doALS {alsace} | R Documentation

## Wrapper function for als, plus some support functions

### Description

Wrapper function for the `als` function in the ALS package, providing a simple interface with sensible defaults for hyphenated data.

### Usage

    doALS(Xl, PureS, maxiter = 100, verbose)
    ## S3 method for class 'ALS'
    print(x, ...)
    ## S3 method for class 'ALS'
    summary(object, ...)
    ## S3 method for class 'ALS'
    plot(x, what = c("spectra", "profiles"), showWindows = TRUE,
                       mat.idx, comp.idx, xlab, ylab, main, ...)
    getTime(x)
    getWavelength(x)

### Arguments

`Xl` | a list of (numerical) data matrices. Missing values are not allowed.
`x, object` | an object of class ALS.
`PureS` | Initial estimates of pure spectral components.
`maxiter` | maximum number of iterations in ALS.
`verbose` | show `als` feedback during optimisation.
`what` | Show spectra or elution profiles
`showWindows` | If showing elution profiles, the window borders and the overlap areas between the windows can be shown (by default). Simply set this parameter to FALSE if this is undesired.
`mat.idx` | If showing elution profiles, one can provide the index of the sample(s) that should be shown. For every sample one plot will be made. Default is to show all.
`comp.idx` | Indices of components to be shown. Default is to show all components.
`xlab, ylab, main, ...` | self-explanatory optional arguments

### Details

The `plot` method can be used to plot the spectral components (one plot for the model) or the elution profiles (one plot for each data matrix, so usually several plots). The `summary` method also returns fit statistics like LOF, R2 and RMS. Extractor functions `getTime` and `getWavelength` provide the vectors of time points and wavelengths from the `ALS` object.

### Value

Function `doALS` returns an object of class "ALS", a list with the following fields:

`CList` | a list of matrices with the elution profiles in the columns. Every matrix in this list corresponds with a matrix in the input.
`S` | a matrix with the spectral components in the columns. These are common for all data matrices.
`rss` | residual sum of squares.
`resid` | a list of residual matrices.
`iter` | number of iterations.
`summ.stats` | summary statistics, providing more information about the fit quality.

See the `als` function for more details; only the `summ.stats` field is not part of the original `als` output.

### Author(s)

Ron Wehrens

### See Also

`als`,`showALSresult`

### Examples

    data(tea)
    new.lambdas <- seq(260, 500, by = 2)
    tea <- lapply(tea.raw, preprocess, dim2 = new.lambdas)
    tea.split <- splitTimeWindow(tea, c(12, 14), overlap = 10)

    Xl <- tea.split[[2]]
    Xl.opa <- opa(Xl, 4)

    Xl.als <- doALS(Xl, Xl.opa)
    Xl.als
    summary(Xl.als)
    plot(Xl.als, "spectra")
    par(mfrow = c(1, 3))
    plot(Xl.als, "profiles", ylim = c(0, 600), mat.idx = 1:3)

[Package alsace version 1.28.0 Index]