R: Construction of Consensus Distance Matrix With SDM

SDM {ape} | R Documentation

## Construction of Consensus Distance Matrix With SDM

### Description

This function implements the SDM method of Criscuolo et al. (2006) for a set of n distance matrices.

### Usage

    SDM(...)

### Arguments

`...` | 2n elements (with n > 1), the first n elements are the distance matrices: these can be (symmetric) matrices, objects of class `"dist"`, or a mix of both. The next n elements are the sequence length from which the matrices have been estimated (can be seen as a degree of confidence in matrices).

### Details

Reconstructs a consensus distance matrix from a set of input distance matrices on overlapping sets of taxa. Potentially missing values in the supermatrix are represented by `NA`. An error is returned if the input distance matrices can not resolve to a consensus matrix.

### Value

a 2-element list containing a distance matrix labelled by the union of the set of taxa of the input distance matrices, and a variance matrix associated to the returned distance matrix.

### Author(s)

Andrei Popescu niteloserpopescu@gmail.com

### References

Criscuolo, A., Berry, V., Douzery, E. J. P. , and Gascuel, O. (2006) SDM: A fast distance-based approach for (super)tree building in phylogenomics. Systematic Biology, 55, 740–755.

### See Also

`bionj`, `fastme`, `njs`, `mvrs`, `triangMtd`

[Package ape version 5.0 Index]