R: Predict Method for PLSR and PCR

predict.mvr {pls} | R Documentation

## Predict Method for PLSR and PCR

### Description

Prediction for mvr (PCR, PLSR) models. New responses or scores are predicted using a fitted model and a new matrix of observations.

### Usage

    ## S3 method for class 'mvr'
    predict(object, newdata, ncomp = 1:object$ncomp, comps,
            type = c("response", "scores"), na.action = na.pass, ...)

### Arguments

`object` | an `mvr` object. The fitted model
`newdata` | a data frame. The new data. If missing, the training data is used.
`ncomp, comps` | vector of positive integers. The components to use in the prediction. See below.
`type` | character. Whether to predict scores or response values
`na.action` | function determining what should be done with missing values in `newdata`. The default is to predict `NA`. See `na.omit` for alternatives.
`...` | further arguments. Currently not used

### Details

When `type` is `"response"` (default), predicted response values are returned. If `comps` is missing (or is `NULL`), predictions for `length(ncomp)` models with `ncomp[1]` components, `ncomp[2]` components, etc., are returned. Otherwise, predictions for a single model with the exact components in `comps` are returned. (Note that in both cases, the intercept is always included in the predictions. It can be removed by subtracting the `Ymeans` component of the fitted model.)

When `type` is `"scores"`, predicted score values are returned for the components given in `comps`. If `comps` is missing or `NULL`, `ncomps` is used instead.

It is also possible to supply a matrix instead of a data frame as `newdata`, which is then assumed to be the X data matrix. Note that the usual checks for the type of the data are then omitted. Also note that this is only possible with `predict`; it will not work in functions like `predplot`, `RMSEP` or `R2`, because they also need the response variable of the new data.

### Value

When `type` is `"response"`, a three dimensional array of predicted response values is returned. The dimensions correspond to the observations, the response variables and the model sizes, respectively.

When `type` is `"scores"`, a score matrix is returned.

### Note

A warning message like 'newdata' had 10 rows but variable(s) found have 106 rows means that not all variables were found in the `newdata` data frame. This (usually) happens if the formula contains terms like `yarn$NIR`. Do not use such terms; use the `data` argument instead. See `mvr` for details.

### Author(s)

Ron Wehrens and Bjørn-Helge Mevik

### See Also

`mvr`, `summary.mvr`, `coef.mvr`, `plot.mvr`

### Examples

    data(yarn)
    nir.mvr <- mvr(density ~ NIR, ncomp = 5, data = yarn[yarn$train,])

    ## Predicted responses for models with 1, 2, 3 and 4 components
    pred.resp <- predict(nir.mvr, ncomp = 1:4, newdata = yarn[!yarn$train,])

    ## Predicted responses for a single model with components 1, 2, 3, 4
    predict(nir.mvr, comps = 1:4, newdata = yarn[!yarn$train,])

    ## Predicted scores
    predict(nir.mvr, comps = 1:3, type = "scores", newdata = yarn[!yarn$train,])

[Package pls version 2.7-0 Index]