Model Evaluation

library(bayesrules)

For Bayesian model evaluation, the bayesrules package has three functions prediction_summary(), classification_summary() and naive_classification_summary() as well as their cross-validation counterparts prediction_summary_cv(), classification_summary_cv(), and naive_classification_summary_cv() respectively.

Functions	Response	Model
`prediction_summary()` `prediction_summary_cv()`	Quantitative	rstanreg
`classification_summary()` `classification_summary_cv()`	Binary	rstanreg
`naive_classification_summary()` `naive_classification_summary_cv()`	Categorical	naiveBayes

Prediction Summary

Given a set of observed data including a quantitative response variable y and an rstanreg model of y, prediction_summary() returns 4 measures of the posterior prediction quality.

Median absolute prediction error (mae) measures the typical difference between the observed y values and their posterior predictive medians (stable = TRUE) or means (stable = FALSE).
Scaled mae (mae_scaled) measures the typical number of absolute deviations (stable = TRUE) or standard deviations (stable = FALSE) that observed y values fall from their predictive medians (stable = TRUE) or means (stable = FALSE).
and 4. within_50 and within_90 report the proportion of observed y values that fall within their posterior prediction intervals, the probability levels of which are set by the user. Although 50% and 90% are the defaults for the posterior prediction intervals, these probability levels can be changed with prob_inner and prob_outer arguments. The example below shows the 60% and 80% posterior prediction intervals.

# Data generation
example_data <- data.frame(x = sample(1:100, 20)) 
example_data$y <- example_data$x*3 + rnorm(20, 0, 5)


# rstanreg model
example_model <- rstanarm::stan_glm(y ~ x,  data = example_data, refresh = FALSE)

# Prediction Summary
prediction_summary(example_model, example_data, 
                   prob_inner = 0.6, prob_outer = 0.80, 
                   stable = TRUE)
       mae mae_scaled within_60 within_80
1 4.190024   1.004458       0.6      0.85

Similarly, prediction_summary_cv() returns the 4 cross-validated measures of a model’s posterior prediction quality for each fold as well as a pooled result. The k argument represents the number of folds to use for cross-validation.

prediction_summary_cv(model = example_model, data = example_data, 
                      k = 2, prob_inner = 0.6, prob_outer = 0.80)
$folds
  fold      mae mae_scaled within_60 within_80
1    1 5.541730  0.7509689       0.5       0.8
2    2 6.377386  0.9820985       0.3       0.6

$cv
       mae mae_scaled within_60 within_80
1 5.959558  0.8665337       0.4       0.7

Classification Summary

Given a set of observed data including a binary response variable y and an rstanreg model of y, the classification_summary() function returns summaries of the model’s posterior classification quality. These summaries include a confusion matrix as well as estimates of the model’s sensitivity, specificity, and overall accuracy. The cutoff argument represents the probability cutoff to classify a new case as positive.

# Data generation
x <- rnorm(20)
z <- 3*x
prob <- 1/(1+exp(-z))
y <- rbinom(20, 1, prob)
example_data <- data.frame(x = x, y = y)


# rstanreg model
example_model <- rstanarm::stan_glm(y ~ x, data = example_data, 
                                    family = binomial, refresh = FALSE)

# Prediction Summary
classification_summary(model = example_model, data = example_data, cutoff = 0.5)                   
$confusion_matrix
 y 0  1
 0 7  1
 1 0 12

$accuracy_rates
                      
sensitivity      1.000
specificity      0.875
overall_accuracy 0.950

The classification_summary_cv() returns the same measures but for cross-validated estimates. The k argument represents the number of folds to use for cross-validation.

classification_summary_cv(model = example_model, data = example_data,
                          k = 2, cutoff = 0.5)                   
$folds
  fold sensitivity specificity overall_accuracy
1    1           1         0.8              0.9
2    2           1         1.0              1.0

$cv
  sensitivity specificity overall_accuracy
1           1         0.9             0.95

Naive Classification Summary

Given a set of observed data including a categorical response variable y and a naiveBayes model of y, the naive_classification_summary() function returns summaries of the model’s posterior classification quality. These summaries include a confusion matrix as well as an estimate of the model’s overall accuracy.

# Data
data(penguins_bayes, package = "bayesrules")

# naiveBayes model
example_model <- e1071::naiveBayes(species ~ bill_length_mm, data = penguins_bayes)

# Naive Classification Summary
naive_classification_summary(model = example_model, data = penguins_bayes, 
                             y = "species")
$confusion_matrix
   species       Adelie Chinstrap       Gentoo
    Adelie 95.39% (145) 0.00% (0)  4.61%   (7)
 Chinstrap  5.88%   (4) 8.82% (6) 85.29%  (58)
    Gentoo  6.45%   (8) 4.84% (6) 88.71% (110)

$overall_accuracy
[1] 0.7587209

Similarly naive_classification_summary_cv() returns the cross validated confusion matrix. The k argument represents the number of folds to use for cross-validation.

naive_classification_summary_cv(model = example_model, data = penguins_bayes, 
                                y = "species", k = 2)
$folds
  fold    Adelie Chinstrap   Gentoo overall_accuracy
1    1 0.9189189 0.1052632 0.900000        0.7325581
2    2 0.9871795 0.2000000 0.828125        0.7906977

$cv
   species       Adelie   Chinstrap       Gentoo
    Adelie 95.39% (145)  0.00%  (0)  4.61%   (7)
 Chinstrap  7.35%   (5) 14.71% (10) 77.94%  (53)
    Gentoo  8.06%  (10)  5.65%  (7) 86.29% (107)