Posted by Sarah Leichty
Robert Gentleman and Duncan Temple Lang lay out a lot of information that relates to what they mean when they talk about the creation of reproducible research. Within the first page, the authors are describing reproducible research as “research papers with accompanying software tools that allow the reader to directly reproduce the results and employ the methods that are presented in the research paper”. The authors are referring to the principle of weaving in personal details about why certain steps are being performed in order to produce a desired outcome. We have practiced this definition multiple times in this class when writing notes within our R scripts about what is being accomplished with each new section of code. For example, during homework 3, my partner and I divided the script into more digestible sections that broke down what functions were needed to complete an objective that would culminate in an end goal. The authors also introduce the idea of a compendium as a process that includes all of the data and software language used in a more workable and understandable format, so that the reader does not have to search for the different parts of a process within appendices or the like. I’m a big fan of the mention of using dynamic documents in which the reader has the option of taking different paths to understand and take in the document. The mention of text chunks reminds me of what we have done with our R codes in class and on homework assignments, so that code makes sense even after a few days or more of not looking at it. This section really sums it all up, “The compendium is a mechanism for associating both the data and the software needed to process the data, together with the text that the author wants to present. A dynamic document provides a means for interweaving the textual description of the problem and the computer code that processes the data to produce the necessary facts, figures and tables that the author wants to present. Finally, the transformer provides the means for turning the dynamic document into different desired outputs such as static papers or web pages”. I think these principles have the potential to have a major impact on the dissemination of information in the future to the public. As of now, papers published in many prestigious journals are contained to a small arena of academics instead of spreading to a more general audience because limitations in what can be derived from simple printed pages of research findings and figures. With a more interactive platform, more could be deduced from figures without the need to directly contact the authors in question.