Assign clone IDs to a tree allowing small polytomies.

Assign clone IDs to a tree allowing small polytomies.

Usage

assign_clones_polytomy(tree, k = Inf, paraphyletic = FALSE, return_df = TRUE)

Arguments

tree

Rooted phylo object with bifurcating or polytomous structure.

k

Positive scalar; maximum clade size that collapses into one clone.

paraphyletic

Logical; if TRUE, leftover unassigned tips below a node are grouped into one clone, otherwise each becomes a singleton.

return_df

Logical; if TRUE, returns a data frame annotated per tip, otherwise an integer vector of clone assignments.

Value

Either a data frame with columns cell, clade, annot, size, frac or an integer vector of clone IDs indexed by tip order.

Details

Finds the root (node never used as a child), recurses over internal nodes, and assigns clone IDs whenever a clade has <= k tips. Tips directly attached to the root are always singleton clones. Ensures all tips receive an assignment, warning if late singletons are required.