TipVolatility: Detect rogue taxa using phylogenetic information distance

In Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

Detect rogue taxa using phylogenetic information distance

Description

Calculate the volatility of each tip: namely, the impact on the mean phylogenetic information distance \insertCiteSmith2020Rogue between trees when that tip is removed. Effective when the number of trees is small.

Usage

TipVolatility(trees)

Arguments

trees

List of trees to analyse.

Value

TipVolatility() returns a named vector listing the volatility index calculated for each leaf.

References

\insertAllCited

See Also

Other tip instability functions: TipInstability()

Examples

library("TreeTools", quietly = TRUE)
trees <- AddTipEverywhere(BalancedTree(8), "Rogue")
trees[] <- lapply(trees, AddTip, "Rogue", "Rogue2")

sb <- TipVolatility(trees)
sbNorm <- 1 + (99 * (sb - min(sb)) / (max(sb - min(sb))))
col <- hcl.colors(128, "inferno")[sbNorm]
plot(consensus(trees), tip.color = col)
plot(ConsensusWithout(trees, names(sb[sb == max(sb)])))

Rogue documentation built on April 1, 2023, 12:14 a.m.