Merge pull request #775 from gjwgit/zy/760_evaluate_rpart_hand

zy/760 EVALUATE: rpart hand as the template for other methods
gjwgit · Jan 14, 2025 · 3f29103 · 3f29103
2 parents cc0d918 + 3f206c7
commit 3f29103
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diff --git a/assets/r/evaluate_measure_error_matrix.R b/assets/r/evaluate_measure_error_matrix.R
@@ -1,11 +1,11 @@
-# Using `actual` and `predicted` generate error matrix with `rattle::errorMatrix()`.
+# Using `actual` and `predicted` generate error matrix.
 #
 # Copyright (C) 2024, Togaware Pty Ltd.
 #
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Monday 2025-01-06 06:59:55 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:16:05 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -29,24 +29,12 @@
 # References:
 #
 # @williams:2017:essentials Chapter 7.
-# https://survivor.togaware.com/datascience/dtrees.html
-# https://survivor.togaware.com/datascience/rpart.html
 # https://survivor.togaware.com/datascience/ for further details.
 
-## #########################################################################
-## #########################################################################
-## #########################################################################
-## 20241220 gjw DO NOT MODIFY THIS FILE WITHOUT DISCUSSION
-## #########################################################################
-## #########################################################################
-## #########################################################################
-
 # Load required packages from the local library into the R session.
 
 library(rattle)       # Generate an error matrix.
 
-####################################
-
 em_count <- rattle::errorMatrix(actual, predicted, count=TRUE)
 ##
 ## 20241229 zy Capture the output of the error matrix and print it to

diff --git a/assets/r/evaluate_measure_hand.R b/assets/r/evaluate_measure_hand.R
@@ -1,12 +1,60 @@
-# PLACE HOLDER FOR NOW - THE CODE CAME FROM evaluate_model_rpart.R
+# Use `actual` and `probability` for David Hand's classifier evaluation.
+#
+# Copyright (C) 2025, Togaware Pty Ltd.
+#
+# License: GNU General Public License, Version 3 (the "License")
+# https://www.gnu.org/licenses/gpl-3.0.en.html
+#
+# Time-stamp: <Friday 2025-01-10 16:03:40 +1100 Graham Williams>
+#
+# Licensed under the GNU General Public License, Version 3 (the "License");
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+# Author: Zheyuan Xu, Graham Williams
 
+# TIMESTAMP
+#
+# References:
+#
+# @williams:2017:essentials Chapter 7.
+# https://survivor.togaware.com/datascience/ for further details.
+
+# Load required packages from the local library into the R session.
+
+library(glue)
+library(hmeasure)     # David Hand's classifier performance measure.
 
 # Evaluate the model using HMeasure.
 
-results <- HMeasure(true.class = actual_rpart_labels, scores = predicted_rpart_probs)
+results <- hmeasure::HMeasure(true.class = actual, scores = probability)
+
+# Create a single SVG file that displays all 4 plots.
+
+svg(filename = glue("TEMPDIR/model_evaluate_hand_{mtype}_{dtype}.svg"), 
+    width = 11, 
+    height = 8)
+
+# Set up a 2x2 layout.
+
+par(mfrow = c(2, 2))
 
-svg("TEMPDIR/model_rpart_evaluate_hand.svg")
+# Generate the four plots in one device.
 
-plotROC(results)
+hmeasure::plotROC(results, which = 1,)
+hmeasure::plotROC(results, which = 2,)
+hmeasure::plotROC(results, which = 3,)
+hmeasure::plotROC(results, which = 4,)
 
 dev.off()
diff --git a/assets/r/evaluate_measure_roc.R b/assets/r/evaluate_measure_roc.R
@@ -1,11 +1,11 @@
-# Using `actual` and `prediction` to generate ROC/AUC plots.
+# Use `actual` and `prediction` to generate ROC/AUC plots.
 #
 # Copyright (C) 2024, Togaware Pty Ltd.
 #
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Monday 2025-01-06 08:23:01 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:16:33 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -29,14 +29,10 @@
 # References:
 #
 # @williams:2017:essentials Chapter 7.
-# https://survivor.togaware.com/datascience/dtrees.html
-# https://survivor.togaware.com/datascience/rpart.html
 # https://survivor.togaware.com/datascience/ for further details.
 
 # Load required packages from the local library into the R session.
 
-library(ggplot2, quietly=TRUE)
-library(glue)
 library(ROCR)
 
 ################################

diff --git a/assets/r/evaluate_riskchart.R b/assets/r/evaluate_riskchart.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Sunday 2024-12-15 10:48:49 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:21:31 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,8 +35,6 @@
 
 # Load required packages from the local library into the R session.
 
-library(ggtext)       # Support markdown in ggplot titles.
-library(glue)         # Format strings: glue().
 library(rattle)       # Generate a risk chart.
 
 ####################################

diff --git a/assets/r/explore_visual_categoric.R b/assets/r/explore_visual_categoric.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Tuesday 2024-12-10 17:23:55 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:23:11 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -33,8 +33,6 @@
 
 # Load required packages from the local library into the R session.
 
-library(ggplot2)
-
 # Preprocess the dataset to generate a temporary dataset `tds` for the
 # plots.
 

diff --git a/assets/r/explore_visual_categoric_nogroupby.R b/assets/r/explore_visual_categoric_nogroupby.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Friday 2024-11-29 10:48:54 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:23:50 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,10 +35,8 @@
 
 # Load required packages from the local library into the R session.
 
-library(ggplot2)
-
 ########################################################################
-# Bar Plot 
+# Bar Plot
 ########################################################################
 
 svg("TEMPDIR/explore_visual_bars.svg", width=10)
@@ -55,7 +53,7 @@ ds %>%
 dev.off()
 
 ########################################################################
-# Dot Plot 
+# Dot Plot
 ########################################################################
 
 svg("TEMPDIR/explore_visual_dots.svg", width=10)
@@ -107,7 +105,7 @@ ggplot(combined_data, aes(y = SELECTED_VAR, x = Frequency)) +
 dev.off()
 
 ########################################################################
-# Mosaic Plot 
+# Mosaic Plot
 ########################################################################
 
 ## # 20241129 gjw A mosaic plot does not make sense for a single variable.

diff --git a/assets/r/explore_visual_numeric.R b/assets/r/explore_visual_numeric.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Tuesday 2024-12-10 17:20:42 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:23:26 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,7 +35,6 @@
 # Load required packages from the local library into the R session.
 
 library(dplyr)
-library(ggplot2)
 library(rattle)
 
 # Preprocess the dataset to generate a temporary dataset `tds` for the

diff --git a/assets/r/explore_visual_numeric_nogroupby.R b/assets/r/explore_visual_numeric_nogroupby.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Friday 2024-11-29 08:38:33 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:24:10 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,7 +35,6 @@
 # https://survivor.togaware.com/datascience/ for further details.
 
 library(dplyr)
-library(ggplot2)
 library(rattle)
 
 ########################################################################
@@ -126,7 +125,7 @@ ds %>%
 dev.off()
 
 ########################################################################
-# BENFORD'S LAW 
+# BENFORD'S LAW
 ########################################################################
 
 # Initialies the parameters.
@@ -161,7 +160,7 @@ len <- nchar(as.character(tds[1, 1]))
 svg("TEMPDIR/explore_visual_benford.svg", width=10)
 
 p <- ggplot2::ggplot(dsm,
-                     ggplot2::aes_string(x      = "digit", 
+                     ggplot2::aes_string(x      = "digit",
                                          y      = "value",
                                          colour = "variable",
                                          shape  = "variable")) +
@@ -189,7 +188,7 @@ dev.off()
 # PAIRS - REQUIRES TWO VARIABLES
 ########################################################################
 
-# Display a pairs plot for the selected variables. 
+# Display a pairs plot for the selected variables.
 
 # Use GGally's ggpairs() to do the hard work.
 
@@ -211,7 +210,7 @@ dev.off()
 ##   ggplot2::theme(panel.grid.major=ggplot2::element_blank(), legend.position="right") +
 ##   ggplot2::xlab(paste("\n\n", "TIMESTAMP", sep=""))
 
-  
+
 # ggplot2::scale_alpha_continuous(guide=FALSE) +
 #  ggplot2::scale_fill_brewer(palette=rattlePalette) +
 #  ggplot2::scale_colour_brewer(palette=rattlePalette)

diff --git a/assets/r/model_build_adaboost.R b/assets/r/model_build_adaboost.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Wednesday 2024-11-27 11:39:42 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:24:26 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -21,16 +21,13 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <https://www.gnu.org/licenses/>.
 #
-# Author: Zheyuan Xu
+# Author: Zheyuan Xu, Graham Williams
 
 # Load required libraries.
 
 library(ada)
 library(caret)
-library(ggplot2)
-library(ggtext)
-library(hmeasure)
-library(rattle) 
+library(rattle)
 library(rpart)
 
 # Define model type and description.
@@ -48,7 +45,7 @@ ada_control <- rpart.control(maxdepth = BOOST_MAX_DEPTH,
 # Train the AdaBoost model.
 
 model_ada <- ada(form,
-                 data    = trds, 
+                 data    = trds,
                  iter    = BOOST_ITERATIONS,
                  type    = "gentle", # Type of boosting.
                  control = ada_control)
@@ -108,7 +105,7 @@ ada_plot <- ada_plot +
 
 # Increase plot limits to make space for the labels.
 
-ada_plot <- ada_plot + 
+ada_plot <- ada_plot +
   scale_y_continuous(expand = expansion(mult = c(0, 0.15))) +
   expand_limits(y = max(importance_df$Importance) * 1.2)
 

diff --git a/assets/r/model_build_conditional_forest.R b/assets/r/model_build_conditional_forest.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Tuesday 2024-12-03 12:39:21 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:22:06 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,8 +35,6 @@
 
 # Load required packages.
 
-library(ggplot2)
-library(ggtext)       # Support markdown in ggplot titles.
 library(kernlab)
 library(party)
 library(rattle)

diff --git a/assets/r/model_build_ctree.R b/assets/r/model_build_ctree.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Monday 2024-12-02 08:42:13 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:01:40 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -35,8 +35,6 @@
 
 # Load required packages from the local library into the R session.
 
-library(ggtext)       # Support markdown in ggplot titles.
-library(hmeasure)
 library(party)        # Conditional inference trees
 library(partykit)     # Enhanced visualization and interpretation
 

diff --git a/assets/r/model_build_linear.R b/assets/r/model_build_linear.R
@@ -5,7 +5,7 @@
 # License: GNU General Public License, Version 3 (the "License")
 # https://www.gnu.org/licenses/gpl-3.0.en.html
 #
-# Time-stamp: <Monday 2024-10-07 17:03:05 +1100 Graham Williams>
+# Time-stamp: <Friday 2025-01-10 16:22:21 +1100 Graham Williams>
 #
 # Licensed under the GNU General Public License, Version 3 (the "License");
 #
@@ -24,7 +24,6 @@
 #
 # Author: Zheyuan Xu
 
-library(ggtext)       # Support markdown in ggplot titles.
 library(rattle)
 
 # Define model type and description.