April 10, 2019
Instructors: Ben Marwick (University of Washington)
Helpers: Matt Harris (AECOM), Liying Wang (University of Washington), Clemens Schmid (RGZM)
In recent years serious concerns about the reproducibility and transparency of research have arisen in many scientific disciplines. These concerns reveal a wide gap between scientific practice and scientific ideals, and threaten to erode public support for research. In this workshop we will provide hands-on training in robust techniques, tools and services (all free) to improve the reproducibility and transparency of archaeological research. Most of these tools relate to the R programming language, which is central to recent developments in social and natural sciences.
This workshop is suited to novices who have never used R before: no prior experience is necessary. The course is aimed at archaeologists doing research at all career stages.
When: April 10, 2019. Add to your Google Calendar. 📅
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). If you have previously installed these programs, please download and install the most recent versions (your version may be outdated and not work with the activities in this workshop). If you have problems or questions, please send us an email at email@example.com . Participants are also required to abide by our Code of Conduct.
Contact: Please email firstname.lastname@example.org for more information. ✉️
|Start time||End time||Topic|
|1:00||1:45||Introduction to R and RStudio|
|2:00||2:45||Writing with RMarkdown|
|3:00||3:45||Git & GitHub|
|4:00||4:45||Data repositories & Open Science Framework|
|4:45||5:00||Good enough practices|
To participate in a this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
Please open the Terminal app, type
git --version and press
Enter/Return. If it's not installed already,
follow the instructions to
Install the "command line
developer tools". Don't click "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your
folder, as they and Git are command line programs.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open in the pop-up dialog. You can watch
a video tutorial about this case.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
We are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. However, we recognise that some groups in our community are subject to historical and ongoing discrimination, and may be vulnerable or disadvantaged. Membership in such a specific group can be on the basis of characteristics such as gender, sexual orientation, disability, physical appearance, body size, race, nationality, sex, colour, ethnic or social origin, pregnancy, citizenship, familial status, veteran status, genetic information, religion or belief, political or any other opinion, membership of a national minority, property, birth, age, or choice of text editor. We do not tolerate harassment of participants on the basis of these categories, or for any other reason.
Harassment is any form of behaviour intended to exclude, intimidate, or cause discomfort. Because we are a diverse community, we may have different ways of communicating and of understanding the intent behind actions. Therefore we have chosen to prohibit certain forms of behaviour in our community, regardless of intent. Prohibited harassing behaviour includes but is not limited to:
written or verbal comments which have the effect of excluding people on the basis of membership of a specific group listed above causing someone to fear for their safety, such as through
Behaviour not explicitly mentioned above may still constitute harassment. The list above should not be taken as exhaustive but rather as a guide to make it easier to enrich all of us and the communities in which we participate. All interactions should be professional regardless of location: harassment is prohibited whether it occurs on- or offline, and the same standards apply to both.
Enforcement of the Code of Conduct will be respectful and not include any harassing behaviors.
Thank you for helping make this a welcoming, friendly community for all.
This code of conduct is an adaptation of the one used by the Software Carpentry Foundation and is a modified version of that used by PyCon, which in turn is forked from a template written by the Ada Initiative and hosted on the Geek Feminism Wiki. Contributors to this document: Adam Obeng, Aleksandra Pawlik, Bill Mills, Carol Willing, Erin Becker, Hilmar Lapp, Kara Woo, Karin Lagesen, Pauline Barmby, Sheila Miguez, Simon Waldman, Tracy Teal.
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, 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]
Matt Harris is the Director of GIS, Data Analysis, & Geoarchaeology in the Cultural Resources Deptartment of AECOM. He is an advanced R user, with a focus on spatial analysis and simulation. He documents many of his explorations using R on his blog. Matt is a member of the SAA Open Science Interest Group, and has previously instructed R to archaeologists via the SAA Online workshops and in person.
Clemens Schmid is an early career archaeologist from Germany. He currently works in a research project about the archaeological site of Olympia (Greece) at the Römisch-Germanisches Zentralmuseum (RGZM) in Mainz. Clemens is an avid R developer and a founding member of the ISAAKiel working group. He developed several R Packages, RStudio Addins and R Shiny Webapps and conducted multiple workshops about R for archaeologists.
Liying Wang is a PhD student of archaeology at the University of Washington. Her PhD research focuses on European culture contact and its impact on indigenous societies in northeastern Taiwan. She recently started using R to analyze archaeological data. She will be a helper in this workshop.