We discuss a method for improving causal inferences called ‘‘Coarsened Exact Matching’’ (CEM), and the new ‘‘Monotonic Imbalance Bounding’’ (MIB) class of matching methods from which CEM is derived. We summarize what is known about CEM and MIB, derive and illustrate several new desirable statistical properties of CEM, and then propose a variety of useful extensions. We show that CEM possesses a wide range of statistical properties not available in most other matching methods but is at the same time exceptionally easy to comprehend and use. We focus on the connection between theoretical properties and practical applications. We also make available easy-to-use open source software for R, Stata, and SPSS that implement all our suggestions.

/pdf/causal-inference-without-balance-checking-coarsened-exact-1xeumfa548.pdf

Causal Inference without Balance Checking: Coarsened Exact Matching

The complete title of this book runs ‘Analyzing Linguistic Data: A Practical Introduction to Statistics using R’ and as such it very well reflects the purpose and spirit of the book. The author guides the reader in about 350 pages from descriptive and basic statistical methods over classification and clustering to (generalised) linear and mixed models. Each of the methods is introduced in the context of concrete linguistic problems and demonstrated on exciting datasets from current research in the language sciences. In line with its practical orientation, the book focuses primarily on using the methods and interpreting the results. This implies that the mathematical treatment of the techniques is held at a minimum if not absent from the book. In return, the reader is provided with very detailed explanations on how to conduct the analyses using R [1]. The first chapter sets the tone being a 20-page introduction to R. For this and all subsequent chapters, the R code is intertwined with the chapter text and the datasets and functions used are conveniently packaged in the languageR package that is available on the Comprehensive R Archive Network (CRAN). With this approach, the author has done an excellent job in enabling researchers and students alike to reproduce the analyses and learn by doing. Another quality as a textbook is the fact that every chapter ends with Workbook sections where the user is invited to exercise his or her analysis skills on supplemental datasets. Full solutions including code, results and comments are given in Appendix A (30 pages). Instructors are therefore very well served by this text, although they might want to balance the book with some more mathematical treatment depending on the target audience. After the introductory chapter on R, the book opens on graphical data exploration. Chapter 3 treats probability distributions and common sampling distributions. Under basic statistical methods (Chapter 4), distribution tests and tests on means and variances are covered. Chapter 5 deals with clustering and classification. Strangely enough, the clustering section has material on PCA, factor analysis, correspondence analysis and includes only one subsection on clustering, devoted notably to hierarchical partitioning methods. The classification part deals with decision trees, discriminant analysis and support vector machines. The regression chapter (Chapter 6) treats linear models, generalised linear models, piecewise linear models and a substantial section on models for lexical richness. The final chapter on mixed models is particularly interesting as it is one of the few text book accounts that introduce the reader to using the (innovative) lme4 package of Douglas Bates which implements linear mixed-effects models. Moreover, the case studies included in this

Analyzing linguistic data: a practical introduction to statistics using R

This paper demonstrates how to use the R package stm for structural topic modeling. The structural topic model allows researchers to flexibly estimate a topic model that includes document-level metadata. Estimation is accomplished through a fast variational approximation. The stm package provides many useful features, including rich ways to explore topics, estimate uncertainty, and visualize quantities of interest.

/pdf/stm-an-r-package-for-structural-topic-models-3vfz80akjf.pdf

stm: An R Package for Structural Topic Models

Background—Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous clinical syndrome in need of improved phenotypic classification. We sought to evaluate whether unbiased clustering analysis using dense phenotypic data (phenomapping) could identify phenotypically distinct HFpEF categories. Methods and Results—We prospectively studied 397 patients with HFpEF and performed detailed clinical, laboratory, ECG, and echocardiographic phenotyping of the study participants. We used several statistical learning algorithms, including unbiased hierarchical cluster analysis of phenotypic data (67 continuous variables) and penalized model-based clustering, to define and characterize mutually exclusive groups making up a novel classification of HFpEF. All phenomapping analyses were performed by investigators blinded to clinical outcomes, and Cox regression was used to demonstrate the clinical validity of phenomapping. The mean age was 65±12 years; 62% were female; 39% were black; and comorbidities wer...

/pdf/phenomapping-for-novel-classification-of-heart-failure-with-4di1t1tgyc.pdf

Phenomapping for novel classification of heart failure with preserved ejection fraction.

Type 2 innate signals stimulate fibro/adipogenic progenitors to facilitate muscle regeneration.

Seriation, i.e., nding a suitable linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem’s combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides an infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.

/pdf/getting-things-in-order-an-introduction-to-the-r-package-3auf64xblb.pdf

Getting Things in Order: An Introduction to the R Package seriation

Two of the prime open-source environments available for machine/statistical learning in data mining and knowledge discovery are the software packages Weka and R which have emerged from the machine learning and statistics communities, respectively. To make the different sets of tools from both environments available in a single unified system, an R package RWeka is suggested which interfaces Weka’s functionality to R. With only a thin layer of (mostly R) code, a set of general interface generators is provided which can set up interface functions with the usual “R look and feel”, re-using Weka’s standardized interface of learner classes (including classifiers, clusterers, associators, filters, loaders, savers, and stemmers) with associated methods.

Open-source machine learning: R meets Weka

This paper describes the ecosystem of R add-on packages developed around the infrastructure provided by the package arules. The packages provide comprehensive functionality for analyzing interesting patterns including frequent itemsets, association rules, frequent sequences and for building applications like associative classification. After discussing the ecosystem's design we illustrate the ease of mining and visualizing rules with a short example.

/pdf/the-arules-r-package-ecosystem-analyzing-interesting-48f1tu5fr6.pdf

The arules R-Package Ecosystem: Analyzing Interesting Patterns from Large Transaction Data Sets

Making friends and communicating on Facebook: Implications for the access to social capital

Identifying the language used will typically be the first step in most natural language
processing tasks. Among the wide variety of language identification methods discussed
in the literature, the ones employing the Cavnar and Trenkle (1994) approach to text
categorization based on character n-gram frequencies have been particularly successful.
This paper presents the R extension package textcat for n-gram based text categorization
which implements both the Cavnar and Trenkle approach as well as a reduced n-gram
approach designed to remove redundancies of the original approach. A multi-lingual
corpus obtained from the Wikipedia pages available on a selection of topics is used to
illustrate the functionality of the package and the performance of the provided language
identification methods. (authors' abstract)

https://www.jstatsoft.org/article/view/v052i06/v52i06.pdf

Christian Buchta

Papers

Getting Things in Order: An Introduction to the R Package seriation

Open-source machine learning: R meets Weka

The arules R-Package Ecosystem: Analyzing Interesting Patterns from Large Transaction Data Sets

Making friends and communicating on Facebook: Implications for the access to social capital

The textcat Package for n-Gram Based TextCategorization in R