trestruct {treestructure}

Detect cryptic population structure in time trees

Description

Detect cryptic population structure in time trees

Usage

trestruct(tre, minCladeSize = 25, minOverlap = -Inf, nsim = 1000,
  level = 0.01, ncpu = 1, verbosity = 1, debugLevel = 0)

Arguments

tre

A tree of type ape::phylo. Must be rooted and binary.

minCladeSize

All clusters within parititon must have at least this many tips.

minOverlap

Threshold time overlap required to find splits in a clade

nsim

Number of simulations for computing null distribution of test statistics

level

Significance level for finding new split within a set of tips

ncpu

If >1 will compute statistics in parallel using multiple CPUs

verbosity

If > 0 will print information about progress of the algorithm

debugLevel

If > 0 will produce additional data in return value

Details

Estimates a partition of a time-scaled tree by contrasting coalescent patterns. The algorithm is premised on a Kingman coalescent null hypothesis and a test statistic is formulated based on the rank sum of node times in the tree.

Value

A TreeStructure object which includes cluster and partitition assignment for each tip of the tree.

References

E.M. Volz, Wiuf, C., Grad, Y., Frost, S., Dennis, A., Didelot, X.D. (2020) Identification of hidden population structure in time-scaled phylogenies.

Author(s)

Erik M Volz <[e-mail]>

Examples

tree <- ape::rcoal(50)
struct <-  trestruct( tree )