DRR-class {dimRed} | R Documentation |

An S4 Class implementing Dimensionality Reduction via Regression (DRR).

DRR is a non-linear extension of PCA that uses Kernel Ridge regression.

`fun`

A function that does the embedding and returns a dimRedResult object.

`stdpars`

The standard parameters for the function.

Dimensionality reduction methods are S4 Classes that either be used
directly, in which case they have to be initialized and a full
list with parameters has to be handed to the `@fun()`

slot, or the method name be passed to the embed function and
parameters can be given to the `...`

, in which case
missing parameters will be replaced by the ones in the
`@stdpars`

.

DRR can take the following parameters:

- ndim
The number of dimensions

- lambda
The regularization parameter for the ridge regression.

- kernel
The kernel to use for KRR, defaults to

`"rbfdot"`

.- kernel.pars
A list with kernel parameters, elements depend on the kernel used,

`"rbfdot"`

uses`"sigma"`

.- pca
logical, should an initial pca step be performed, defaults to

`TRUE`

.- pca.center
logical, should the data be centered before the pca step. Defaults to

`TRUE`

.- pca.scale
logical, should the data be scaled before the pca ste. Defaults to

`FALSE`

.- fastcv
logical, should

`fastCV`

from the CVST package be used instead of normal cross-validation.- fastcv.test
If

`fastcv = TRUE`

, separate test data set for fastcv.- cv.folds
if

`fastcv = FALSE`

, specifies the number of folds for crossvalidation.- fastkrr.nblocks
integer, higher values sacrifice numerical accuracy for speed and less memory, see below for details.

- verbose
logical, should the cross-validation results be printed out.

Wraps around `drr`

, see there for details. DRR is
a non-linear extension of principal components analysis using Kernel
Ridge Regression (KRR, details see `constructKRRLearner`

and `constructFastKRRLearner`

). Non-linear
regression is used to explain more variance than PCA. DRR provides
an out-of-sample extension and a backward projection.

The most expensive computations are matrix inversions therefore the
implementation profits a lot from a multithreaded BLAS library.
The best parameters for each KRR are determined by cross-validaton
over all parameter combinations of `lambda`

and
`kernel.pars`

, using less parameter values will speed up
computation time. Calculation of KRR can be accelerated by
increasing `fastkrr.nblocks`

, it should be smaller than
n^1/3 up to sacrificing some accuracy, for details see
`constructFastKRRLearner`

. Another way to speed up
is to use `pars$fastcv = TRUE`

which might provide a more
efficient way to search the parameter space but may also miss the
global maximum, I have not ran tests on the accuracy of this method.

Laparra, V., Malo, J., Camps-Valls, G., 2015. Dimensionality Reduction via Regression in Hyperspectral Imagery. IEEE Journal of Selected Topics in Signal Processing 9, 1026-1036. doi:10.1109/JSTSP.2015.2417833

Other dimensionality reduction methods:
`AutoEncoder-class`

,
`DiffusionMaps-class`

,
`DrL-class`

,
`FastICA-class`

,
`FruchtermanReingold-class`

,
`HLLE-class`

,
`Isomap-class`

,
`KamadaKawai-class`

,
`MDS-class`

,
`NNMF-class`

,
`PCA-class`

,
`PCA_L1-class`

,
`UMAP-class`

,
`dimRedMethod-class`

,
`dimRedMethodList()`

,
`kPCA-class`

,
`nMDS-class`

,
`tSNE-class`

```
## Not run:
if(requireNamespace(c("kernlab", "DRR"), quietly = TRUE)) {
dat <- loadDataSet("variable Noise Helix", n = 200)[sample(200)]
emb <- embed(dat, "DRR", ndim = 3)
plot(dat, type = "3vars")
plot(emb, type = "3vars")
# We even have function to reconstruct, also working for only the first few dimensions
rec <- inverse(emb, getData(getDimRedData(emb))[, 1, drop = FALSE])
plot(rec, type = "3vars")
}
## End(Not run)
```

[Package *dimRed* version 0.2.6 Index]