resolvePolytomies {dowser}

Resolve polytomies to have the minimum number of single timepoint clades

Description

Resolve polytomies to have the minimum number of single timepoint clades

Usage

resolvePolytomies(
  phy,
  clone,
  minlength = 0.001,
  time = "time",
  sequence = "sequence_id",
  germline = "Germline",
  verbose = FALSE
)

Arguments

phy

Tree object

clone

airrClone data object corresponding to phy

minlength

Branch lengths to collapse in trees

time

Column name holding numeric time information

sequence

Column name holding sequence ID

germline

Germline sequence name

verbose

Print lots of rubbish while running?

Details

Iteratively identifies polytomies (clusters of < minlength branches), prunes each descendant branch, combines clades with the same timepoint before grouping them back together. Checks to make sure that the divergence of each tip is the same after resolution.

Value

A phylo tree object in which polytomies are resolved to have the minimum number of single timepoint clades.

See Also

Uses output from getTrees during correlationTest.