R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics by Ben Baumer, et.al.
Abstract:
Nolan and Temple Lang argue that “the ability to express statistical computations is an essential skill.” A key related capacity is the ability to conduct and present data analysis in a way that another person can understand and replicate. The copy-and-paste workflow that is an artifact of antiquated user-interface design makes reproducibility of statistical analysis more difficult, especially as data become increasingly complex and statistical methods become increasingly sophisticated. R Markdown is a new technology that makes creating fully-reproducible statistical analysis simple and painless. It provides a solution suitable not only for cutting edge research, but also for use in an introductory statistics course. We present evidence that R Markdown can be used effectively in introductory statistics courses, and discuss its role in the rapidly-changing world of statistical computation. (emphasis in original)
The author’s third point for R Markdown I would have made the first:
Third, the separation of computing from presentation is not necessarily honest… More subtly and less perniciously, the copy-and-paste paradigm enables, and in many cases even encourages, selective reporting. That is, the tabular output from R is admittedly not of presentation quality. Thus the student may be tempted or even encouraged to prettify tabular output before submitting. But while one is fi ddling with margins and headers, it is all too tempting to remove rows or columns that do not suit the student’s purpose. Since the commands used to generate the table are not present, the reader is none the wiser.
Although I have to admit that reproducibility has a lot going for it.
Can you imagine reproducible analysis from the OMB? Complete with machine readable data sets? Or for any other agency reports. Or for that matter, for all publications by registered lobbyists. That could be real interesting.
Open Analysis (OA) as a natural successor to Open Data.
That works for me.
You?
PS: More resources:
Create Dynamic R Statistical Reports Using R Markdown
Writing papers using R Markdown
If journals started requiring R Markdown as a condition for publication, some aspects of research would become more transparent.
Some will say that authors will resistl
Assume Science or Nature has accepted your article on the condition of your use of R Markdown.
Honestly, are you really going to say no?
I first saw this in a tweet by Scott Chamberlain.