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Mastering Machine Learning with R, Second Edition

You're reading from   Mastering Machine Learning with R, Second Edition Advanced prediction, algorithms, and learning methods with R 3.x

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Product type Paperback
Published in Apr 2017
Publisher Packt
ISBN-13 9781787287471
Length 420 pages
Edition 2nd Edition
Languages
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Author (1):
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Cory Lesmeister Cory Lesmeister
Author Profile Icon Cory Lesmeister
Cory Lesmeister
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Table of Contents (17) Chapters Close

Preface 1. A Process for Success 2. Linear Regression - The Blocking and Tackling of Machine Learning FREE CHAPTER 3. Logistic Regression and Discriminant Analysis 4. Advanced Feature Selection in Linear Models 5. More Classification Techniques - K-Nearest Neighbors and Support Vector Machines 6. Classification and Regression Trees 7. Neural Networks and Deep Learning 8. Cluster Analysis 9. Principal Components Analysis 10. Market Basket Analysis, Recommendation Engines, and Sequential Analysis 11. Creating Ensembles and Multiclass Classification 12. Time Series and Causality 13. Text Mining 14. R on the Cloud 15. R Fundamentals 16. Sources

Modeling and evaluation


For the modeling process, we will follow the following steps:

  1. Extract the components and determine the number to retain.
  2. Rotate the retained components.
  3. Interpret the rotated solution.
  4. Create the factor scores.
  5. Use the scores as input variables for regression analysis and evaluate the performance on the test data.

There are many different ways and packages to conduct PCA in R, including what seems to be the most commonly used prcomp() and princomp() functions in base R. However, for my money, it seems that the psych package is the most flexible with the best options.

Component extraction

To extract the components with the psych package, you will use the principal() function. The syntax will include the data and whether or not we want to rotate the components at this time:

> pca <- principal(train.scale, rotate="none")

You can examine the components by calling the pca object that we created. However, my primary intent is to determine what should be the number of components...

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