This is a module of the CIEE Living Data Project. Access to this Canvas site and associated materials is restricted to registered participants. To find out more about the Living Data Project, visit <https://www.ciee-icee.ca/ldp.html>. ### **Teaching team** #### Lead instructor(s): - Prof. Jason Pither, University of British Columbia---Okanagan ([jason.pither\@ubc.ca](mailto:jason.pither@ubc.ca)) #### LDP postdocs: - Dr. Gracielle Higino, University of British Columbia---Vancouver ([higino\@zoology.ubc.ca](mailto:higino@zoology.ubc.ca)) - Dr. Mike Lavender, University of Regina ([thomas.lavender\@uregina.ca](mailto:thomas.lavender@uregina.ca)) - Dr. Sam Straus, McGill University and Université de Montréal ([samantha.straus\@mcgill.ca](mailto:samantha.straus@mcgill.ca)) #### Teaching assistants: - Liam Johnson, University of British Columbia---Okanagan ([liamgwj\@mail.ubc.ca](mailto:liamgwj@mail.ubc.ca))  ### **Course description** This course aims to transform the way that ecologists and evolutionary biologists work: to increase productivity, improve accountability and transparency, and meet need demands for research reproducibility. Trainees will learn how to integrate recommended practices in Open Science into their individual and collaborative research workflows, and use digital platforms and tools to facilitate collaboration, ensure transparency, enable pre-registrations, and implement version control and provenance tracking. Here is a visual [Roadmap](https://miro.com/app/board/uXjVPa119Jk=/?share_link_id=18768530888) for the course, produced by Gracielle. Our collaborative notes will be built and hosted [here](https://docs.google.com/document/d/1bn7-71HmH7C31cP4KYqUIyDp4IxxvXfQB5miFUBYOic/edit?usp=sharing). ### **Meeting times** 06 September to 29 September 2022 Tue/Thu 8:00 am - 9:30 am PDT\ Tue/Thu 9:00 am - 10:30 am CST + MDT\ Tue/Thu 11:00 am - 12:30 pm EDT **NOTE: All lesson plans will be viewable in the [Modules](https://canvas.ubc.ca/courses/97661/modules) page once they're finalized.** **Week 1**: Tue 06 Sep ([Session 1](https://canvas.ubc.ca/courses/97661/pages/session-1-introductions-slash-background "Session 1 - Introductions / Background")), Thu 08 Sep ([Session 2](https://canvas.ubc.ca/courses/97661/pages/session-2-project-initialization-part-1 "Session 2 - Project initialization (Part 1)"))\ **Week 2**: Tue 13 Sep ([Session 3](https://canvas.ubc.ca/courses/97661/pages/session-3-project-initialization-part-2 "Session 3 - Project initialization (Part 2)")), Thu 15 Sep ([Session 4](https://canvas.ubc.ca/courses/97661/pages/session-4-linking-osf-to-github-and-zotero-and-an-intro-to-markdown "Session 4 - Linking OSF to GitHub & Zotero, and an Intro to Markdown"))\ **Week 3**: Tue 20 Sep (Session 5), Thu 22 Sep ([Session 6](https://canvas.ubc.ca/courses/97661/pages/session-6-licensing-your-work-and-citing-packages "Session 6 - Licensing your work and citing packages"))\ **Week 4**: Tue 27 Sep (Session 7), Thu 29 Sep (Session 8) ### **Zoom link** Join Zoom Meeting\ <https://ubc.zoom.us/j/66142968972?pwd=c1dGR3p1cmVSWVlKaGZOeVptYzhSUT09> Meeting ID: 661 4296 8972\ Passcode: 572345 [+1 778 907 2071](tel:+17789072071) (Vancouver)\ [+1 647 374 4685](tel:+16473744685) (Toronto)\ [+1 204 272 7920](tel:+12042727920) (Manitoba)\ [+1 438 809 7799](tel:+14388097799) (Montreal)\ [+1 587 328 1099](tel:+15873281099) (Alberta)\ [+1 613 209 3054](tel:+16132093054) (Ottawa) ### **Delivery format** - 8 sessions, 1.5 hours per session - The first session will provide an overview of the course and a general background - In sessions 2 through 7, with guidance from instructors, students will work through a mini-project (the same project for all students), start to finish, following best practices in reproducible and transparent research. Some sessions will include peer-evaluation and group discussions. - The final session 8 will provide a wrap-up and reflection on the skills and tools learned ### **Anticipated time commitment** We anticipate the outside class time commitment to be in line with other 1-credit courses. This will include readings and some preparatory activities in advance of sessions (1 hour per session).  Work outside of class may take an additional 15 hours total. ### **Pre-requisites** - Graduate-level thesis in ecology, evolutionary biology, or environmental science - Introductory R programming experience ### **Preparing for the course and for individual sessions** There are a variety of tasks you must complete prior individual sessions. These are described in detail [here](https://canvas.ubc.ca/courses/97661/pages/pre-session-tasks "Pre-session tasks").  ### **Required materials** - Personal computer with videoconferencing ability and reliable internet access - R and RStudio - Please see [these instructions](https://canvas.ubc.ca/courses/97661/pages/instructions-for-students-r-and-rstudio "Instructions for students: R and RStudio") for installing the latest versions R and RStudio, or checking which versions you're currently running **Note**: we focus on the use of open-source and free software and tools to maximize accessibility. ### **Learning outcomes** - Describe why Open Science principles and practices are required - Identify common Questionable Research Practices in ecology and evolution - Describe proximate and systemic barriers to practicing Open Science - Describe incentives and programs designed to promote best practices in OS - Describe the connections between best practices in Open Science, research reliability, and research productivity - Successfully implement and practice reproducible workflows - Successful use of various free / open source tools that facilitate reproducible workflows, including R / RStudio / R Markdown, Zotero - Demonstrated use of version control systems including Git/Github, [OSF](https://osf.io) - Successful implementation of a computationally reproducible project - Familiarity with the purpose and steps of pre-registration ### **Assessments** - During the course, you will practice **creating and managing your own fully reproducible research project**. The main assignment is to have exactly that by the last day of class. However, this assignment is expected to be **built gradually**, so you will have to complete tasks every week. - A peer will be assigned to review your project from week 2 to week 4, and you will review a peer's project too. **Students will grade each other** based on these reviews, so you have to complete your tasks before you grade your peer.  - There are deadlines, but there are also no-questions-asked extensions. If you can deliver a fully reproducible project by September 29, you're good! However, **it's fundamental that you communicate with your peer reviewer if you can't meet the deadlines**. The progress and evaluation of your work is a synchronized dance between you and your reviewer, so work together! - Detailed descriptions of the requirements for each week are on the [assignments](https://canvas.ubc.ca/courses/97661/assignments "Assignments") page. - Detailed checklist for the assignments can be found [here](https://canvas.ubc.ca/courses/97661/pages/final-assignment-checklist). ### **Online resources** All relevant course materials will be housed on **Canvas**. A public [Zotero group library](https://www.zotero.org/groups/2573952/living_data_project/library) is available for this course. It includes the suggested/required readings, and other relevant citations. Once complete, all public materials for this and associated courses will also be archived and made available on the Open Science Framework (OSF) component and wiki pages for the Living Data Project. ### **Office hours / Getting help** #### Office hours Postdocs will host weekly open office hours where you can ask questions about course material, assignments, LDP training opportunities, career development, etc. Students are welcome to attend any office hours that work with their schedule. - **Wednesdays** \@ 1:00 pm - 2:00 pm EDT / 11:00 am - 12:00 pm CST + MDT / 10:00 am - 11:00 am PDT (Mike and Liam)\ [Join Zoom meeting](https://uregina-ca.zoom.us/j/94741619853?pwd=UENFM3ZKTmNEY1pVdFNaSyt5QzFrUT09) (meeting ID: 947 4161 9853; passcode: 890794)\ - **Thursdays** \@ 4:00 pm - 5:00 pm EDT / 2:00 pm - 3:00 pm CST + MDT / 1:00 pm - 2:00 pm PDT (Gracielle and Sam)\ [Join Zoom meeting](https://ubc.zoom.us/j/61974399606?pwd=M3p3cERMMkV2RzdpZ2g1Q0M5MDdLZz09) (meeting ID: 619 7439 9606; passcode: 986168)\ #### Getting help For help with course material, students are encouraged to contact their primary mentor as follows: - **UBC-V** and **CIEE member universities\***: Gracielle Higino ([higino\@zoology.ubc.ca](mailto:higino@zoology.ubc.ca)) - **Regina** and **UBC-O**: Mike Lavender([thomas.lavender\@uregina.ca](mailto:thomas.lavender@uregina.ca)) - **UdeM**, **McGill**, and **CSEE-affiliated students\*\***: Sam Straus ([samantha.straus\@mcgill.ca](mailto:samantha.straus@mail.mcgill.ca)) **\*** Other CIEE member universities: Carleton, Simon Fraser, Guelph, Manitoba, UQaM, Queen's, Toronto **\*\*** CSEE-affiliated students: participants from all other Canadian universities You can email the postdocs or course instructor directly from Canvas by navigating to your [Inbox](https://canvas.ubc.ca/conversations#filter=type=inbox) (this will send an email through the address you used to create your CWL). If you cannot reach your designated mentor, please feel free to contact another instructor or teaching assistant. ### **Code of conduct** Participation in this course and all other functions of the Living Data Project requires adherence to our [Code of Conduct](https://canvas.ubc.ca/courses/97661/pages/ldp-code-of-conduct "LDP Code of Conduct"). Please review the Code of Conduct before the beginning of the first class. **International students at UBC are directed to read [this statement](https://canvas.ubc.ca/courses/97661/pages/statement-for-review-by-international-students-at-ubc "Statement for review by international students at UBC").** ### **Territorial acknowledgement** The Living Data Project is a collaborative effort by researchers at institutions across Canada. We collectively acknowledge that we live and work on the traditional, ancestral, treaty, and unceded territories of many Indigenous peoples, including the Coast Salish Peoples, xwməθkwəy̓əm (Musqueam), Syilx (Okanagan), nêhiyawak (Cree), anihšināpēk (Saulteaux), Dakota, Lakota, Nakoda, Attawanderon, Mississaugas, kanien'kehà:ka (Mohawk), and Haudenosaunee, and the homeland of the Métis/Michif Nation. The LDP brings together instructors and students from many different places with distinct Indigenous traditions and colonial histories. We encourage all participants to seek more information about the traditional territories on which they live: <https://native-land.ca>