Add Chapter 14 notes (#16)

* Add Chapter 5 notes

* Add Chapter 6 notes

* Use DALEX.

* Use randomForest.

* Add Chapter 10 - CP profiles notes

* Add 'rms' package to DESCRIPTION file

* Add patchwork to imports.

* Add Chapter 14 notes

* Add Chapter 15 notes

* Comment out explainer function for lmr/rf models. Substitute with .rds files.

---------

Co-authored-by: Jon Harmon <[email protected]>

14_introduction-to-dataset-level-exploration.Rmd

@@ -2,12 +2,20 @@
 
 **Learning objectives:**
 
-- THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
-
-## SLIDE 1 {-}
-
-- ADD SLIDES AS SECTIONS (`##`).
-- TRY TO KEEP THEM RELATIVELY SLIDE-LIKE; THESE ARE NOTES, NOT THE BOOK ITSELF.
+-  Dataset-level (global) explanations
+-  Understand how do the model predictions perform overall
+-  Model variable importance
+-  Understand how does a selected variable influence the model’s predictions
+-  Discover whether there are observations where the model yields wrong predictions
+
+## Part III - Contents
+
+-  Model overall performance measures (`Chapter 15`)
+-  Variable importance measures (`Chapter 16`)
+-  Partial-dependence  profiles (`Chapter 17`)
+-  Local-dependence and accumulated-local profiles (`Chapter 18`)
+-  Residuals diagnostics plots (`Chapter 19`)
+-  Summary of dataset-level exploration (`Chapter 20`)
 
 ## Meeting Videos {-}
 

15_model-performance-measures.Rmd

@@ -1,15 +1,102 @@
+---
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
 # Model-performance Measures
 
 **Learning objectives:**
 
-- THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
+-  Model performance measures and evaluation
+-  Goodness-of-fit (GoF)
+-  Goodness-of-prediction (GoP)
 
-## SLIDE 1 {-}
+## Introduction
 
-- ADD SLIDES AS SECTIONS (`##`).
-- TRY TO KEEP THEM RELATIVELY SLIDE-LIKE; THESE ARE NOTES, NOT THE BOOK ITSELF.
+-  Model evaluation (how reliable are the model's predictions?)
+-  Model comparison (compare two or more models and decide which is the best model)
+-  Out-of-sample and out-of-time comparisons (how the model performs with new, unseen data)
 
-## Meeting Videos {-}
+## Method
+
+![Source: Table 15.1](img/15-model-performance-measures/ch_15_table_1.jpg)
+
+## Example: Apartment prices
+
+![Source: Figure 15.1](img/15-model-performance-measures/figure-15.1.png)
+
+## Example: Titanic data
+
+![Source: Table 15.2](img/15-model-performance-measures/table_15.2.png)
+
+![Source: Figure 15.2](img/15-model-performance-measures/figure-15.2.png)
+
+![Source: Figure 15.3](img/15-model-performance-measures/figure-15.3.png)
+
+![Source: Figure 15.4](img/15-model-performance-measures/figure-15.4.png)
+
+## Pros and cons
+
+Pros
+
+-   Most used continuous dependent variable metrics (RMSE, MAD, $R^2$) provide a fairly simple way to compare the suitability of predicted and actual values.
+
+ -  For binary/categorical dependent variables, the use of ROC-AUC and lift charts provide a comprehensive metric to compare models performance.
+
+Cons
+
+-   Some continuous dependent variable mtrics (i.e., RMSE) can be sensitive to outliers.
+
+-   Binary dependent variable metrics can vary on the selected cut-off values used for creating predictions.
+
+## R code snippetts
+
+Let's retrieve the `titanic_imputed` dataset, and the `titanic_lmr` and `titanic_rf` models.
+```{r 15-load-objects}
+titanic_imputed <- archivist::aread("pbiecek/models/27e5c")
+titanic_lmr <- archivist::aread("pbiecek/models/58b24")
+titanic_rf <- archivist::aread("pbiecek/models/4e0fc")
+```
+
+Construct the explainers
+```{r 15-construct-explainers}
+library("rms")
+library("randomForest")
+library("DALEX")
+
+# explain_lmr <- explain(model = titanic_lmr, 
+#                        data = titanic_imputed[, -9],
+#                        y = titanic_imputed$survived == "yes", 
+#                        type = "classification",
+#                        label = "Logistic Regression")
+explain_lmr <- readRDS("./explainers/explain_lmr.rds")
+
+# explain_rf <- explain(model = titanic_rf,  
+#                       data = titanic_imputed[, -9],
+#                       y = titanic_imputed$survived == "yes", 
+#                       label = "Random Forest")
+explain_rf <- readRDS("./explainers/explain_rf.rds")
+```
+
+Function `model_performance()` calculates, by default, a set of selected model-performance measures.
+
+```{r 15-model-performance-rf}
+(eva_rf <- DALEX::model_performance(explain_rf))
+```
+
+```{r 15-model-performance-lmr}
+(eva_lr <- DALEX::model_performance(explain_lmr))
+```
+
+Plot the residual histograms and precision-recall curves for both models.
+```{r 15-plots}
+library("patchwork")
+
+p1 <- plot(eva_rf, eva_lr, geom = "histogram")
+p2 <- plot(eva_rf, eva_lr, geom = "prc")
+
+p1 + p2
+```
 
 ### Cohort 1 {-}