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Practical Machine Learning with R
Practical Machine Learning with R

Practical Machine Learning with R: Define, build, and evaluate machine learning models for real-world applications

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Practical Machine Learning with R

Data Cleaning and Pre-processing

Learning Objectives

By the end of this chapter, you will be able to:

  • Perform the sort, rank, filter, subset, normalize, scale, and join operations in an R data frame.
  • Identify and handle outliers, missing values, and duplicates gracefully using the MICE and rpart packages.
  • Perform undersampling and oversampling on a dataset.
  • Apply the concepts of ROSE and SMOTE to handle unbalanced data.

This chapter covers the important concepts of handling data and making the data ready for analysis.

Introduction

Data cleaning and preparation takes about 70% of the effort in the entire process of a machine learning project. This step is essential because the quality of the data determines the accuracy of the prediction model. A clean dataset should contain good samples of the scenarios that we want to predict, and this will give us good prediction results. Also, the data should be balanced, which means that every category we want to predict should have similar number of samples. For example, if we want to predict whether it will rain or not on any particular day, and if the sample data size is 100, the data could contain 40 samples for It will rain and 60 samples for It will not rain today, or vice versa. However, if the ratio is 20:80 or 30:70, it is an unbalanced dataset, and this will not yield good results for the minority class.

In the following section, we will look at the essential operations performed on data frames in R. These operations will help us to manipulate and analyze...

Advanced Operations on Data Frames

In the previous chapter, we performed a number of operations on data frames, including rbind(). There are many more operations that can be performed on data frames, which are very useful while preparing the data for the model. The following exercises will describe these operations in detail and illustrate them through their corresponding implementation in R:

  • The order function: The order function is used to sort a data frame. We can specify ascending or descending order using the "-" symbol.
  • The sort function: The sort function can also be used to sort the data. The order can be specified as "decreasing=TRUE" or "decreasing"="FALSE".
  • The rank function: The rank function is used to rank the values in the data in a numerical manner.

Sorting, ordering, and ranking are operations that act as techniques to identify outliers. Outliers are values that are either too big or too small and do not fit in the value...

Identifying the Input and Output Variables

For any dataset, we should identify the input variables and the output variables. For the iris dataset, the input variables are the following:

  1. SepalLength
  2. SepalWidth
  3. PetalLength
  4. PetalWidth

The output variable, or the field to be predicted, is Species.

Identifying the Category of Prediction

Based on the category of prediction, we will perform different pre-processing steps. The category of prediction could be any of these:

  • Categorical Prediction: In this type of prediction, the output to be predicted will have class values such as yes, no, or given categories.
  • Numeric Prediction: In a numeric prediction, the output that will be predicted is a numeric value, such as predicting the cost of a house.

Handling Missing Values, Duplicates, and Outliers

In any dataset, we might have missing values, duplicate values, or outliers. We need to ensure that these are handled appropriately so that the data used by the model is clean.

Handling Missing Values

Missing values in a data frame can affect the model during the training process. Therefore, they need to be identified and handled during the pre-processing stage. They are represented as NA in a data frame. Using the example that follows, we will see how to identify a missing value in a dataset.

Using the is.na(), complete.cases(), and md.pattern() functions, we will identify the missing values.

The is.na() function, as the name suggests, returns TRUE for those elements marked NA or, for numeric or complex vectors, NaN (Not a Number) , and FALSE. The complete.cases() function returns TRUE if the value is missing and md.pattern() gives a summary of the missing values.

Exercise 12: Identifying the Missing Values

In the following example, we are adding...

Handling Outliers

Any datapoint with a value that is very different from the other data points is an outlier. Outliers can affect the training process negatively and therefore they need to be handled gracefully. In the following section, we will illustrate via examples both the process of detecting an outlier and the techniques used to handle them.

Exercise 16: Identifying Outlier Values

The outlier package can detect the outlier values. Using the opposite=TRUE parameter will fetch the outliers from the other side of dataset. The outlier values can be verified using a boxplot.

  1. Attach the outlier package:

    library(outliers)

  2. Detect outliers:

    #Detect outliers

    outlier(PimaIndiansDiabetes[,1:4])

    The output is as follows:

    pregnant  glucose pressure  triceps

          17        0        0       99

    Detect outliers from the other end:

    #This...

Summary

In this chapter, we learned how to perform several operations on a data frame, including scaling, standardizing, and normalizing. Also, we covered the sorting, ranking, and joining operations with their implementations in R. We discussed the need for pre-processing of the data; and identified and handled outliers, missing values, and duplicate values.

Next, we moved on to the sampling of data. It is important for the data to contain a reasonable sample of each class that is to be predicted. If the data is imbalanced, it can affect our predictions in a negative manner. Therefore, we can use either the undersampling, oversampling, ROSE, or SMOTE techniques imbalanced to ensure that the dataset is representative of all the classes that we want to predict. This can be done using the MICE, rpart, ROSE, and caret packages.

In the next chapter, we will cover feature engineering in detail, where we will focus on extracting features to create models.

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Key benefits

  • Gain a comprehensive overview of different machine learning techniques
  • Explore various methods for selecting a particular algorithm
  • Implement a machine learning project from problem definition through to the final model

Description

With huge amounts of data being generated every moment, businesses need applications that apply complex mathematical calculations to data repeatedly and at speed. With machine learning techniques and R, you can easily develop these kinds of applications in an efficient way. Practical Machine Learning with R begins by helping you grasp the basics of machine learning methods, while also highlighting how and why they work. You will understand how to get these algorithms to work in practice, rather than focusing on mathematical derivations. As you progress from one chapter to another, you will gain hands-on experience of building a machine learning solution in R. Next, using R packages such as rpart, random forest, and multiple imputation by chained equations (MICE), you will learn to implement algorithms including neural net classifier, decision trees, and linear and non-linear regression. As you progress through the book, you’ll delve into various machine learning techniques for both supervised and unsupervised learning approaches. In addition to this, you’ll gain insights into partitioning the datasets and mechanisms to evaluate the results from each model and be able to compare them. By the end of this book, you will have gained expertise in solving your business problems, starting by forming a good problem statement, selecting the most appropriate model to solve your problem, and then ensuring that you do not overtrain it.

Who is this book for?

If you are a data analyst, data scientist, or a business analyst who wants to understand the process of machine learning and apply it to a real dataset using R, this book is just what you need. Data scientists who use Python and want to implement their machine learning solutions using R will also find this book very useful. The book will also enable novice programmers to start their journey in data science. Basic knowledge of any programming language is all you need to get started.

What you will learn

  • Define a problem that can be solved by training a machine learning model
  • Obtain, verify and clean data before transforming it into the correct format for use
  • Perform exploratory analysis and extract features from data
  • Build models for neural net, linear and non-linear regression, classification, and clustering
  • Evaluate the performance of a model with the right metrics
  • Implement a classification problem using the neural net package
  • Employ a decision tree using the random forest library
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Table of Contents

6 Chapters
An Introduction to Machine Learning Chevron down icon Chevron up icon
Data Cleaning and Pre-processing Chevron down icon Chevron up icon
Feature Engineering Chevron down icon Chevron up icon
Introduction to neuralnet and Evaluation Methods Chevron down icon Chevron up icon
Linear and Logistic Regression Models Chevron down icon Chevron up icon
Unsupervised Learning Chevron down icon Chevron up icon

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Los ejercicios y actividades propuestos en este libro son esenciales para el aprendizaje efectivo de Machine Learning. Los autores incluyen en el texto soluciones detalladas de unos y otras, de modo que puedes contrastar lo que has hecho con las respuestas correctas.Incluyen capítulos sobre limpieza y preprocesamiento de datos (la parte más ardua y costosa en tiempo de un análisis de aprendizaje automático), el cálculo mediante diversos métodos de la importancia relativa de las variables dentro de una base de datos, las redes neuronales artificiales y las diversas métricas para calibrar su idoneidad en modelos de clasificación (exactitud, precisión, sensibilidad, puntuación F1) y en modelos de regresión (coeficiente de determinación, raíz cuadrada del error cuadrático medio, error medio absoluto, entre otros).El grueso del libro está consagrado al aprendizaje supervisado. Sólo en el último capítulo, el 6º, se introduce el aprendizaje no supervisado, con especial atención a la técnica de k-means clustering.Hay que advertir, eso sí, que los autores apenas se detienen a explicar cómo se escribe código en R ni tampoco aclaran la mayoría de los conceptos estadísticos que emplean. Todo esto lo dan por sabido en el que leyere. De modo que este libro, con ser excelente y muy didáctico, no es para primerizos en el área.
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