book

Machine Learning with R - Second Edition

by Brett Lantz

July 2015

Beginner to intermediate

452 pages

11h 33m

English

Packt Publishing

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What this book covers

Downloading the example codeDownloading the color images of this bookErrataPiracyQuestions
The origins of machine learning
Machine learning successesThe limits of machine learningMachine learning ethics
Data storageAbstractionGeneralizationEvaluation
Types of input dataTypes of machine learning algorithmsMatching input data to algorithms
Installing R packagesLoading and unloading R packages
R data structuresVectorsFactorsListsData framesMatrixes and arrays
Saving, loading, and removing R data structuresImporting and saving data from CSV files
Exploring the structure of dataExploring numeric variablesMeasuring the central tendency – mean and medianMeasuring spread – quartiles and the five-number summaryVisualizing numeric variables – boxplotsVisualizing numeric variables – histogramsUnderstanding numeric data – uniform and normal distributionsMeasuring spread – variance and standard deviationExploring categorical variablesMeasuring the central tendency – the modeExploring relationships between variablesVisualizing relationships – scatterplotsExamining relationships – two-way cross-tabulations
Understanding nearest neighbor classificationThe k-NN algorithmMeasuring similarity with distanceChoosing an appropriate kPreparing data for use with k-NNWhy is the k-NN algorithm lazy?
Step 1 – collecting dataStep 2 – exploring and preparing the dataTransformation – normalizing numeric dataData preparation – creating training and test datasetsStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performanceTransformation – z-score standardizationTesting alternative values of k
Understanding Naive BayesBasic concepts of Bayesian methodsUnderstanding probabilityUnderstanding joint probabilityComputing conditional probability with Bayes' theoremThe Naive Bayes algorithmClassification with Naive BayesThe Laplace estimatorUsing numeric features with Naive Bayes
Step 1 – collecting dataStep 2 – exploring and preparing the dataData preparation – cleaning and standardizing text dataData preparation – splitting text documents into wordsData preparation – creating training and test datasetsVisualizing text data – word cloudsData preparation – creating indicator features for frequent wordsStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performance
Understanding decision treesDivide and conquerThe C5.0 decision tree algorithmChoosing the best splitPruning the decision tree
Step 1 – collecting dataStep 2 – exploring and preparing the dataData preparation – creating random training and test datasetsStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performanceBoosting the accuracy of decision treesMaking mistakes more costlier than others
Separate and conquerThe 1R algorithmThe RIPPER algorithmRules from decision treesWhat makes trees and rules greedy?
Step 1 – collecting dataStep 2 – exploring and preparing the dataStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performance
Understanding regressionSimple linear regressionOrdinary least squares estimationCorrelationsMultiple linear regression
Step 1 – collecting dataStep 2 – exploring and preparing the dataExploring relationships among features – the correlation matrixVisualizing relationships among features – the scatterplot matrixStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performanceModel specification – adding non-linear relationshipsTransformation – converting a numeric variable to a binary indicatorModel specification – adding interaction effectsPutting it all together – an improved regression model
Adding regression to trees
Step 1 – collecting dataStep 2 – exploring and preparing the dataStep 3 – training a model on the dataVisualizing decision treesStep 4 – evaluating model performanceMeasuring performance with the mean absolute errorStep 5 – improving model performance
Understanding neural networksFrom biological to artificial neuronsActivation functionsNetwork topologyThe number of layersThe direction of information travelThe number of nodes in each layerTraining neural networks with backpropagation
Step 1 – collecting dataStep 2 – exploring and preparing the dataStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performance
Classification with hyperplanesThe case of linearly separable dataThe case of nonlinearly separable dataUsing kernels for non-linear spaces
Step 1 – collecting dataStep 2 – exploring and preparing the dataStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performance
Understanding association rulesThe Apriori algorithm for association rule learningMeasuring rule interest – support and confidenceBuilding a set of rules with the Apriori principle
Step 1 – collecting dataStep 2 – exploring and preparing the dataData preparation – creating a sparse matrix for transaction dataVisualizing item support – item frequency plotsVisualizing the transaction data – plotting the sparse matrixStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performanceSorting the set of association rulesTaking subsets of association rulesSaving association rules to a file or data frame
Understanding clusteringClustering as a machine learning taskThe k-means clustering algorithmUsing distance to assign and update clustersChoosing the appropriate number of clusters
Step 1 – collecting dataStep 2 – exploring and preparing the dataData preparation – dummy coding missing valuesData preparation – imputing the missing valuesStep 3 – training a model on the dataStep 4 – evaluating model performanceStep 5 – improving model performance
Measuring performance for classificationWorking with classification prediction data in RA closer look at confusion matricesUsing confusion matrices to measure performanceBeyond accuracy – other measures of performanceThe kappa statisticSensitivity and specificityPrecision and recallThe F-measureVisualizing performance trade-offsROC curves
The holdout methodCross-validationBootstrap sampling
Tuning stock models for better performanceUsing caret for automated parameter tuningCreating a simple tuned modelCustomizing the tuning process
Understanding ensemblesBaggingBoostingRandom forestsTraining random forestsEvaluating random forest performance
Working with proprietary files and databasesReading from and writing to Microsoft Excel, SAS, SPSS, and Stata filesQuerying data in SQL databases
Downloading the complete text of web pagesScraping data from web pagesParsing XML documentsParsing JSON from web APIs
Analyzing bioinformatics dataAnalyzing and visualizing network data
Managing very large datasetsGeneralizing tabular data structures with dplyrMaking data frames faster with data.tableCreating disk-based data frames with ffUsing massive matrices with bigmemoryLearning faster with parallel computingMeasuring execution timeWorking in parallel with multicore and snowTaking advantage of parallel with foreach and doParallelParallel cloud computing with MapReduce and HadoopGPU computingDeploying optimized learning algorithmsBuilding bigger regression models with biglmGrowing bigger and faster random forests with bigrfTraining and evaluating models in parallel with caret

Content preview from Machine Learning with R - Second Edition

Improving the performance of R

R has a reputation for being slow and memory-inefficient, a reputation that is at least somewhat earned. These faults are largely unnoticed on a modern PC for datasets of many thousands of records, but datasets with a million records or more can exceed the limits of what is currently possible with consumer-grade hardware. The problem worsens if the dataset contains many features or if complex learning algorithms are being used.

Note

CRAN has a high-performance computing task view that lists packages pushing the boundaries of what is possible in R. It can be viewed at http://cran.r-project.org/web/views/HighPerformanceComputing.html.

Packages that extend R past the capabilities of the base software are being developed ...