R: Bhattacharyya Coefficient

bhattacharyya {bio3d} | R Documentation

## Bhattacharyya Coefficient

### Description

Calculate the Bhattacharyya Coefficient as a similarity between two modes objects.

### Usage

    bhattacharyya(...)

    ## S3 method for class 'enma'
    bhattacharyya(enma, covs=NULL, ncore=NULL, ...)

    ## S3 method for class 'array'
    bhattacharyya(covs, ncore=NULL, ...)

    ## S3 method for class 'matrix'
    bhattacharyya(a, b, q=90, n=NULL, ...)

    ## S3 method for class 'nma'
    bhattacharyya(...)

    ## S3 method for class 'pca'
    bhattacharyya(...)

### Arguments

`enma` | an object of class `"enma"` obtained from function `nma.pdbs`.
`covs` | an array of covariance matrices of equal dimensions.
`ncore` | number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.
`a` | covariance matrix to be compared with `b`.
`b` | covariance matrix to be compared with `a`.
`q` | a numeric value (in percent) determining the number of modes to be compared.
`n` | the number of modes to be compared.
`...` | arguments passed to associated functions.

### Details

Bhattacharyya coefficient provides a means to compare two covariance matrices derived from NMA or an ensemble of conformers (e.g. simulation or X-ray conformers).

### Value

Returns the similarity coefficient(s).

### Author(s)

Lars Skjaerven

### References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. Fuglebakk, E. et al. (2013) JCTC 9, 5618–5628.

### See Also

Other similarity measures: `sip`, `covsoverlap`, `rmsip`.

[Package bio3d version 2.3-4 Index]