Reproducible Research and Reports with R

We have all had the experience of having performed a laborious calculation in a spreadsheet program only to later be required to redo the analysis because of the availability of additional data, the discovery of an error, or because the analysis is part of a recurring report (e.g., monthly quality indicators). At that point we may have to return and begin the calculation all over, except we may not even remember what we did, or we may inadvertently perform the analysis in a slightly different way each time. Another common issue is that we may have a data set so large that using a spreadsheet program may be impractical—move scroll bar, watch program freeze, go for coffee. Then there's all the help you did not ask for. Has your spreadsheet program ever converted your data points into dates against your will? (1) Another challenge we have all faced is the preparation of an elaborate figure, the complexity of which makes the use of standard software tools unworkable. The problem of retracing your statistical steps is not merely one of inconvenience. There are serious medical consequences to errors attributable to the effects of spreadsheet programs and software operated through a graphical user interface (2). Fundamentally, the issue is one of reproducibility. The opacity of graphical user interface–based statistical analysis and the importance of research transparency and reproducibility have been highlighted by scientific scandals that could have been avoided through a reproducible research paradigm (3). Anytime we manipulate data with mouse moves, a record of what we have actually done (cleansing, outlier removal, statistical methodology) is lost, and if we made a mistake, it will not be traceable. However, if we prepare our analysis in a programming language, we and others can see what we did, provided we have left the original data set undisturbed. Even better, if we could combine the statistical analysis and authorship process, we could produce an entirely reproducible and transparent scientific report. In the past 10 years there have been serious efforts in the statistical and computational sciences to build tools for creating reports and research papers that are themselves a computer program, down to the tables, the figures, the inline quotations of summative statistics, the handling of references and internal cross-references. If written properly, alteration of a single point of raw data will be reflected throughout the paper when the code to generate the paper is rerun. In light of recent developments in so-called “big data” and “data science,” doubtless the reader is aware of the open-source and freely available R statistical programming language, which can be used to perform all manner of analyses in healthcare and laboratory medicine research. However, parallel to the prolific expansion of the language itself and the massive user base has been the development of tools specifically directed at the production of reproducible reports. These programs can read in the raw data, clean it up, format it properly, perform all calculations, and then generate the output in nearly any desired format: static HTML, HTML Dashboards, PDF, Word, Excel, and PowerPoint. The program can then push the output to a local folder, e-mail it, and even send alerts by text message. The manuscript, having calculated this z score, stores it in a variable, denoted z.score. The calculated value, (z = 3.0902), can then be embedded in the document, as it has been in this sentence. As a more elaborate example of an embedded figure built in real time, Fig. 1 shows a rose plot of turnaround time breakdown for stat ward collections over the course of a year. The code to generate this plot and this entire manuscript is provided as an online supplement (see Data Supplement that accompanies the online version of this article at http://www.jalm.org/content/vol4/issue3). Although there are obvious complexities associated with publishing raw data and source code (particularly if there may be yet-undiscovered findings), it is our belief that the death knell has been sounded for the traditional scientific publishing paradigm of presentation of description and findings but without raw data and source code (5) and that open and reproducible publications will become normative in time. RMarkdown and a number of related open-source tools make automated reports and reproducible research possible.

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