# TipInstability: Tip instability In Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

## Description

`TipInstability()` calculates the instability of each leaf in a tree. Unstable leaves are likely to display roguish behaviour.

## Usage

 ```1 2 3 4 5 6 7 8 9``` ```TipInstability( trees, log = TRUE, average = "mean", deviation = "sd", checkTips = TRUE ) ColByStability(trees, log = TRUE, average = "mean", deviation = "sd") ```

## Arguments

 `trees` List of trees to analyse. `log` Logical specifying whether to log-transform distances when calculating leaf stability. `average` Character specifying whether to use `'mean'` or `'median'` tip distances to calculate leaf stability. `deviation` Character specifying whether to use `'sd'` or `'mad'` to calculate leaf stability. `checkTips` Logical specifying whether to check that tips are numbered consistently.

## Details

\insertCite

SmithCons;textualRogue defines the instability of a pair of leaves as the median absolute divergence in the graph geodesic (the number of edges in the shortest path between the leaves) across all trees, normalized against the mean graph geodesic. The instability of a single leaf is the mean instability of all pairs that include that leaf; higher values characterise leaves whose position is more variable between trees.

Other concepts of leaf instability include

• The 'taxonomic instability index', as implemented in Mesquite: described by \insertCiteThomson2010;textualRogue as ∑[x, y, j != i] (D[ijx] - D[ijy] / (D[ijx] - D[ijy])^2 ), where D[ijx] is the patristic distance (i.e. length of edges) between leaves i and j in tree x.

• the average stability of triplets (i.e. quartets including the root) that include the leaf \insertCiteThorley1999Rogue, implemented in "Phyutility" \insertCiteSmith2008Rogue; and related to 'positional congruence' measures \insertCiteEstabrook1992,Pol2009Rogue.

## References

\insertAllCited

Other tip instability functions: `TipVolatility()`
 ```1 2 3 4 5``` ```library("TreeTools", quietly = TRUE) trees <- AddTipEverywhere(BalancedTree(8), 'Rogue')[3:6] plot(consensus(trees), tip.col = ColByStability(trees)) instab <- TipInstability(trees, log = FALSE, ave = 'mean', dev = 'mad') plot(ConsensusWithout(trees, names(instab[instab > 0.2]))) ```