Publications by Author: James Honaker

We provide an overview of PSI ("a Private data Sharing Interface"), a system we are developing to enable researchers in the social sciences and other fields to share and explore privacy-sensitive datasets with the strong privacy protections of differential privacy.  (See software here and our OpenDP.org project which builds on this paper.)

We extend a unified and easy-to-use approach to measurement error and missing data. In our companion article, Blackwell, Honaker, and King give an intuitive overview of the new technique, along with practical suggestions and empirical applications. Here, we offer more precise technical details, more sophisticated measurement error model specifications and estimation procedures, and analyses to assess the approach’s robustness to correlated measurement errors and to errors in categorical variables. These results support using the technique to reduce bias and increase efficiency in a wide variety of empirical research.

Although social scientists devote considerable effort to mitigating measurement error during data collection, they often ignore the issue during data analysis. And although many statistical methods have been proposed for reducing measurement error-induced biases, few have been widely used because of implausible assumptions, high levels of model dependence, difficult computation, or inapplicability with multiple mismeasured variables. We develop an easy-to-use alternative without these problems; it generalizes the popular multiple imputation (MI) framework by treating missing data problems as a limiting special case of extreme measurement error, and corrects for both. Like MI, the proposed framework is a simple two-step procedure, so that in the second step researchers can use whatever statistical method they would have if there had been no problem in the first place. We also offer empirical illustrations, open source software that implements all the methods described herein, and a companion paper with technical details and extensions (Blackwell, Honaker, and King, 2017b).

The vast majority of social science research presently uses small (MB or GB scale) data sets. These fixed-scale data sets are commonly downloaded to the researcher's computer where the analysis is performed locally, and are often shared and cited with well-established technologies, such as the Dataverse Project (see Dataverse.org), to support the published results.  The trend towards Big Data -- including large scale streaming data -- is starting to transform research and has the potential to impact policy-making and our understanding of the social, economic, and political problems that affect human societies.  However, this research poses new challenges in execution, accountability, preservation, reuse, and reproducibility. Downloading these data sets to a researcher’s computer is infeasible or not practical; hence, analyses take place in the cloud, require unusual expertise, and benefit from collaborative teamwork and novel tool development. The advantage of these data sets in how informative they are also means that they are much more likely to contain highly sensitive personally identifiable information. In this paper, we discuss solutions to these new challenges so that the social sciences can realize the potential of Big Data.

Amelia II is a complete R package for multiple imputation of missing data. The package implements a new expectation-maximization with bootstrapping algorithm that works faster, with larger numbers of variables, and is far easier to use, than various Markov chain Monte Carlo approaches, but gives essentially the same answers. The program also improves imputation models by allowing researchers to put Bayesian priors on individual cell values, thereby including a great deal of potentially valuable and extensive information. It also includes features to accurately impute cross-sectional datasets, individual time series, or sets of time series for different cross-sections. A full set of graphical diagnostics are also available. The program is easy to use, and the simplicity of the algorithm makes it far more robust; both a simple command line and extensive graphical user interface are included.

Amelia II software web site

Applications of modern methods for analyzing data with missing values, based primarily on multiple imputation, have in the last half-decade become common in American politics and political behavior. Scholars in these fields have thus increasingly avoided the biases and inefficiencies caused by ad hoc methods like listwise deletion and best guess imputation. However, researchers in much of comparative politics and international relations, and others with similar data, have been unable to do the same because the best available imputation methods work poorly with the time-series cross-section data structures common in these fields. We attempt to rectify this situation. First, we build a multiple imputation model that allows smooth time trends, shifts across cross-sectional units, and correlations over time and space, resulting in far more accurate imputations. Second, we build nonignorable missingness models by enabling analysts to incorporate knowledge from area studies experts via priors on individual missing cell values, rather than on difficult-to-interpret model parameters. Third, since these tasks could not be accomplished within existing imputation algorithms, in that they cannot handle as many variables as needed even in the simpler cross-sectional data for which they were designed, we also develop a new algorithm that substantially expands the range of computationally feasible data types and sizes for which multiple imputation can be used. These developments also made it possible to implement the methods introduced here in freely available open source software that is considerably more reliable than existing strategies.

We propose a remedy for the discrepancy between the way political scientists analyze data with missing values and the recommendations of the statistics community. Methodologists and statisticians agree that "multiple imputation" is a superior approach to the problem of missing data scattered through one’s explanatory and dependent variables than the methods currently used in applied data analysis. The discrepancy occurs because the computational algorithms used to apply the best multiple imputation models have been slow, difficult to implement, impossible to run with existing commercial statistical packages, and have demanded considerable expertise. We adapt an algorithm and use it to implement a general-purpose, multiple imputation model for missing data. This algorithm is considerably easier to use than the leading method recommended in statistics literature. We also quantify the risks of current missing data practices, illustrate how to use the new procedure, and evaluate this alternative through simulated data as well as actual empirical examples. Finally, we offer easy-to-use that implements our suggested methods. (Software: AMELIA)