Another Benefit of Publicly Version-Controlled Research

I've been thinking quite a bit lately about why and how political scientists should publicly version control their research projects. By research projects, I mean data, manuscript, and code. And by publicly version control, I mean use Git to version-control and post a public GitHub repository, from the beginning of the project, so that other researchers are free to follow and borrow as needed. Below I quickly summarize some of the benefits of version control and discuss another benefit that Git and GitHub have had on my own research.

My thinking about public version control for research projects began Zach Jones' discussion of the idea in a recent Political Methodologist. Teaching the linear models class here at UB last semester solidified its importance in my mind. We used Dropbox for version control and sharing, but Git and GitHub are better.

Several recent articles and posts outline why researchers (as opposed to programmers) might use Git and GitHub. Here's a brief summary:

  1. A paper by Karthik Ram.
  2. A short essay by Zach Jones.
  3. A short essay by Christopher Gandrud.

If I've missed something, please let me know.

There are a lot of good reasons to do this:

  • History. We all use version control. Most of us do it poorly. Using Git/GitHub, I'm learning to do it better. Git/GitHub offers a formal way to easily maintain a complete history of a project. In general, it's good to avoid filenames like new_final_carlisle_v3c_updated.docx. A recent comic makes this point clear. We need a method of updating files while keeping track of the old versions so that we can go back if needed. But the approach of giving different filenames to different version is inefficient at best. My approach of keeping "old files" in a designated folder is no better. Git/GitHub solves these issues. Second, Git allows you to tag a project at certain stages, such as "Initial submission to AJPS." After getting an invitation to revise and resubmit and making the required changes, I can compare the current version of the project to the (now several months old) version I initially submitted. This makes writing response memos much easier.
  • Transparency. Zach Jones most clearly makes the point that Git/GitHub increases transparency in the context of political science research. Git/GitHub essentially allows others to actively monitor the progress of a project or study its past development. Related to the motivation to using GitHub in an open manner is the idea of an "open notebook." Carl Boettiger is one of the most well-know proponents of open notebooks. This kind of openness provides a wonderful opportunity to receive comments and suggestions from a wide audience. This allows other to catch errors that might otherwise go unnoticed. It also gives readers a formal avenue to make suggestions, not to mention keeping a complete history of the suggestions and any subsequent discussion. GitHub allows the public to open issues, which is a wonderful way to receive and organize feedback on a paper.
  • Accessibility. Christopher Gandrud makes the point clearly in a clearly in a recent edition of The Political Methodologist, though he discusses accessibility purely in the context of building data sets. But similar arguments could be made for code. I recently had a graduate student express interest in some MRP estimates of state-level opinion on the Affordable Care Act. I told her that I had spent some time collecting surveys and writing code to produce the estimates. I noted that, ideally, she would not duplicate my work, but, if possible, build on it. I was able to point her to the GitHub repository for the project, which hopefully she'll find useful as a starting point for her own work. As part of my experience supervising replication projects as part of graduate methods classes and my own experience with replication data, the clean, final versions of the data that researchers typically post publicly do not allow future researchers to build on easily build on previous work. If authors posted the raw data and all the (possibly long and messy) code to do the cleaning and recoding, it would be much easier for future researcher to build on past contribution. Indeed, research shows that making the data and code freely available lowers the barriers to reuse and increases citations.

But these are the commonly cited reasons for using Git and GitHub. But in my practice, I've found another reason, perhaps more important than the above.

One thing that I first noticed in my students, but now I see that I'm just as guilty of, is "the race to a regression." That is, I devote the absolute minimum required effort (or less) to everything leading up to the regression. My attitude is usually that I'll go back later and clean up everything, double checking along the way, if the line of investigation "proves useful" (i.e., provides stars). I rarely go back later. I find that the script  let_me_just_try_this_really_quickly.R quickly becomes a part of  analysis.R . This is bad practice and careless.

Instead of a race to the regression, Git encourages me to develop projects a little more carefully, thinking about projects in tiny steps, each to be made public, and each done right and summarized in a nice commit message. The care in my research has noticeably improved. I think about how to do something better, do it better, and explain it in a commit message that I can refer to later.

In my view, project development in Git/GitHub works best when users make small, discrete changes to a project. This takes some thought and discipline, but it is the best way to go. I'm guilty of coming back from a conference and making dozens of small changes to an existing projects, incorporating all the suggestions in a single update. I just did it after the State Politics and Policy Conference. It is a poor way to go about developing a project. It is a poor way to keep track of things. It is a poor strategy, but I'm learning.

Publishing Replication Studies

I was at a replication panel at ISA on Friday and the editor of the APSR, John Ishiyama, offered his thoughts on publishing replications in the APSR. I tweeted about it, which generated quite a discussion (relative to my other Tweets, at least). John discusses these thoughts in more detail in this paper that was previously discussed on the Political Science Replication Blog.

The editors of the APSR have been discussing this issue for some time. In many ways this was prompted by several recent exchanges we had with a scholar who had obtained the replication data from the authors of a manuscript that had appeared in an earlier issue of the Review (in 2010, prior to the University of North Texas’ team taking the reins of the journal). After obtaining the replication data from the authors of the original piece (with the editors’ help) they proceeded to attempt to replicate the results, but were unable to do so. The authors notified us and asked where to publish such a replication study. Our policy at the APSR (which was also the policy of all of our predecessors and the policy of most major journals in the social sciences as well ) is not to publish works that are only replication studies because they do not represent the kind of original work we publish in the Review.

There are very good reasons for APSR’s policy, and we strongly believe in continuing it. We do believe, however, that a very good point was made. A venue for the publication of replication studies is necessary, especially the discipline aspires to raise the degree of scientific rigor in the field. However, as editors of the APSR we are also reluctant to publish such studies in the Review, because this would open up a “cheap” way for authors to have their work published in the APSR, and every Tom, Dick, and Harriet (pardon the expression) could potentially seek to replicate some study, just to get published in the Review. Most all other major journals in the field, we believe, do not to publish solely replication studies (certainly this is true of APSR, AJPS and JOP, as well as the major international relations journals).

I feel that all journals (including the APSR) should evaluate articles on the strength of the contribution, not the time spent working on the paper (I guess this is what John means by "cheap"). In my mind, if an article makes a claim that is deemed a substantial contribution worthy of the APSR, then an article that refutes this claim has made a similar contribution. 

Further, I don't think that most replication studies start out as witch hunts with "Tom, Dick, and Harriet" looking for a "cheap" publication in the APSR. Every replication that I've been a part of and that my students have worked on started as extensions trying to build on the original research.

I can certainly speak for myself. I'm never "out to get" the original authors. I never start out trying to destroy someone else's work. I replicate studies for two reasons. First, I'm trying to build on their work. Second, I'm trying to make a methodological point to help strengthen future work. Along the way, I've found many "mistakes" (or at least things that people citing/believing the key findings should be aware of). In one case, the results changed dramatically when I slightly changed the model specification--the specification the author reports seemed to be the only one with the appropriate stars. In another example, a single case drove all of the authors' key findings. (In both cases, I swept the mistakes under the rug and proceeded as though everything was hunky-dory.) In both cases, a summary of the findings deserves publication in good journals, but I don't expect either to ever see daylight.

Finally, I don't think it would be such a bad thing if the APSR took responsibility for its publications and published papers by "every Tom, Dick, and Harriet" informing us that some of the the major results we're all citing in the APSR are (or might be) wrong. It might be "cheap," but perhaps that makes it a good investment.

More on Product Terms and Interaction in Logistic Regression Models

I noticed that Bill Berry, Justin Esarey, and Jackie DeMeritt's (BDE) long-time R&R'ed paper at AJPS is finally forthcoming. I really like seeing highly applied, but rigorous, work like this being published at top journals. You should definitely have a look at their paper if you use logit or probit models to argue for interaction.

First, the background. BDE published a paper back in 2010 that examines whether researchers need to include a product term in order to argue for interaction.  This first paper examines the situation in which the researcher expects interaction due to compression (when the researcher expects changes in predicted probabilities to be smaller and the probabilities approach zero and one). BDE argue that the logit model with no product term is able to capture this type of interaction and, therefore, no product term is needed in this situation. I've previously discussed this paper here and mentioned that I have a paper arguing that one should include a product term even when interaction is expected on the basis of compression alone. While I disagree with his particular situation, the rest of the paper is fantastic. In particular, I've found their advice about hypothesizing interaction in terms of \(Pr(Y)\) or \(Y^*\) especially valuable.

In the forthcoming paper, BDE extend their analysis to the situation in which researchers expect effects (i.e., changes in predicted probabilities) to vary, but do not have a theoretically motivated specification. They refer to this as "specification ambiguity." In this situation, I was delighted to read that BDE recommend always include a product term. They find that excluding the product term biases the researcher toward finding interaction. This is the same reason I disagree with their recommendation to exclude product term in the situation of strong theory. With the publication of this new paper, the literature is almost where I'd like it to be, with the exception of the tiny point I mentioned above.

Creating Marginal Effect Plots for Linear Regression Models in R

Suppose we estimate the model \(E(y) = \beta_0 + \beta_xx + \beta_zz + \beta_{xz}xz\) and want to calculate the the marginal effect of \(x\) on \(E(y)\) as \(z\) varies \(\left(\dfrac{\partial E(y)}{\partial x}\right)\) and its 90% confidence interval. Brambor, Clark, and Golder describe exactly how to do this and provide Stata code. Below is a bit of R code to do something similar. (Click here to continue reading.)

compactr is now on CRAN

I've been working on a package called compactr  that helps create nice-looking plots in R and it is now up on CRAN.

You can get it by typing

directly into the command line in R. See how it works by typing  example(eplot)  or reading the details here. Below I describe the basic structure and functions. (Click here to continue reading.)

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