Description Usage Arguments Details Value References Author(s) Examples
Detect cryptic population structure in time trees
1 2 |
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 |
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.
A TreeStructure object which includes cluster and partitition assignment for each tip of the tree.
E.M. Volz, Wiuf, C., Grad, Y., Frost, S., Dennis, A., Didelot, X.D. (2020) Identification of hidden population structure in time-scaled phylogenies.
Erik M Volz <erik.volz@gmail.com>
1 2 | tree <- ape::rcoal(50)
struct <- trestruct( tree )
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