Reproducible Research

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Course Date: 04 August 2014 to 01 September 2014 (4 weeks)

Price: free

Course Summary

Learn the concepts and tools behind reporting modern data analyses in a reproducible manner. This is the fifth course in the Johns Hopkins Data Science Specialization.

Estimated Workload: 3-5 hours/week

Course Instructors

Roger Peng

Roger D. Peng is an Associate Professor of Biostatistics at the Johns Hopkins Bloomberg School of Public Health and a Co-Editor of the Simply Statistics blog. He received his Ph.D. in Statistics from the University of California, Los Angeles and is a prominent researcher in the areas of air pollution and health risk assessment and statistical methods for environmental data. He created the course Statistical Programming at Johns Hopkins as a way to introduce students to the computational tools for data analysis. Dr. Peng is also a national leader in the area of methods and standards for reproducible research and is the Reproducible Research editor for the journal Biostatistics. His research is highly interdisciplinary and his work has been published in major substantive and statistical journals, including the Journal of the American Medical Association and the Journal of the Royal Statistical Society. Dr. Peng is the author of more than a dozen software packages implementing statistical methods for environmental studies, methods for reproducible research, and data distribution tools. He has also given workshops, tutorials, and short courses in statistical computing and data analysis.

Jeff Leek

Jeff Leek is an Assistant Professor of Biostatistics at the Johns Hopkins Bloomberg School of Public Health and co-editor of the Simply Statistics Blog. He received his Ph.D. in Biostatistics from the University of Washington and is recognized for his contributions to genomic data analysis and statistical methods for personalized medicine. His data analyses have helped us understand the molecular mechanisms behind brain development, stem cell self-renewal, and the immune response to major blunt force trauma. His work has appeared in the top scientific and medical journals Nature, Proceedings of the National Academy of Sciences, Genome Biology, and PLoS Medicine. He created Data Analysis as a component of the year-long statistical methods core sequence for Biostatistics students at Johns Hopkins. The course has won a teaching excellence award, voted on by the students at Johns Hopkins, every year Dr. Leek has taught the course.

Brian Caffo

Brian Caffo, PhD is a professor in the Department of Biostatistics at the Johns Hopkins University Bloomberg School of Public Health. He graduated from the Department of Statistics at the University of Florida in 2001. He works in the fields of computational statistics and neuroinformatics and co-created the SMART ( working group. He has been the recipient of the Presidential Early Career Award for Scientist (PECASE) and Engineers and Bloomberg School of Public Health Golden Apple and AMTRA teaching awards.

Course Description

This course focuses on the concepts and tools behind reporting modern data analyses in a reproducible manner. Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them.  The need for reproducibility is increasing dramatically as data analyses become more complex, involving larger datasets and more sophisticated computations. Reproducibility allows for people to focus on the actual content of a data analysis, rather than on superficial details reported in a written summary. In addition, reproducibility makes an analysis more useful to others because the data and code that actually conducted the analysis are available. This course will focus on literate statistical analysis tools which allow one to publish data analyses in a single document that allows others to easily execute the same analysis to obtain the same results.


How do the courses in the Data Science Specialization depend on each other?
We have created a handy course dependency chart to help you see how the nine courses in the specialization depend on each other.

Will I get a Statement of Accomplishment after completing this class?

Yes. Students who successfully complete the class will receive a Statement of Accomplishment signed by the instructor.

What resources will I need for this class?
A computer is needed on which the R software environment can be installed (recent Mac, Windows, or Linux computers are sufficient).

How does this course fit into the Data Science Specialization?

This is the fifth course in the Specialization. We strongly recommend that you first take The Data Scientist's Toolbox and R Programming before taking this course.


In this course you will learn to write a document using R markdown, integrate live R code into a literate statistical program, compile R markdown documents using knitr and related tools, and organize a data analysis so that it is reproducible and accessible to others.


There will be weekly video lectures,  quizzes, peer assessments.

As part of this class you will be required to set up a GitHub and an RPubs account. GitHub is a tool for collaborative code sharing and editing. RPubs is a web site for publishing data analyses from R. During this course and other courses in the Specialization you will be submitting links to files you publicly place in your GitHub account as part of peer evaluation. If you are concerned about preserving your anonymity you will need to set up an anonymous GitHub and RPubs accounts and be careful not to include any information you do not want made available to peer evaluators.

Course Workload

3-5 hours/week

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