R: Collapsed Coalescent Intervals

collapsed.intervals {ape} | R Documentation

## Collapsed Coalescent Intervals

### Description

This function takes a `"coalescentIntervals"` objects and collapses neighbouring coalescent intervals into a single combined interval so that every collapsed interval is larger than `epsilon`. Collapsed coalescent intervals are used, e.g., to obtain the generalized skyline plot (`skyline`). For `epsilon = 0` no interval is collapsed.

### Usage

    collapsed.intervals(ci, epsilon=0)

### Arguments

`ci` | coalescent intervals (i.e. an object of class `"coalescentIntervals"`).
`epsilon` | collapsing parameter that controls the amount of smoothing (allowed range: from `0` to `ci$total.depth`)

### Details

Proceeding from the tips to the root of the tree each small interval is pooled with the neighboring interval closer to the root. If the neighboring interval is also small, then pooling continues until the composite interval is larger than `epsilon`. Note that this approach prevents the occurrence of zero-length intervals at the present. For more details see Strimmer and Pybus (2001).

### Value

An object of class `"collapsedIntervals"` with the following entries:

`lineages` | A vector with the number of lineages at the start of each coalescent interval.
`interval.length` | A vector with the length of each coalescent interval.
`collapsed.interval` | A vector indicating for each coalescent interval to which collapsed interval it belongs.
`interval.count` | The total number of coalescent intervals.
`collapsed.interval.count` | The number of collapsed intervals.
`total.depth` | The sum of the lengths of all coalescent intervals.
`epsilon` | The value of the underlying smoothing parameter.

### Author(s)

Korbinian Strimmer

### References

Strimmer, K. and Pybus, O. G. (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution, 18, 2298–2305.

### See Also

`coalescent.intervals`,`skyline`.

### Examples

    data("hivtree.table") # example tree
    # colescent intervals from vector of interval lengths
    ci <- coalescent.intervals(hivtree.table$size)
    ci
    # collapsed intervals
    cl1 <- collapsed.intervals(ci,0)
    cl2 <- collapsed.intervals(ci,0.0119)
    cl1
    cl2

[Package ape version 5.6-2 Index]