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Networks have permeated everyday life through everyday realities like the Internet, social networks, and viral marketing. As such, network analysis is an important growth area in the quantitative sciences, with roots in social network analysis going back to the 1930s and graph theory going back centuries. Measurement and analysis are integral components of network research. As a result, statistical methods play a critical role in network analysis. This book is the first of its kind in network research. It can be used as a stand-alone resource in which multiple R packages are used to illustrate how to conduct a wide range of network analyses, from basic manipulation and visualization, to summary and characterization, to modeling of network data. The central package is igraph, which provides extensive capabilities for studying network graphs in R. This text builds on Eric D. Kolaczyk’s book Statistical Analysis of Network Data (Springer, 2009).
In recent years there has been an explosion of network data – that is, measu- ments that are either of or from a system conceptualized as a network – from se- ingly all corners of science. The combination of an increasingly pervasive interest in scienti c analysis at a systems level and the ever-growing capabilities for hi- throughput data collection in various elds has fueled this trend. Researchers from biology and bioinformatics to physics, from computer science to the information sciences, and from economics to sociology are more and more engaged in the c- lection and statistical analysis of data from a network-centric perspective. Accordingly, the contributions to statistical methods and modeling in this area have come from a similarly broad spectrum of areas, often independently of each other. Many books already have been written addressing network data and network problems in speci c individual disciplines. However, there is at present no single book that provides a modern treatment of a core body of knowledge for statistical analysis of network data that cuts across the various disciplines and is organized rather according to a statistical taxonomy of tasks and techniques. This book seeks to ll that gap and, as such, it aims to contribute to a growing trend in recent years to facilitate the exchange of knowledge across the pre-existing boundaries between those disciplines that play a role in what is coming to be called ‘network science.
Probabilistic Foundations of Statistical Network Analysis presents a fresh and insightful perspective on the fundamental tenets and major challenges of modern network analysis. Its lucid exposition provides necessary background for understanding the essential ideas behind exchangeable and dynamic network models, network sampling, and network statistics such as sparsity and power law, all of which play a central role in contemporary data science and machine learning applications. The book rewards readers with a clear and intuitive understanding of the subtle interplay between basic principles of statistical inference, empirical properties of network data, and technical concepts from probability theory. Its mathematically rigorous, yet non-technical, exposition makes the book accessible to professional data scientists, statisticians, and computer scientists as well as practitioners and researchers in substantive fields. Newcomers and non-quantitative researchers will find its conceptual approach invaluable for developing intuition about technical ideas from statistics and probability, while experts and graduate students will find the book a handy reference for a wide range of new topics, including edge exchangeability, relative exchangeability, graphon and graphex models, and graph-valued Levy process and rewiring models for dynamic networks. The author’s incisive commentary supplements these core concepts, challenging the reader to push beyond the current limitations of this emerging discipline. With an approachable exposition and more than 50 open research problems and exercises with solutions, this book is ideal for advanced undergraduate and graduate students interested in modern network analysis, data science, machine learning, and statistics. Harry Crane is Associate Professor and Co-Director of the Graduate Program in Statistics and Biostatistics and an Associate Member of the Graduate Faculty in Philosophy at Rutgers University. Professor Crane’s research interests cover a range of mathematical and applied topics in network science, probability theory, statistical inference, and mathematical logic. In addition to his technical work on edge and relational exchangeability, relative exchangeability, and graph-valued Markov processes, Prof. Crane’s methods have been applied to domain-specific cybersecurity and counterterrorism problems at the Foreign Policy Research Institute and RAND’s Project AIR FORCE. ? ? ? ? ? ?
Presenting a comprehensive resource for the mastery of network analysis in R, the goal of Network Analysis with R is to introduce modern network analysis techniques in R to social, physical, and health scientists. The mathematical foundations of network analysis are emphasized in an accessible way and readers are guided through the basic steps of network studies: network conceptualization, data collection and management, network description, visualization, and building and testing statistical models of networks. As with all of the books in the Use R! series, each chapter contains extensive R code and detailed visualizations of datasets. Appendices will describe the R network packages and the datasets used in the book. An R package developed specifically for the book, available to readers on GitHub, contains relevant code and real-world network datasets as well.
​This pioneering book teaches readers to use R within four core analytical areas applicable to the Humanities: networks, text, geospatial data, and images. This book is also designed to be a bridge: between quantitative and qualitative methods, individual and collaborative work, and the humanities and social sciences. Humanities Data with R does not presuppose background programming experience. Early chapters take readers from R set-up to exploratory data analysis (continuous and categorical data, multivariate analysis, and advanced graphics with emphasis on aesthetics and facility). Following this, networks, geospatial data, image data, natural language processing and text analysis each have a dedicated chapter. Each chapter is grounded in examples to move readers beyond the intimidation of adding new tools to their research. Everything is hands-on: networks are explained using U.S. Supreme Court opinions, and low-level NLP methods are applied to short stories by Sir Arthur Conan Doyle. After working through these examples with the provided data, code and book website, readers are prepared to apply new methods to their own work. The open source R programming language, with its myriad packages and popularity within the sciences and social sciences, is particularly well-suited to working with humanities data. R packages are also highlighted in an appendix. This book uses an expanded conception of the forms data may take and the information it represents. The methodology will have wide application in classrooms and self-study for the humanities, but also for use in linguistics, anthropology, and political science. Outside the classroom, this intersection of humanities and computing is particularly relevant for research and new modes of dissemination across archives, museums and libraries. ​
Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.
Graphical models in their modern form have been around since the late 1970s and appear today in many areas of the sciences. Along with the ongoing developments of graphical models, a number of different graphical modeling software programs have been written over the years. In recent years many of these software developments have taken place within the R community, either in the form of new packages or by providing an R interface to existing software. This book attempts to give the reader a gentle introduction to graphical modeling using R and the main features of some of these packages. In addition, the book provides examples of how more advanced aspects of graphical modeling can be represented and handled within R. Topics covered in the seven chapters include graphical models for contingency tables, Gaussian and mixed graphical models, Bayesian networks and modeling high dimensional data.

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