Research Compendia with R

https://nevrome.github.io/rrtools.tutorial.mpi2020
Github: https://github.com/nevrome/rrtools.tutorial.mpi2020

This tutorial was compiled by Clemens Schmid for a workshop on reproducible research and data management at MPI-SHH in January 2020. It’s based on and inspired by two workshops prepared by Ben Marwick for the SAA2019 conference and Brown University Digital Archaeology Lab.

The research compendium

The following figure by Marwick 2017 illustrates one implementation of this workflow.

R for reproducible research

rrtools setup

rrtools workflow

rrtools advanced

Further reading

Eglen, S. J., Marwick, B., Halchenko, Y. O., Hanke, M., Sufi, S., Gleeson, P., … & Wachtler, T. (2017). Toward standard practices for sharing computer code and programs in neuroscience. Nature Neuroscience 20(6), 770-773. [DOI] [preprint] [PDF]

Marwick, B. 2017 Computational reproducibility in archaeological research: Basic principles and a case study of their implementation. Journal of Archaeological Method and Theory 24(2), 424-450. [DOI] [preprint] [code & data]

Marwick 2017 Using R and Related Tools for Reproducible Research in Archaeology. In Kitzes, J., Turek, D., & Deniz, F. (Eds.) The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences. Oakland, CA: University of California Press. [online]

Marwick, B., & Birch, S. 2018 A Standard for the Scholarly Citation of Archaeological Data as an Incentive to Data Sharing. Advances in Archaeological Practice 1-19. [DOI] [preprint] [PDF] [code & data]

Marwick, B., Boettiger, C., & Mullen, L. 2017 Packaging data analytical work reproducibly using R (and friends). The American Statistician [DOI] [preprint]

Marwick, B, d’Alpoim Guedes, J., Barton, C. M., Bates, L. A., Baxter, M., Bevan, A., Bollwerk, E. A., Bocinsky, R. K., Brughmans, T., Carter, A. K., Conrad, C., Contreras, D. A., Costa, S., Crema, E. R., Daggett, A., Davies, B., Drake, B. L., Dye, T. S., France, P., Fullagar, R., Giusti, D., Graham, S., Harris, M. D., Hawks, J., Health, S., Huffer, D., Kansa, E. C., Kansa, S. W., Madsen, M. E., Melcher, J., Negre, J., Neiman, F. D., Opitz, R., Orton, D. C., Przstupa, P., Raviele, M., Riel-Savatore, J., Riris, P., Romanowska, I., Smith, J., Strupler, N., Ullah, I. I., Van Vlack, H. G., VanValkenburgh, N., Watrall, E. C., Webster, C., Wells, J., Winters, J., and Wren, C. D. (2017) Open science in archaeology. SAA Archaeological Record, 17(4), pp. 8-14. [PDF] [preprint]

Ram, K. B. Marwick 2017 Building Towards a Future Where Reproducible, Open Science is the Norm. In Kitzes, J., Turek, D., & Deniz, F. (Eds.) The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences. Oakland, CA: University of California Press. [online]

Rokem, A., B. Marwick, V. Staneva 2017 Assessing Reproducibility. In Kitzes, J., Turek, D., & Deniz, F. (Eds.) The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences. Oakland, CA: University of California Press. University of California Press. [online]

Clemens Schmid

January 2020