resolvePolytomies - 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?
Value¶
A phylo tree object in which polytomies are resolved to
have the minimum number of single timepoint clades.
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.
See also¶
Uses output from getTrees during correlationTest.