TipInstability | R Documentation |

`TipInstability()`

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

```
TipInstability(
trees,
log = TRUE,
average = "mean",
deviation = "sd",
checkTips = TRUE,
parallel = FALSE
)
ColByStability(
trees,
log = TRUE,
average = "mean",
deviation = "sd",
pal = hcl.colors(131, "inferno")[1:101]
)
```

`trees` |
List of trees to analyse. |

`log` |
Logical specifying whether to log-transform distances when calculating leaf stability. |

`average` |
Character specifying whether to use |

`deviation` |
Character specifying whether to use |

`checkTips` |
Logical specifying whether to check that tips are numbered consistently. |

`parallel` |
Logical specifying whether parallel execution should take place in C++. |

`pal` |
A vector listing a sequence of colours to be used for plotting. The earliest entries will be assigned to the most stable tips. |

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

`\sum\limits_{(x, y), j \neq i}{\frac{|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.

`ColByStability()`

returns a named character vector that assigns a
colour to each leaf in `trees`

according to their stability.

Martin R. Smith (martin.smith@durham.ac.uk)

Other tip instability functions:
`TipVolatility()`

```
library("TreeTools", quietly = TRUE)
# Generate some trees with a rogue taxon
trees <- AddTipEverywhere(BalancedTree(8), "Rogue")[3:6]
# Display the strict consensus
plot(consensus(trees), tip.col = ColByStability(trees))
# Add a legend for the colour scale used
PlotTools::SpectrumLegend(
"bottomleft", bty = "n", # No box
legend = c("Unstable", "", "Stable"),
palette = hcl.colors(131, "inferno")[1:101]
)
# Calculate leaf stability
instab <- TipInstability(trees, log = FALSE, ave = "mean", dev = "mad")
# Plot a consensus that omits the least stable leaves
plot(ConsensusWithout(trees, names(instab[instab > 0.2])))
```

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