nestedcv (version 0.9.0)

outercv: Outer cross-validation of selected models

Description

This is a convenience function designed to use a single loop of cross-validation to quickly evaluate performance of specific models (random forest, naive Bayes, lm, glm) with fixed hyperparameters and no tuning. If tuning of parameters on data is required, full nested CV with inner CV is needed to tune model hyperparameters (see nestcv.train).

Usage

outercv(y, ...)
# S3 method for default
outercv(
  y,
  x,
  model,
  filterFUN = NULL,
  filter_options = NULL,
  weights = NULL,
  balance = NULL,
  balance_options = NULL,
  modifyX = NULL,
  modifyX_useY = FALSE,
  modifyX_options = NULL,
  outer_method = c("cv", "LOOCV"),
  n_outer_folds = 10,
  outer_folds = NULL,
  parallel_mode = NULL,
  cv.cores = 1,
  predict_type = "prob",
  outer_train_predict = FALSE,
  returnList = FALSE,
  final = TRUE,
  na.option = "pass",
  verbose = FALSE,
  suppressMsg = verbose,
  ...
)
# S3 method for formula
outercv(
  formula,
  data,
  model,
  outer_method = c("cv", "LOOCV"),
  n_outer_folds = 10,
  outer_folds = NULL,
  parallel_mode = NULL,
  cv.cores = 1,
  predict_type = "prob",
  outer_train_predict = FALSE,
  verbose = FALSE,
  suppressMsg = verbose,
  ...,
  na.action = na.fail
)

Value

An object with S3 class "outercv"

call

the matched call

output

Predictions on the left-out outer folds

outer_result

List object of results from each outer fold containing predictions on left-out outer folds, model result and number of filtered predictors at each fold.

dimx

vector of number of observations and number of predictors

outer_folds

List of indices of outer test folds

final_fit

Final fitted model on whole data

final_vars

Column names of filtered predictors entering final model

roc

ROC AUC for binary classification where available.

summary

Overall performance summary. Accuracy and balanced accuracy for classification. ROC AUC for binary classification. RMSE for regression.

Arguments

y

Response vector

...

Optional arguments passed to the function specified by model.

x

Matrix or dataframe of predictors

model

Character value or function of the model to be fitted.

filterFUN

Filter function, e.g. ttest_filter or relieff_filter. Any function can be provided and is passed y and x. Ideally returns a numeric vector with indices of filtered predictors. The custom function can return a character vector of names of the filtered predictors, but this will not work with the penalty.factor argument in nestcv.glmnet(). Not available if outercv is called with a formula.

filter_options

List of additional arguments passed to the filter function specified by filterFUN.

weights

Weights applied to each sample for models which can use weights. Note weights and balance cannot be used at the same time. Weights are not applied in filters.

balance

Specifies method for dealing with imbalanced class data. Current options are "randomsample" or "smote". Not available if outercv is called with a formula. See randomsample() and smote()

balance_options

List of additional arguments passed to the balancing function

modifyX

Character string specifying the name of a function to modify x. This can be an imputation function for replacing missing values, or a more complex function which alters or even adds columns to x. The required return value of this function depends on the modifyX_useY setting.

modifyX_useY

Logical value whether the x modifying function makes use of response training data from y. If FALSE then the modifyX function simply needs to return a modified x object. If TRUE then the modifyX function must return a model type object on which predict() can be called, so that train and test partitions of x can be modified independently.

modifyX_options

List of additional arguments passed to the x modifying function

outer_method

String of either "cv" or "LOOCV" specifying whether to do k-fold CV or leave one out CV (LOOCV) for the outer folds

n_outer_folds

Number of outer CV folds

outer_folds

Optional list containing indices of test folds for outer CV. If supplied, n_outer_folds is ignored.

parallel_mode

Either "mclapply", "parLapply" or "future". This determines which parallel backend to use. The default is parallel::mclapply on unix/mac and parallel::parLapply on windows.

cv.cores

Number of cores for parallel processing of the outer loops. Ignored if parallel_mode = "future".

predict_type

Only used with binary classification. Calculation of ROC AUC requires predicted class probabilities from fitted models. Most model functions use syntax of the form predict(..., type = "prob"). However, some models require a different type to be specified, which can be passed to predict() via predict_type.

outer_train_predict

Logical whether to save predictions on outer training folds to calculate performance on outer training folds.

returnList

Logical whether to return list of results after main outer CV loop without concatenating results. Useful for debugging.

final

Logical whether to fit final model.

na.option

Character value specifying how NAs are dealt with. "omit" is equivalent to na.action = na.omit. "omitcol" removes cases if there are NA in 'y', but columns (predictors) containing NA are removed from 'x' to preserve cases. Any other value means that NA are ignored (a message is given).

verbose

Logical whether to print messages and show progress

suppressMsg

Logical whether to suppress messages and printed output from model functions. This is necessary when using forked multicore parallelisation.

formula

A formula describing the model to be fitted

data

A matrix or data frame containing variables in the model.

na.action

Formula S3 method only: a function to specify the action to be taken if NAs are found. The default action is for the procedure to fail. An alternative is na.omit, which leads to rejection of cases with missing values on any required variable. (NOTE: If given, this argument must be named.)

Details

Some predictive model functions do not have an x & y interface. If the function specified by model requires a formula, x & y will be merged into a dataframe with model() called with a formula equivalent to y ~ ..

The S3 formula method for outercv is not really recommended with large data sets - it is envisaged to be primarily used to compare performance of more basic models e.g. lm() specified by formulae for example incorporating interactions. NOTE: filtering is not available if outercv is called with a formula - use the x-y interface instead.

An alternative method of tuning a single model with fixed parameters is to use nestcv.train with tuneGrid set as a single row of a data.frame. The parameters which are needed for a specific model can be identified using caret::modelLookup().

Case weights can be passed to model function which accept these, however outercv assumes that these are passed to the model via an argument named weights.

Note that in the case of model = "lm", although additional arguments e.g. subset, weights, offset are passed into the model function via "..." the scoping is known to go awry. Avoid using these arguments with model = "lm".

NA handling differs between the default S3 method and the formula S3 method. The na.option argument takes a character string, while the more typical na.action argument takes a function.

Examples

if (requireNamespace("randomForest")) {
## Classification example

## sigmoid function
sigmoid <- function(x) {1 / (1 + exp(-x))}

# load iris dataset and simulate a binary outcome
data(iris)
dt <- iris[, 1:4]
colnames(dt) <- c("marker1", "marker2", "marker3", "marker4")
dt <- as.data.frame(apply(dt, 2, scale))
x <- dt
y2 <- sigmoid(0.5 * dt$marker1 + 2 * dt$marker2) > runif(nrow(dt))
y2 <- factor(y2)

## Random forest
library(randomForest)
cvfit <- outercv(y2, x, "randomForest")
summary(cvfit)
plot(cvfit$roc)

## Mixture discriminant analysis (MDA)
if (requireNamespace("mda", quietly = TRUE)) {
  library(mda)
  cvfit <- outercv(y2, x, "mda", predict_type = "posterior")
  summary(cvfit)
}


## Example with continuous outcome
y <- -3 + 0.5 * dt$marker1 + 2 * dt$marker2 + rnorm(nrow(dt), 0, 2)
dt$outcome <- y

## simple linear model - formula interface
cvfit <- outercv(outcome ~ ., data = dt, model = "lm")
summary(cvfit)

## random forest for regression
cvfit <- outercv(y, x, "randomForest")
summary(cvfit)

## example with lm_filter() to reduce input predictors
cvfit <- outercv(y, x, "randomForest", filterFUN = lm_filter,
                 filter_options = list(nfilter = 2, p_cutoff = NULL))
summary(cvfit)
}