Factor Analysis and Dimension Reduction in R provides coverage, with worked examples, of a large number of dimension reduction procedures along with model performance metrics to compare them. Factor analysis in the form of principal components analysis (PCA) or principal factor analysis (PFA) is familiar to most social scientists. However, what is less familiar is understanding that factor analysis is a subset of the more general statistical family of dimension reduction methods. The social scientist's toolkit for factor analysis problems can be expanded to include the range of solutions this book presents. In addition to covering FA and PCA with orthogonal and oblique rotation, this book’s coverage includes higher-order factor models, bifactor models, models based on binary and ordinal data, models based on mixed data, generalized low-rank models, cluster analysis with GLRM, models involving supplemental variables or observations, Bayesian factor analysis, regularized factor analysis, testing for unidimensionality, and prediction with factor scores. The second half of the book deals with other procedures for dimension reduction. These include coverage of kernel PCA, factor analysis with multidimensional scaling, locally linear embedding models, Laplacian eigenmaps, diffusion maps, force directed methods, t-distributed stochastic neighbor embedding, independent component analysis (ICA), dimensionality reduction via regression (DRR), non-negative matrix factorization (NNMF), Isomap, Autoencoder, uniform manifold approximation and projection (UMAP) models, neural network models, and longitudinal factor analysis models. In addition, a special chapter covers metrics for comparing model performance. Features of this book include: Numerous worked examples with replicable R code Explicit comprehensive coverage of data assumptions Adaptation of factor methods to binary, ordinal, and categorical data Residual and outlier analysis Visualization of factor results Final chapters that treat integration of factor analysis with neural network and time series methods Presented in color with R code and introduction to R and RStudio, this book will be suitable for graduate-level and optional module courses for social scientists, and on quantitative methods and multivariate statistics courses.

The process of developing predictive models includes many stages. Most resources focus on the modeling algorithms but neglect other critical aspects of the modeling process. This book describes techniques for finding the best representations of predictors for modeling and for nding the best subset of predictors for improving model performance. A variety of example data sets are used to illustrate the techniques along with R programs for reproducing the results.

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Although there are several good books on principal component methods (PCMs) and related topics, we felt that many of them are either too theoretical or too advanced. This book provides a solid practical guidance to summarize, visualize and interpret the most important information in a large multivariate data sets, using principal component methods in R. The visualization is based on the factoextra R package that we developed for creating easily beautiful ggplot2-based graphs from the output of PCMs. This book contains 4 parts. Part I provides a quick introduction to R and presents the key features of FactoMineR and factoextra. Part II describes classical principal component methods to analyze data sets containing, predominantly, either continuous or categorical variables. These methods include: Principal Component Analysis (PCA, for continuous variables), simple correspondence analysis (CA, for large contingency tables formed by two categorical variables) and Multiple CA (MCA, for a data set with more than 2 categorical variables). In Part III, you'll learn advanced methods for analyzing a data set containing a mix of variables (continuous and categorical) structured or not into groups: Factor Analysis of Mixed Data (FAMD) and Multiple Factor Analysis (MFA). Part IV covers hierarchical clustering on principal components (HCPC), which is useful for performing clustering with a data set containing only categorical variables or with a mixed data of categorical and continuous variables.

A practical source for performing essential statistical analyses and data management tasks in R Univariate, Bivariate, and Multivariate Statistics Using R offers a practical and very user-friendly introduction to the use of R software that covers a range of statistical methods featured in data analysis and data science. The author— a noted expert in quantitative teaching —has written a quick go-to reference for performing essential statistical analyses and data management tasks in R. Requiring only minimal prior knowledge, the book introduces concepts needed for an immediate yet clear understanding of statistical concepts essential to interpreting software output. The author explores univariate, bivariate, and multivariate statistical methods, as well as select nonparametric tests. Altogether a hands-on manual on the applied statistics and essential R computing capabilities needed to write theses, dissertations, as well as research publications. The book is comprehensive in its coverage of univariate through to multivariate procedures, while serving as a friendly and gentle introduction to R software for the newcomer. This important resource: Offers an introductory, concise guide to the computational tools that are useful for making sense out of data using R statistical software Provides a resource for students and professionals in the social, behavioral, and natural sciences Puts the emphasis on the computational tools used in the discovery of empirical patterns Features a variety of popular statistical analyses and data management tasks that can be immediately and quickly applied as needed to research projects Shows how to apply statistical analysis using R to data sets in order to get started quickly performing essential tasks in data analysis and data science Written for students, professionals, and researchers primarily in the social, behavioral, and natural sciences, Univariate, Bivariate, and Multivariate Statistics Using R offers an easy-to-use guide for performing data analysis fast, with an emphasis on drawing conclusions from empirical observations. The book can also serve as a primary or secondary textbook for courses in data analysis or data science, or others in which quantitative methods are featured.

Multiple factor analysis (MFA) enables users to analyze tables of individuals and variables in which the variables are structured into quantitative, qualitative, or mixed groups. Written by the co-developer of this methodology, Multiple Factor Analysis by Example Using R brings together the theoretical and methodological aspects of MFA. It also inc

This textbook integrates important mathematical foundations, efficient computational algorithms, applied statistical inference techniques, and cutting-edge machine learning approaches to address a wide range of crucial biomedical informatics, health analytics applications, and decision science challenges. Each concept in the book includes a rigorous symbolic formulation coupled with computational algorithms and complete end-to-end pipeline protocols implemented as functional R electronic markdown notebooks. These workflows support active learning and demonstrate comprehensive data manipulations, interactive visualizations, and sophisticated analytics. The content includes open problems, state-of-the-art scientific knowledge, ethical integration of heterogeneous scientific tools, and procedures for systematic validation and dissemination of reproducible research findings. Complementary to the enormous challenges related to handling, interrogating, and understanding massive amounts of complex structured and unstructured data, there are unique opportunities that come with access to a wealth of feature-rich, high-dimensional, and time-varying information. The topics covered in Data Science and Predictive Analytics address specific knowledge gaps, resolve educational barriers, and mitigate workforce information-readiness and data science deficiencies. Specifically, it provides a transdisciplinary curriculum integrating core mathematical principles, modern computational methods, advanced data science techniques, model-based machine learning, model-free artificial intelligence, and innovative biomedical applications. The book’s fourteen chapters start with an introduction and progressively build foundational skills from visualization to linear modeling, dimensionality reduction, supervised classification, black-box machine learning techniques, qualitative learning methods, unsupervised clustering, model performance assessment, feature selection strategies, longitudinal data analytics, optimization, neural networks, and deep learning. The second edition of the book includes additional learning-based strategies utilizing generative adversarial networks, transfer learning, and synthetic data generation, as well as eight complementary electronic appendices. This textbook is suitable for formal didactic instructor-guided course education, as well as for individual or team-supported self-learning. The material is presented at the upper-division and graduate-level college courses and covers applied and interdisciplinary mathematics, contemporary learning-based data science techniques, computational algorithm development, optimization theory, statistical computing, and biomedical sciences. The analytical techniques and predictive scientific methods described in the book may be useful to a wide range of readers, formal and informal learners, college instructors, researchers, and engineers throughout the academy, industry, government, regulatory, funding, and policy agencies. The supporting book website provides many examples, datasets, functional scripts, complete electronic notebooks, extensive appendices, and additional materials.

Processing multimedia content has emerged as a key area for the application of machine learning techniques, where the objectives are to provide insight into the domain from which the data is drawn, and to organize that data and improve the performance of the processes manipulating it. Arising from the EU MUSCLE network, this multidisciplinary book provides a comprehensive coverage of the most important machine learning techniques used and their application in this domain.

Gain sharp insights into your data and solve real-world data science problems with R—from data munging to modeling and visualization About This Book Handle your data with precision and care for optimal business intelligence Restructure and transform your data to inform decision-making Packed with practical advice and tips to help you get to grips with data mining Who This Book Is For If you are a data scientist or R developer who wants to explore and optimize your use of R's advanced features and tools, this is the book for you. A basic knowledge of R is required, along with an understanding of database logic. What You Will Learn Connect to and load data from R's range of powerful databases Successfully fetch and parse structured and unstructured data Transform and restructure your data with efficient R packages Define and build complex statistical models with glm Develop and train machine learning algorithms Visualize social networks and graph data Deploy supervised and unsupervised classification algorithms Discover how to visualize spatial data with R In Detail R is an essential language for sharp and successful data analysis. Its numerous features and ease of use make it a powerful way of mining, managing, and interpreting large sets of data. In a world where understanding big data has become key, by mastering R you will be able to deal with your data effectively and efficiently. This book will give you the guidance you need to build and develop your knowledge and expertise. Bridging the gap between theory and practice, this book will help you to understand and use data for a competitive advantage. Beginning with taking you through essential data mining and management tasks such as munging, fetching, cleaning, and restructuring, the book then explores different model designs and the core components of effective analysis. You will then discover how to optimize your use of machine learning algorithms for classification and recommendation systems beside the traditional and more recent statistical methods. Style and approach Covering the essential tasks and skills within data science, Mastering Data Analysis provides you with solutions to the challenges of data science. Each section gives you a theoretical overview before demonstrating how to put the theory to work with real-world use cases and hands-on examples.

Although there are several good books on unsupervised machine learning, we felt that many of them are too theoretical. This book provides practical guide to cluster analysis, elegant visualization and interpretation. It contains 5 parts. Part I provides a quick introduction to R and presents required R packages, as well as, data formats and dissimilarity measures for cluster analysis and visualization. Part II covers partitioning clustering methods, which subdivide the data sets into a set of k groups, where k is the number of groups pre-specified by the analyst. Partitioning clustering approaches include: K-means, K-Medoids (PAM) and CLARA algorithms. In Part III, we consider hierarchical clustering method, which is an alternative approach to partitioning clustering. The result of hierarchical clustering is a tree-based representation of the objects called dendrogram. In this part, we describe how to compute, visualize, interpret and compare dendrograms. Part IV describes clustering validation and evaluation strategies, which consists of measuring the goodness of clustering results. Among the chapters covered here, there are: Assessing clustering tendency, Determining the optimal number of clusters, Cluster validation statistics, Choosing the best clustering algorithms and Computing p-value for hierarchical clustering. Part V presents advanced clustering methods, including: Hierarchical k-means clustering, Fuzzy clustering, Model-based clustering and Density-based clustering.