findOutliers {clstutils} | R Documentation

## Identify outlier objects given a square distance matrix.

### Description

Outliers are defined as elements with edge length to the centermost element > cutoff. The distance threshold (cutoff) can be either specified, or calculated as a quantile of all pairwise distances in the matrix.

### Usage

    findOutliers(mat, quant, cutoff)

### Arguments

`mat` | square matrix of distances
`quant` | given all pairwise distances x, calculate distance threshold as quantile(x, quant). Values closer to 0 are more stringent.
`cutoff` | an absolute cutoff overriding quant

### Value

Returns a boolean vector corresponding to margin of mat; outliers have a value of TRUE.

### Author(s)

Noah Hoffman

### Examples

    library(ape)
    data(seqs)
    data(seqdat)
    dmat <- ape::dist.dna(seqs[seqdat$tax_name == 'Enterococcus faecium',],
            pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
    summary(dmat[lower.tri(dmat)])
    outliers <- findOutliers(dmat, cutoff=0.015)
    table(outliers)

[Package clstutils version 1.42.0 Index]