`step_pls()`

creates a *specification* of a recipe step that will convert
numeric data into one or more new dimensions.

## Arguments

- recipe
A recipe object. The step will be added to the sequence of operations for this recipe.

- ...
One or more selector functions to choose variables for this step. See

`selections()`

for more details.- role
For model terms created by this step, what analysis role should they be assigned? By default, the new columns created by this step from the original variables will be used as

*predictors*in a model.- trained
A logical to indicate if the quantities for preprocessing have been estimated.

- num_comp
The number of components to retain as new predictors. If

`num_comp`

is greater than the number of columns or the number of possible components, a smaller value will be used. If`num_comp = 0`

is set then no transformation is done and selected variables will stay unchanged, regardless of the value of`keep_original_cols`

.- predictor_prop
The maximum number of original predictors that can have non-zero coefficients for each PLS component (via regularization).

- outcome
When a single outcome is available, character string or call to

`dplyr::vars()`

can be used to specify a single outcome variable.- options
A list of options to

`mixOmics::pls()`

,`mixOmics::spls()`

,`mixOmics::plsda()`

, or`mixOmics::splsda()`

(depending on the data and arguments).- preserve
Use

`keep_original_cols`

instead to specify whether the original predictor data should be retained along with the new features.- res
A list of results are stored here once this preprocessing step has been trained by

`prep()`

.- columns
A character string of the selected variable names. This field is a placeholder and will be populated once

`prep()`

is used.- prefix
A character string for the prefix of the resulting new variables. See notes below.

- keep_original_cols
A logical to keep the original variables in the output. Defaults to

`FALSE`

.- skip
A logical. Should the step be skipped when the recipe is baked by

`bake()`

? While all operations are baked when`prep()`

is run, some operations may not be able to be conducted on new data (e.g. processing the outcome variable(s)). Care should be taken when using`skip = TRUE`

as it may affect the computations for subsequent operations.- id
A character string that is unique to this step to identify it.

## Value

An updated version of `recipe`

with the new step added to the
sequence of any existing operations.

## Details

PLS is a supervised version of principal component analysis that requires the outcome data to compute the new features.

This step requires the Bioconductor mixOmics package. If not installed, the step will stop with a note about installing the package.

The argument `num_comp`

controls the number of components that will be retained
(the original variables that are used to derive the components are removed from
the data). The new components will have names that begin with `prefix`

and a
sequence of numbers. The variable names are padded with zeros. For example, if
`num_comp < 10`

, their names will be `PLS1`

- `PLS9`

. If `num_comp = 101`

,
the names would be `PLS1`

- `PLS101`

.

Sparsity can be encouraged using the `predictor_prop`

parameter. This affects
each PLS component, and indicates the maximum proportion of predictors with
non-zero coefficients in each component. `step_pls()`

converts this
proportion to determine the `keepX`

parameter in `mixOmics::spls()`

and
`mixOmics::splsda()`

. See the references in `mixOmics::spls()`

for details.

## Tidying

The `tidy()`

method returns the coefficients that are
usually defined as

$$W(P'W)^{-1}$$

(See the Wikipedia article below)

When applied to data, these values are usually scaled by a column-specific
norm. The `tidy()`

method applies this same norm to the coefficients shown
above. When you `tidy()`

this step, a tibble with columns `terms`

(the
selectors or variables selected), `components`

, and `values`

is returned.

## Tuning Parameters

This step has 2 tuning parameters:

`num_comp`

: # Components (type: integer, default: 2)`predictor_prop`

: Proportion of Predictors (type: double, default: 1)

## References

https://en.wikipedia.org/wiki/Partial_least_squares_regression

Rohart F, Gautier B, Singh A, Lê Cao K-A (2017) *mixOmics: An R package for
'omics feature selection and multiple data integration*. PLoS Comput Biol
13(11): e1005752. doi:10.1371/journal.pcbi.1005752

## See also

Other multivariate transformation steps:
`step_classdist_shrunken()`

,
`step_classdist()`

,
`step_depth()`

,
`step_geodist()`

,
`step_ica()`

,
`step_isomap()`

,
`step_kpca_poly()`

,
`step_kpca_rbf()`

,
`step_kpca()`

,
`step_mutate_at()`

,
`step_nnmf_sparse()`

,
`step_nnmf()`

,
`step_pca()`

,
`step_ratio()`

,
`step_spatialsign()`

## Examples

```
# requires the Bioconductor mixOmics package
data(biomass, package = "modeldata")
biom_tr <-
biomass %>%
dplyr::filter(dataset == "Training") %>%
dplyr::select(-dataset, -sample)
biom_te <-
biomass %>%
dplyr::filter(dataset == "Testing") %>%
dplyr::select(-dataset, -sample, -HHV)
dense_pls <-
recipe(HHV ~ ., data = biom_tr) %>%
step_pls(all_numeric_predictors(), outcome = "HHV", num_comp = 3)
sparse_pls <-
recipe(HHV ~ ., data = biom_tr) %>%
step_pls(all_numeric_predictors(), outcome = "HHV", num_comp = 3, predictor_prop = 4 / 5)
## -----------------------------------------------------------------------------
## PLS discriminant analysis
data(cells, package = "modeldata")
cell_tr <-
cells %>%
dplyr::filter(case == "Train") %>%
dplyr::select(-case)
cell_te <-
cells %>%
dplyr::filter(case == "Test") %>%
dplyr::select(-case, -class)
dense_plsda <-
recipe(class ~ ., data = cell_tr) %>%
step_pls(all_numeric_predictors(), outcome = "class", num_comp = 5)
sparse_plsda <-
recipe(class ~ ., data = cell_tr) %>%
step_pls(all_numeric_predictors(), outcome = "class", num_comp = 5, predictor_prop = 1 / 4)
```