boostMDS {chroGPS} | R Documentation

## Improve goodness-of-fit of a given MDS solution in terms of R-square.

### Description

Given a distance matrix and a valid MDS representation for it, improve the R-square correlation between observed and approximated distances until converged is reached for a given threshold.

### Usage

    boostMDS(D, Y, rate = 0.01, maxit = 50, tol = 0.001, samplesize,
    verbose = TRUE, scale = FALSE, seed = 149, plt = FALSE, mc.cores = 1)

### Arguments

`D` | Distance matrix.
`Y` | Matrix with points from a valid MDS solution for the distances in D.
`rate` | Grid step rate, start with 0.1 which usually is a good compromise, try also 0.01, 1, 10.
`maxit` | Maximum number of iterations.
`tol` | Tolerace for R-square convergence.
`samplesize` | When there are over 100 points to represent, the gradiend descent step size is determined using a fraction `samplesize` of the original data points. By default 0.01 with a minimum of 100 points, which typically gives very stable results. Setting large `samplesize` can significantly increase the computational cost.
`verbose` | Give details of the gains in R-square and step size.
`scale` | Whether to scale the MDS coordinates in the output MDS.
`seed` | A random seed to be used in the resampling process if samplesize < 1.
`plt` | Whether to plot the intermediate solutions or not.
`mc.cores` | Number of cores to use in parallelized grid step size search.

### Value

The function returns a matrix with the coordinates of a valid MDS solution for distance matrix D where the R-square correlation has been improved. However, have in mind that an MDS solution with better R-square does not necessarily mean the solution is easier to interpret. As with any MDS approach, a balance must be found between pure 'technical' goodness-of-fit and usefulness of the delivered solution in terms of answering the original hypothesis.

### References

boostMDS is based on hitMDS (High-Throughput Multidimensional Scaling, see see http://dig.ipk-gatersleben.de/hitmds/hitmds.html for details)

### Examples

    # Not run, see also chroGPS-manual.pdf file for examples
    #data(geneSample)
    #d = distGPS(geneSample,uniqueRows=TRUE)
    #m = mds(d,type='isoMDS')
    #m
    #plot(m)
    #m = boostMDS(d@d,m@points)
    #plot(m)

[Package chroGPS version 2.4.0 Index]