perrySelect: Model selection via resampling-based prediction error...
In aalfons/perry: Resampling-Based Prediction Error Estimation for Regression Models

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Combine resampling-based prediction error results for various models into one object and select the model with the best prediction performance.

perrySelect(
  ...,
  .list = list(...),
  .reshape = FALSE,
  .selectBest = c("min", "hastie"),
  .seFactor = 1
)

`...`	objects inheriting from class `"perry"` or `"perrySelect"` that contain prediction error results.
`.list`	a list of objects inheriting from class `"perry"` or `"perrySelect"`. If supplied, this is preferred over objects supplied via the ... argument.
`.reshape`	a logical indicating whether objects with more than one column of prediction error results should be reshaped to have only one column (see “Details”).
`.selectBest`	a character string specifying a criterion for selecting the best model. Possible values are `"min"` (the default) or `"hastie"`. The former selects the model with the smallest prediction error. The latter is useful for nested models or for models with a tuning parameter controlling the complexity of the model (e.g., penalized regression). It selects the most parsimonious model whose prediction error is no larger than `.seFactor` standard errors above the prediction error of the best overall model. Note that the models are thereby assumed to be ordered from the most parsimonious one to the most complex one. In particular a one-standard-error rule is frequently applied.
`.seFactor`	a numeric value giving a multiplication factor of the standard error for the selection of the best model. This is ignored if `.selectBest` is `"min"`.

Keep in mind that objects inheriting from class "perry" or "perrySelect" may contain multiple columns of prediction error results. This is the case if the response is univariate but the function to compute predictions (usually the predict method of the fitted model) returns a matrix.

The .reshape argument determines how to handle such objects. If .reshape is FALSE, all objects are required to have the same number of columns and the best model for each column is selected. A typical use case for this behavior would be if the investigated models contain prediction error results for a raw and a reweighted fit. It might then be of interest to researchers to compare the best model for the raw estimators with the best model for the reweighted estimators.

If .reshape is TRUE, objects with more than one column of results are first transformed with perryReshape to have only one column. Then the best overall model is selected.

It should also be noted that the argument names of .list, .reshape, .selectBest and .seFacor start with a dot to avoid conflicts with the argument names used for the objects containing prediction error results.

An object of class "perrySelect" with the following components:

pe: a data frame containing the estimated prediction errors for the models. In case of more than one resampling replication, those are average values over all replications.
se: a data frame containing the estimated standard errors of the prediction loss for the models.
reps: a data frame containing the estimated prediction errors for the models from all replications. This is only returned in case of more than one resampling replication.
splits: an object giving the data splits used to estimate the prediction error of the models.
y: the response.
yHat: a list containing the predicted values for the models. Each list component is again a list containing the corresponding predicted values from all replications.
best: an integer vector giving the indices of the models with the best prediction performance.
selectBest: a character string specifying the criterion used for selecting the best model.
seFactor: a numeric value giving the multiplication factor of the standard error used for the selection of the best model.

To ensure comparability, the prediction errors for all models are required to be computed from the same data splits.

Andreas Alfons

Hastie, T., Tibshirani, R. and Friedman, J. (2009) The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer, 2nd edition.

perryFit, perryTuning

library("perryExamples")
data("coleman")
set.seed(1234)  # set seed for reproducibility

## set up folds for cross-validation
folds <- cvFolds(nrow(coleman), K = 5, R = 10)

## compare LS, MM and LTS regression

# perform cross-validation for an LS regression model
fitLm <- lm(Y ~ ., data = coleman)
cvLm <- perry(fitLm, splits = folds,
              cost = rtmspe, trim = 0.1)

# perform cross-validation for an MM regression model
fitLmrob <- lmrob(Y ~ ., data = coleman)
cvLmrob <- perry(fitLmrob, splits = folds,
                 cost = rtmspe, trim = 0.1)

# perform cross-validation for an LTS regression model
fitLts <- ltsReg(Y ~ ., data = coleman)
cvLts <- perry(fitLts, splits = folds,
               cost = rtmspe, trim = 0.1)

# compare cross-validation results
perrySelect(LS = cvLm, MM = cvLmrob, LTS = cvLts)