cal_validate_isotonic_boot: Measure performance with and without using bagged isotonic...

In topepo/probably: Tools for Post-Processing Predicted Values

Measure performance with and without using bagged isotonic regression calibration

Description

This function uses resampling to measure the effect of calibrating predicted values.

Usage

cal_validate_isotonic_boot(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  metrics = NULL,
  save_pred = FALSE,
  ...
)

## S3 method for class 'resample_results'
cal_validate_isotonic_boot(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  metrics = NULL,
  save_pred = FALSE,
  ...
)

## S3 method for class 'rset'
cal_validate_isotonic_boot(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  metrics = NULL,
  save_pred = FALSE,
  ...
)

## S3 method for class 'tune_results'
cal_validate_isotonic_boot(
  .data,
  truth = NULL,
  estimate = NULL,
  metrics = NULL,
  save_pred = FALSE,
  ...
)

Arguments

.data	An rset object or the results of tune::fit_resamples() with a .predictions column.
truth	The column identifier for the true class results (that is a factor). This should be an unquoted column name.
estimate	A vector of column identifiers, or one of dplyr selector functions to choose which variables contains the class probabilities. It defaults to the prefix used by tidymodels (.pred_). The order of the identifiers will be considered the same as the order of the levels of the truth variable.
metrics	A set of metrics passed created via yardstick::metric_set()
save_pred	Indicates whether to a column of post-calibration predictions.
...	Options to pass to cal_estimate_isotonic_boot(), such as the times argument.

Details

These functions are designed to calculate performance with and without calibration. They use resampling to measure out-of-sample effectiveness. There are two ways to pass the data in:

• If you have a data frame of predictions, an rset object can be created via rsample functions. See the example below.

• If you have already made a resampling object from the original data and used it with tune::fit_resamples(), you can pass that object to the calibration function and it will use the same resampling scheme. If a different resampling scheme should be used, run tune::collect_predictions() on the object and use the process in the previous bullet point.

Please note that these functions do not apply to tune_result objects. The notion of "validation" implies that the tuning parameter selection has been resolved.

collect_predictions() can be used to aggregate the metrics for analysis.

Value

The original object with a .metrics_cal column and, optionally, an additional .predictions_cal column. The class cal_rset is also added.

Performance Metrics

By default, the average of the Brier scores (classification calibration) or the root mean squared error (regression) is returned. Any appropriate yardstick::metric_set() can be used. The validation function compares the average of the metrics before, and after the calibration.

See Also

https://www.tidymodels.org/learn/models/calibration/, cal_estimate_isotonic_boot()

Examples

library(dplyr)

segment_logistic %>%
  rsample::vfold_cv() %>%
  cal_validate_isotonic_boot(Class)

topepo/probably documentation built on Oct. 21, 2024, 3:28 a.m.