R: Set or return options for the pls package

pls.options {pls} | R Documentation

## Set or return options for the pls package

### Description

A function to set options for the pls package, or to return the current options.

### Usage

    pls.options(...)

### Arguments

`...` | a single list, a single character vector, or any number of named arguments (name = value).

### Details

If called with no arguments, or with an empty list as the single argument, `pls.options` returns the current options.

If called with a character vector as the single argument, a list with the arguments named in the vector are returned.

If called with a non-empty list as the single argument, the list elements should be named, and are treated as named arguments to the function.

Otherwise, `pls.options` should be called with one or more named arguments name = value. For each argument, the option named name will be given the value value.

The recognised options are:

mvralg

  The fit method to use in `mvr` and `mvrCv`. The value should be one of the allowed methods. Defaults to `"kernelpls"`. Can be overridden with the argument `method` in `mvr` and `mvrCv`.

pcralg

  The fit method to use in `pcr`. The value should be one of the allowed methods. Defaults to `"svdpc"`. Can be overridden with the argument `method` in `pcr`.

plsralg

  The fit method to use in `plsr`. The value should be one of the allowed methods. Defaults to `"kernelpls"`. Can be overridden with the argument `method` in `plsr`.

cpplsalg

  The fit method to use in `cppls`. The value should be one of the allowed methods. Defaults to `"cppls"`. Can be overridden with the argument `method` in `cppls`.

parallel

  Specification of how the cross-validation (CV) in `mvr` should be performed. If the specification is `NULL` (default) or `1`, the CV is done serially, otherwise it is done in parallel using functionality from the `parallel` package.

  If it is an integer greater than 1, the CV is done in parallel with the specified number of processes, using `mclapply`.

  If it is a cluster object created by `makeCluster`, the CV is done in parallel on that cluster, using `parLapply`. The user should stop the cluster herself when it is no longer needed, using `stopCluster`.

  Finally, if the specification is an unevaluated call to `makeCluster`, the call is evaluated, and the CV is done in parallel on the resulting cluster, using `parLapply`. In this case, the cluster will be stopped (with `stopCluster`) after the CV. Thus, in the final case, the cluster is created and destroyed for each CV, just like when using `mclapply`.

w.tol

  The tolerance used for removing values close to 0 in the vectors of loading weights in `cppls`. Defaults to .Machine$double.eps.

X.tol

  The tolerance used for removing predictor variables with L1 norms close to 0 in `cppls`. Defaults to 10^-12.

### Value

A list with the (possibly changed) options. If any named argument (or list element) was provided, the list is returned invisibly.

### Note

The function is a slight modification of the function `sm.options` from the package sm.

### Author(s)

Bjørn-Helge Mevik and Ron Wehrens

### Examples

    ## Return current options:
    pls.options()
    pls.options("plsralg")
    pls.options(c("plsralg", "pcralg"))

    ## Set options:
    pls.options(plsralg = "simpls", mvralg = "simpls")
    pls.options(list(plsralg = "simpls", mvralg = "simpls")) # Equivalent
    pls.options()

    ## Restore `factory settings':
    rm(.pls.Options)
    pls.options()

[Package pls version 2.7-0 Index]