cal_plot_breaks: Probability calibration plots via binning

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

Probability calibration plots via binning

Description

A plot is created to assess whether the observed rate of the event is about the same as the predicted probability of the event from some model.

A sequence of even, mutually exclusive bins are created from zero to one. For each bin, the data whose predicted probability falls within the range of the bin is used to calculate the observed event rate (along with confidence intervals for the event rate). If the predictions are well calibrated, the fitted curve should align with the diagonal line.

Usage

cal_plot_breaks(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  num_breaks = 10,
  conf_level = 0.9,
  include_ribbon = TRUE,
  include_rug = TRUE,
  include_points = TRUE,
  event_level = c("auto", "first", "second"),
  ...
)

## S3 method for class 'data.frame'
cal_plot_breaks(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  num_breaks = 10,
  conf_level = 0.9,
  include_ribbon = TRUE,
  include_rug = TRUE,
  include_points = TRUE,
  event_level = c("auto", "first", "second"),
  ...,
  .by = NULL
)

## S3 method for class 'tune_results'
cal_plot_breaks(
  .data,
  truth = NULL,
  estimate = dplyr::starts_with(".pred"),
  num_breaks = 10,
  conf_level = 0.9,
  include_ribbon = TRUE,
  include_rug = TRUE,
  include_points = TRUE,
  event_level = c("auto", "first", "second"),
  ...
)

## S3 method for class 'grouped_df'
cal_plot_breaks(
  .data,
  truth = NULL,
  estimate = NULL,
  num_breaks = 10,
  conf_level = 0.9,
  include_ribbon = TRUE,
  include_rug = TRUE,
  include_points = TRUE,
  event_level = c("auto", "first", "second"),
  ...
)

Arguments

.data	An ungrouped data frame object containing predictions and probability columns.
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.
num_breaks	The number of segments to group the probabilities. It defaults to 10.
conf_level	Confidence level to use in the visualization. It defaults to 0.9.
include_ribbon	Flag that indicates if the ribbon layer is to be included. It defaults to TRUE.
include_rug	Flag that indicates if the Rug layer is to be included. It defaults to TRUE. In the plot, the top side shows the frequency the event occurring, and the bottom the frequency of the event not occurring.
include_points	Flag that indicates if the point layer is to be included.
event_level	single string. Either "first" or "second" to specify which level of truth to consider as the "event". Defaults to "auto", which allows the function decide which one to use based on the type of model (binary, multi-class or linear)
...	Additional arguments passed to the tune_results object.
.by	The column identifier for the grouping variable. This should be a single unquoted column name that selects a qualitative variable for grouping. Default to NULL. When .by = NULL no grouping will take place.

Value

A ggplot object.

See Also

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

cal_plot_logistic(), cal_plot_windowed()

Examples

library(ggplot2)
library(dplyr)

cal_plot_breaks(
  segment_logistic,
  Class,
  .pred_good
)

cal_plot_logistic(
  segment_logistic,
  Class,
  .pred_good
)

cal_plot_windowed(
  segment_logistic,
  Class,
  .pred_good
)

# The functions support dplyr groups

model <- glm(Class ~ .pred_good, segment_logistic, family = "binomial")

preds <- predict(model, segment_logistic, type = "response")

gl <- segment_logistic %>%
  mutate(.pred_good = 1 - preds, source = "glm")

combined <- bind_rows(mutate(segment_logistic, source = "original"), gl)

combined %>%
  cal_plot_logistic(Class, .pred_good, .by = source)

# The grouping can be faceted in ggplot2
combined %>%
  cal_plot_logistic(Class, .pred_good, .by = source) +
  facet_wrap(~source) +
  theme(legend.position = "")

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