trestruct: Detect cryptic population structure in time trees

In emvolz-phylodynamics/treestructure: Detect Population Structure Within Phylogenetic Trees

Detect cryptic population structure in time trees

Description

Detect cryptic population structure in time trees

Usage

trestruct(
  tre,
  minCladeSize = 25,
  minOverlap = -Inf,
  nodeSupportValues = FALSE,
  nodeSupportThreshold = 95,
  nsim = 1000,
  level = 0.01,
  ncpu = 1,
  verbosity = 1,
  debugLevel = 0
)

Arguments

tre	A tree of type ape::phylo. Must be rooted. If the tree has multifurcations, it will be converted to a binary tree before processing.
minCladeSize	All clusters within partition must have at least this many tips.
minOverlap	Threshold time overlap required to find splits in a clade
nodeSupportValues	Node support values such as produced by bootrap or Bayesian credibility scores. Must be logical or vector with length equal to number of internal nodes in the tree. If numeric, these values should be between 0 and 100.
nodeSupportThreshold	Threshold node support value between 0 and 100. Nodes with support lower than this threshold will not be tested.
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. If node support values are available (as computed by bootstrap procedures), the method can optionally exclude designation of structure on poorly supported nodes. The method will not designate structure on nodes with zero branch length relative to their immediate ancestor.

Value

A TreeStructure object which includes cluster and partition 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 )

emvolz-phylodynamics/treestructure documentation built on March 1, 2025, 3:47 p.m.