Box-Cox transformation from Feature Engineering by Max Kuhn and Kjell Johnson

Welcome to rtichoke blog!

This blog will be dedicated to the {rtichoke} package, which means that it will contain posts that are related to performance metrics and the possible related usability of {rtichoke}.

Replications

To make the package easier to use I plan to reproduce other people’s code with rtichoke, posts of this kind will be available under the category “replications”.

My first choice is to replicate the first example from the book “Feature Engineering and Selection: A Practical Approach for Predictive Models by Max Kuhn and Kjell Johnson”.

In this example you can see how Box-Cox transformation improves the discrimination capability of the logistic regression model without using any additional information.

Original Code

The code is almost identical to the original code that can be found on github.

Preparing the Data

library(caret)
library(tidymodels)
library(ggplot2)


data(segmentationData)

segmentationData <- 
  segmentationData |> 
  dplyr::select(EqSphereAreaCh1, PerimCh1, Class, Case) |> 
  setNames(c("PredictorA", "PredictorB", "Class", "Case")) |> 
  mutate(Class = factor(ifelse(Class == "PS", "One", "Two")))

example_train <- 
  segmentationData |> 
  dplyr::filter(Case == "Train") |> 
  dplyr::select(-Case)

example_test  <- 
  segmentationData |> 
  dplyr::filter(Case == "Test") |> 
  dplyr::select(-Case)

Training the Models

example_ctrl <- 
  trainControl(method = "none",
               classProbs = TRUE,
               summaryFunction = twoClassSummary)

natural_terms <- train(Class ~ PredictorA + PredictorB,
                       data = example_train,
                       method = "glm",
                       metric = "ROC",
                       trControl = example_ctrl)

trans_terms <- train(Class ~ PredictorA + PredictorB,
                     data = example_train,
                     method = "glm",
                     preProc = "BoxCox",
                     metric = "ROC",
                     trControl = example_ctrl)

Creating Predictions

original_probs <- predict(natural_terms, example_test, type = "prob")[,1]

transformed_probs <- predict(trans_terms, example_test, type = "prob")[,1]

outcomes <- example_test$Class == "One"

Creating ROC Curve with yardstick

natural_dat <-
  example_test |> 
  mutate(
    prob = original_probs) |> 
  roc_curve(Class, prob) |> 
  mutate(Format = "Natural Units")

trans_dat <-
  example_test |> 
  mutate(
    prob = transformed_probs) |> 
  roc_curve(Class, prob) |> 
  mutate(Format = "Inverse Units") 

both_dat <- 
  bind_rows(natural_dat, trans_dat) |>
  mutate(
    Format = factor(Format, levels = c("Natural Units", "Inverse Units")))

trans_roc_plot <- 
  ggplot(both_dat) +
  geom_step(aes(x = 1 - specificity, y = sensitivity, color = Format)) + 
  coord_equal() + 
  xlab("False Positive Rate") + 
  ylab("True Positive Rate") + 
  theme(legend.position = c(.8, .2)) + 
  scale_colour_manual(
    values = c("Natural Units" = "grey", 
               "Inverse Units" = "black")) + 
  geom_abline(intercept = 0, slope = 1, col = "grey", lty = 2) +
  theme_classic()

trans_roc_plot

rtichoke code

Creating ROC Curve with rtichoke

library(rtichoke)

create_roc_curve(
  probs = list(
    "Natural Units" = original_probs,
    "Inverse Units" = transformed_probs
  ),
  reals = list(
    outcomes
  ),
  size = 350, 
  color_values = c("grey", "black")
)

library(rtichoke)

create_roc_curve(
  probs = list(
    "Natural Units" = original_probs,
    "Inverse Units" = transformed_probs
  ),
  reals = list(
    outcomes
  ),
  stratified_by = "ppcr",
  size = 350, 
  color_values = c("grey", "black")
)