TipVolatility: Detect rogue taxa using phylogenetic information distance

Description Usage Arguments Value References See Also Examples

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

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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

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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 Jan. 13, 2022, 5:07 p.m.