Bioconductor: open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

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.

In this article, we introduce a Stata implementation of coarsened exact matching, a new method for improving the estimation of causal effects by reducing imbalance in covariates between treated and control groups. Coarsened exact matching is faster, is easier to use and understand, requires fewer assumptions, is more easily automated, and possesses more attractive statistical properties for many applications than do existing matching methods. In coarsened exact matching, users temporarily coarsen their data, exact match on these coarsened data, and then run their analysis on the uncoarsened, matched data. Coarsened exact matching bounds the degree of model dependence and causal effect estimation error by ex ante user choice, is monotonic imbalance bounding (so that reducing the maximum imbalance on one variable has no effect on others), does not require a separate procedure to restrict data to common support, meets the congruence principle, is approximately invariant to measurement error, balances all nonlinearities and interactions in sample (i.e., not merely in expectation), and works with multiply imputed datasets. Other matching methods inherit many of the coarsened exact matching method's properties when applied to further match data preprocessed by coarsened exact matching. The cem command implements the coarsened exact matching algorithm in Stata.

We introduce a new "Monotonic Imbalance Bounding" (MIB) class of matching methods for causal inference with a surprisingly large number of attractive statistical properties. MIB generalizes and extends in several new directions the only existing class, "Equal Percent Bias Reducing" (EPBR), which is designed to satisfy weaker properties and only in expectation. We also offer strategies to obtain specific members of the MIB class, and analyze in more detail a member of this class, called Coarsened Exact Matching, whose properties we analyze from this new perspective. We offer a variety of analytical results and numerical simulations that demonstrate how members of the MIB class can dramatically improve inferences relative to EPBR-based matching methods.

This program is designed to improve causal inference via a method of matching that is widely applicable in observational data and easy to understand and use (if you understand how to draw a histogram, you will understand this method). The program implements the coarsened exact matching (CEM) algorithm, described below. CEM may be used alone or in combination with any existing matching method. This algorithm, and its statistical properties, are described in Iacus, King, and Porro (2008).

The growing usage of social media by a wider audience of citizens sharply increases the possibility of investigating the web as a device to explore and track political preferences. In the present paper we apply a method recently proposed by other social scientists to three different scenarios, by analyzing on one side the online popularity of Italian political leaders throughout 2011, and on the other the voting intention of French Internet users in both the 2012 presidential ballot and the subsequent legislative election. While Internet users are not necessarily representative of the whole population of a country's citizens, our analysis shows a remarkable ability for social media to forecast electoral results, as well as a noteworthy correlation between social media and the results of traditional mass surveys. We also illustrate that the predictive ability of social media analysis strengthens as the number of citizens expressing their opinion online increases, provided that the citizens act consistently on these opinions.

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