R: Optimise several baseline algorithms on a data set

doOptim {baseline} | R Documentation

## Optimise several baseline algorithms on a data set

### Description

Tests several baseline algorithms with one predictor for a given data set. The baseline algorithms are represented as a list of `baselineAlgTest` objects, and the predictor as a `predictionTest` object.

### Usage

    doOptim(baselineTests, X, y, predictionTest, postproc = NULL,
            tmpfile = "tmp.baseline", verbose = FALSE, cleanTmp = FALSE)

### Arguments

`baselineTests` | a list of `baselineAlgTest` objects. The baseline algorithms and parameter values to test
`X` | A matrix. The spectra to use in the test
`y` | A vector or matrix. The response(s) to use in the test
`predictionTest` | A `predictionTest` object. The predictor and parameter values to use in the test
`postproc` | A function, used to postprocess the baseline corrected spectra prior to prediction testing. The function should take a matrix of spectra as its only argument, and return a matrix of postprocessed spectra
`tmpfile` | The basename of the files used to store intermediate calculations for checkpointing. Defaults to `"tmp.baseline"`
`verbose` | Logical, specifying whether the test should print out progress information. Default is `FALSE`
`cleanTmp` | Logical, specifying whether the intermediate files should be deleted when the optimisation has finished. Default is `FALSE`

### Details

The function loops through the baseline algorithm tests in `baselineTests`, testing each of them with the given data and prediction test, and collects the results. The results of each baseline algorithm test is saved in a temporary file so that if the optimisation is interrupted, it can be re-run and will use the pre-calculated results. If `cleanTmp` is `TRUE`, the temporary files are deleted when the whole optimisation has finished.

### Value

A list with components

`baselineTests` | The `baselineTests` argument
`results` | A list with the `baselineAlgResult` objects for each baseline test
`minQualMeas` | The minimum quality measure value
`baselineAlg.min` | The name of the baseline algorithm giving the minimum quality measure value
`param.min` | A list with the parameter values corresponding to the minimum quality measure value

### Author(s)

BjÃ¸rn-Helge Mevik and Kristian Hovde Liland

### See Also

`baselineAlgTest`,`predictionTest`

[Package baseline version 1.2-1 Index]