont_tree, Host_to_Symbiont_df): could not find function "collapse_monophyletic"