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<p>Productivity and Reproducibility in Ecology & Evolution</p> <h4>Instructors:</h4> <ul> <li>Jason Pither (UBC, Okanagan campus)<ul> <li>jason &lt;dot&gt; pither [at] ubc &lt;dot&gt; ca&lt;/dot&gt;&lt;/dot&gt;</li> </ul> </li> <li>Gavin Simpson (U. Regina)<ul> <li>gavin &lt;dot&gt; simpson [at] uregina &lt;dot&gt; ca&lt;/dot&gt;&lt;/dot&gt;</li> </ul> </li> <li>postdocs from the Living Data Project</li> </ul> <p><strong>Course Description</strong><br> This course aims to transform the way that ecologists and evolutionary biologists work: to increase productivity, improve accountability, and meet new requirements for research reproducibility. Trainees will learn how to integrate open science best practices 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. </p> <p><strong>Meeting Times:</strong> </p> <ul> <li>9:00-10:30am PST British Columbia</li> <li>10 - 11:30 CST Saskatchewan</li> <li>11:00am-12:30pm CDT Manitoba</li> <li>noon-1:30pm EST Ontario/Quebec</li> </ul> <p>Week 1: Tues Sept 29, Thurs Oct 1<br> Week 2: Tues Oct 6, Thurs Oct 8<br> Week 3: Tues Oct 13, Thurs Oct 15<br> MID-TERM BREAK (U. Montréal)<br> Week 4: Tues Oct 27, Thurs Oct 29 </p> <p><strong>Pre-requisites</strong><br> - Graduate-level thesis in Ecology or Evolutionary Biology - Introductory R programming experience (i.e. base R)</p> <p><strong>Delivery format</strong><br> - 8 sessions, 1.5 hours per session - Sessions are delivered as mini-workshops, typically including an introductory lecture component, followed by hands-on activities </p> <p><strong>Online Resources:</strong><br> All materials for this and associated courses will be available on the wiki pages the <a href="https://osf.io/uwzx5/wiki/home/" rel="nofollow">OSF site</a> for the Living Data Project. </p> <p><strong>Assessment</strong> - Assignment (30%) - Group project (70%) </p> <p><strong>Workload</strong> 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 hr per session). Outside work on assignments and group project may take an additional 15-25 h total. </p> <p><strong>Required materials</strong><br> - Personal computer with videoconferencing ability - Internet access </p> <p><strong>NOTE</strong>: We focus on the use of open-source and free software and tools to maximize accessibility </p> <p><strong>Logistics</strong></p> <p>For help on course material, students are encouraged to contact their primary mentor as follows (but if you cannot reach then, feel free to contact another instructor): </p> <ul> <li>UBC-V and Regina* - Ellen Bledsoe (ellen [dot] bledsoe [at] weecology [dot] org) after Oct 6 </li> <li>UdeM, McGill*, SFU - Joey Burant (jburant[at] uoguelph [dot] ca) </li> <li>UBC-O - Mauro Sugawara (sugawara [at] zoology [dot] ubc [dot] ca) </li> <li>Carleton, Manitoba, UQAM, Toronto - Bruno Carturan (bruno [dot] carturan [at] ubc [dot] ca)</li> </ul> <p>*<em>including students doing transfer credits via these universities</em></p> <p>Participation in this course requires adherence to the Living Data Project <a href="https://osf.io/u2abx/wiki/home/" rel="nofollow">Code of Conduct</a></p> <p>We have set-up a <strong>course chat forum</strong> and an <strong>assignment submission portal</strong> on OSF. This is the preferred platform, but the instructional team can also accommodate students who prefer not to use OSF. Instructions on how to set-up and use OSF for these purposes is found <a href="https://osf.io/ghwua/wiki/Instructions%20for%20Students/" rel="nofollow">here</a> and we are happy to help you with any questions. </p> <p><strong>International students at UBC</strong> are directed to read <a href="https://osf.io/k4x2f/wiki/home/" rel="nofollow">this</a> statement</p> <hr> <h3>Approximate schedule of topics and activities (8 sessions)</h3> <hr> <h4><strong>Session 1: Sept. 29</strong></h4> <p><strong>In-session:</strong></p> <ol> <li><strong>Introductions</strong> (15 min)</li> <li>Introduction to instructors, postdocs, and teaching assistants </li> <li>Overview of the course and expectations re. activities and assignments, and code of conduct</li> <li>Refer to web resources, including instructions for assignment submission etc...</li> <li> <p>Inform students of privacy requirements and cautions</p> </li> <li> <p><strong>Lecture</strong> (35 min)</p> </li> <li>The reproducibility crisis and the Open Science movement</li> <li> <p>See: <a href="https://osf.io/2xzya/" rel="nofollow">session 1 lecture slides</a></p> </li> <li> <p><strong>Activities</strong> (25 min)</p> </li> <li>Breakout rooms, 1 for each postdoc/TA</li> <li>Quick intros and state what research interests are</li> <li>Time-permitting: what part of "Open Science" resonates most for you?</li> <li>Ensure R/RStudio installed</li> <li>Set up <a href="https://osf.io" rel="nofollow">OSF account</a>, including adding affiliation info; see <a href="https://osf.io/uwzx5/wiki/4.%20Instructions%20for%20students/" rel="nofollow">Instructions to students</a></li> <li>set up <a href="https://github.com" rel="nofollow">Github account</a> (or do on own time)</li> <li>Set up <a href="https://www.zotero.org" rel="nofollow">Zotero account</a> (or do on own time), Chrome/Firefox extension and <a href="zotfile.com" rel="nofollow">zotfile</a> add-on</li> <li><a href="https://people.ok.ubc.ca/vdunbar/BIOL/Zotero/ZoteroBIOL.html" rel="nofollow">Getting started with Zotero</a></li> </ol> <hr> <h4><strong>Session 2: Oct. 1</strong></h4> <p><strong>Pre-session:</strong></p> <p><strong>Suggested activities:</strong> </p> <ul> <li>Read this <a href="https://www.cos.io/blog/5-ways-to-optimize-your-research-workflow-with-osf" rel="nofollow">website</a> about the online collaboration platform <strong>OSF</strong> (which hosts these course materials)</li> </ul> <p><strong>In-session:</strong></p> <ol> <li><strong>Q & A / Admin</strong> (5-10 min) </li> <li> <p>Address questions </p> </li> <li> <p><strong>Workshop: Matthew Vis-Dunbar (UBC Library) & Jason Pither</strong> (60 minutes)</p> </li> <li>overview of the OSF collaboration platform</li> <li>students create their own OSF project <ul> <li>add collaborators, permissions</li> <li>notifications</li> <li>commenting</li> <li>wiki pages</li> <li>file check-out / updates</li> <li>add-ons</li> </ul> </li> </ol> <hr> <h4><strong>Session 3: Oct. 6</strong></h4> <p><strong>Pre-session:</strong></p> <p><strong>Note for students</strong>: PDFs of suggested pre-readings are available in the private Course Communications component <a href="https://osf.io/z9h8m/" rel="nofollow">here</a>.</p> <p><strong>Suggested reading:</strong></p> <ul> <li>Fraser, H., Parker, T., Nakagawa, S., Barnett, A. & Fidler, F. (2018). Questionable research practices in ecology and evolution. PLOS ONE, 13, e0200303.<a href="https://doi.org/10.1371/journal.pone.0200303" rel="nofollow">doi.org/10.1371/journal.pone.0200303</a></li> <li>Roche, D.G., Kruuk, L.E.B., Lanfear, R., and Binning, S.A. (2015). Public data archiving in ecology and evolution: how well are we doing? PLoS Biology, 13, e1002295. <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002295" rel="nofollow">doi.org/10.1371/journal.pbio.1002295</a></li> </ul> <p><strong>In-session:</strong></p> <ol> <li><strong>Q & A / Admin</strong> (5-10 min) </li> <li> <p>Address questions </p> </li> <li> <p><strong>Lecture: Jason Pither</strong> (30 min)</p> </li> <li>Questionable Research Practices</li> <li>Intro to Pre-registration & Registered Reports</li> <li> <p>See: <a href="https://osf.io/7d2kf/" rel="nofollow">session 3 lecture slides</a></p> </li> <li> <p><strong>Activities</strong> (45 minutes)</p> </li> <li>RStudio (20 min)</li> <li>Pre-recorded video (Gavin)</li> <li>Projects</li> <li>Environment settings</li> <li> <p><a href="https://datacarpentry.org/semester-biology/materials/project-structure/" rel="nofollow">Directory structure</a> / relative paths</p> </li> <li> <p>Demo of Zotero functionality (25 min)</p> </li> <li><a href="https://www.youtube.com/watch?v=Hm0TboOcAuM&feature=emb_logo" rel="nofollow">General Introduction</a><ul> <li><a href="https://www.zotero.org/support/groups" rel="nofollow">sharing / groups</a> </li> <li>Chrome / Firefox extensions</li> <li><a href="https://zotfile.com" rel="nofollow">Zotfile</a> functionality</li> <li>PDF storage</li> <li>notes, highlighting, export notes</li> <li>export bibtex</li> <li><a href="https://www.zotero.org/support/kb/mendeley_import" rel="nofollow">importing from Mendeley</a></li> </ul> </li> <li> <p>See: <a href="https://osf.io/ek2xf/" rel="nofollow">session 3 activity materials</a> (make sure to download all three files)</p> </li> <li> <p><strong>Post-session activities</strong> (45 minutes)</p> </li> <li>Check out this short <a href="https://ox.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=db83bd17-4c08-466b-9ced-ac60012e7573" rel="nofollow">Introduction to Pre-registrations</a> from Dr. Malika Ihle (Oxford University).</li> </ol> <hr> <h4><strong>Session 4: Oct. 8</strong></h4> <p><strong>Pre-session activities</strong></p> <ul> <li>RMarkdown & Literate Programming (Gavin, pre-recorded: <a href="https://youtu.be/xsHDSxUmh-g" rel="nofollow">YouTube</a>)</li> </ul> <p><strong>Suggested readings:</strong> </p> <ul> <li> <p>Nilsen, E.B., Bowler, D.E. & Linnell, J.D.C. (2020). Exploratory and confirmatory research in the open science era. Journal of Applied Ecology, 57, 842–847. <a href="https://doi.org/10.1111/1365-2664.13571" rel="nofollow">https://doi.org/10.1111/1365-2664.13571</a></p> </li> <li> <p>Fraser, H., Barnett, A., Parker, T.H. & Fidler, F. (2020). The role of replication studies in ecology. Ecology and Evolution, 10, 5197–5207. <a href="https://doi.org/10.1002/ece3.6330" rel="nofollow">https://doi.org/10.1002/ece3.6330</a></p> </li> <li> <p><strong>Q & A / Admin</strong> (5-10 min) </p> </li> <li> <p>Address questions </p> </li> <li> <p><strong>Lecture: Jason Pither</strong> (25 min)</p> </li> <li>Confirmatory vs Exploratory research</li> <li>Replication in Ecology, Evolution, Environmental research</li> <li> <p>See: <a href="https://osf.io/7kfd5/" rel="nofollow">session 4 lecture slides</a></p> </li> <li> <p><strong>Hands-on activities</strong> (60 minutes)</p> </li> <li> <p>R Markdown Part 1</p> </li> <li>literate programming do's and don'ts</li> <li>citations in Markdown - Better BibTeX </li> <li>figures, tables, equations</li> <li>brief intro to Bookdown</li> <li><code>osfr</code> demonstration (<em>time permitting</em>)</li> <li>See: <a href="https://osf.io/m8nv7/" rel="nofollow">R Markdown tutorial (part 1)</a> and <a href="https://osf.io/eujrp/" rel="nofollow">osfr demonstration</a>. Please download the full zip file. </li> </ul> <hr> <h4><strong>Session 5: Oct. 13</strong></h4> <p><strong>Pre-session:</strong></p> <p><strong>Suggested reading:</strong></p> <ul> <li>Nosek, B.A., Ebersole, C.R., DeHaven, A.C., and Mellor, D.T. (2018). The preregistration revolution. PNAS, 115, 2600-2606. <a href="https://www.pnas.org/content/115/11/2600" rel="nofollow">doi/10.1073/pnas.1708274114</a>.</li> <li>Parker, T.H., Forstmeier, W., Koricheva, J., Fidler, F., Hadfield, J.D., Chee, Y.E., et al. (2016). Transparency in Ecology and Evolution: Real Problems, Real Solutions. Trends in Ecology & Evolution, 31, 711–719. <a href="https://doi.org/10.1016/j.tree.2016.07.002" rel="nofollow">doi.org/10.1016/j.tree.2016.07.002</a> </li> </ul> <p><strong>Supporting resources:</strong> </p> <ul> <li><a href="https://osf.io/y8aqx/" rel="nofollow">Tools for Transparency in Ecology and Evolution</a></li> <li><a href="https://www.nature.com/documents/nr-reporting-summary-flat.pdf" rel="nofollow">Nature reporting summary checklist for authors</a></li> <li><a href="https://science.sciencemag.org/content/sci/suppl/2020/03/05/science.aba9757.DC1/aba9757_MDAR_Reproducibility_Checklist.pdf" rel="nofollow">Science - MDAR author checklist</a></li> <li><a href="http://www.shinyapps.org/apps/ShortTransparencyChecklist/" rel="nofollow">Shiny app transparency checklist</a></li> <li><a href="https://www.carl-abrc.ca/advancing-research/scholarly-communication/info-for-authors/" rel="nofollow">Canadian Association of Research Libraries resources on helping authors understand author rights, and use of metrics</a></li> <li><a href="https://beckerguides.wustl.edu/authors/eri" rel="nofollow">Tips for enhancing your impact</a> from Washington University</li> <li><a href="https://guides.library.duq.edu/c.php?g=363731&p=2457553" rel="nofollow">Enhancing Discoverability tips/guidelines</a> from Duquesne University</li> </ul> <p><strong>In-session activities</strong></p> <ol> <li> <p><strong>Lecture material</strong></p> <ul> <li><strong><a href="https://osf.io/aqxuj/" rel="nofollow">Lecture slides</a></strong> Jason Pither (15 min) </li> <li>TOP guidelines / author checklists</li> <li> <p>Ensuring discoverability of your outputs</p> </li> <li> <p><strong><a href="https://youtu.be/GBoLKvWWQZg" rel="nofollow">Recorded Lecture (please view before session)</a></strong>: Gavin Simpson (65 min <a href="https://osf.io/hc4r7/" rel="nofollow">Slidedeck</a>)</p> </li> <li>Overview of Open Access </li> <li>Preprints</li> <li>Copyright (creative commons etc..)</li> <li>ORCID</li> </ul> </li> <li> <p><strong>Discussion</strong> (20 min)</p> </li> <li> <p><strong>Activities</strong></p> </li> <li>R Markdown Part 2</li> <li>using journal templates from <code>rticles</code></li> <li>authoring pre-registrations with <a href="https://github.com/crsh/prereg" rel="nofollow"><code>prereg</code> R package</a></li> <li>collaborative authoring in Markdown</li> <li><a href="https://rmarkdown.rstudio.com/lesson-11.html" rel="nofollow">creating slides using R Markdown</a></li> <li>See: <a href="https://osf.io/wqdvk/" rel="nofollow">R Markdown tutorial (part 2)</a>. Please download the full zip file.</li> </ol> <hr> <h4><strong>Session 6: Oct. 15</strong></h4> <p><strong>Pre-session activities</strong></p> <ol> <li><strong>Introduction to version control with git & GitHub</strong> (Gavin, <a href="https://osf.io/w5xme/" rel="nofollow">slidedeck</a>, <a href="https://youtu.be/zlhR4vzIahM" rel="nofollow">YouTube video</a> (30 mins))</li> </ol> <p><strong>In-session activities</strong></p> <ol> <li> <p><strong>Q & A / Admin</strong> (5-10 min) </p> <ul> <li>Address questions </li> </ul> </li> <li> <p><strong>Workshop: Gavin Simpson</strong> (30 min)</p> <ul> <li>Git & Github</li> <li>version control</li> <li>setup Git with RStudio</li> <li>push/pull/commit</li> <li>collaborating and sharing</li> <li><a href="https://happygitwithr.com/index.html" rel="nofollow">Instructions to install and use Git and Github with RStudio</a></li> </ul> </li> </ol> <hr> <h4><strong>Session 7: Oct. 27</strong></h4> <p><strong>Pre-session activities</strong></p> <p><strong>Suggested readings:</strong> </p> <ul> <li>Ali-Khan, S.E., Jean, A. & Gold, E.R. (2018). Identifying the challenges in implementing open science. MNI Open Res, 2, 5.<a href="https://mniopenresearch.org/articles/2-5/v1" rel="nofollow">link</a></li> </ul> <p><strong>In-session activities</strong></p> <ol> <li><strong>Q & A / Admin</strong> (5-10 min) </li> <li> <p>Address questions </p> </li> <li> <p><strong>~~Lecture / Discussion~~</strong> Please refer to this <a href="https://osf.io/uwzx5/wiki/5.%20Open%20Science%20Barriers%20%26%20Incentives/" rel="nofollow">Wiki page (in progress)</a> for information on these topics: </p> </li> <li>Barriers to practicing Open Science</li> <li>Solutions and Incentives</li> <li><a href="https://sfdora.org/" rel="nofollow">DORA</a></li> <li> <p>Examples of Open Science practices and Initiatives</p> </li> <li> <p><strong>Hands-on activities</strong> (60 minutes)</p> </li> <li>package/version management, containerization with <code>renv</code></li> <li>determining package dependencies </li> <li>provenance documentation</li> <li>See: <a href="https://osf.io/dnf9x/" rel="nofollow">virtual environments mini-tutorial</a>.</li> </ol> <hr> <h4><strong>Session 8: Oct. 29</strong></h4> <p><strong>Pre-session activities</strong></p> <p><strong>Required readings:</strong> </p> <ol> <li> <p>The <a href="https://ocsdnet.org" rel="nofollow">Open and Collaborative Science in Development Network</a> provides some excellent insights on how Open Science can progress to help address systemic inequalities and biases in conventional western science. Please read their very short <a href="https://ocsdnet.org/manifesto/open-science-manifesto/" rel="nofollow">manifesto</a>, which provides a good entry point. </p> </li> <li> <p><a href="https://www.americanscientist.org/article/open-science-isnt-always-open-to-all-scientists" rel="nofollow">Open science isn’t always open to all scientists</a></p> </li> </ol> <p><strong>Additional readings (related to discussion):</strong> </p> <ul> <li><a href="https://www.sciencemag.org/careers/2020/10/science-s-english-dominance-hinders-diversity-community-can-work-toward-change" rel="nofollow">Science’s English dominance hinders diversity</a></li> <li><a href="https://fnigc.ca/splash/" rel="nofollow">OCAP® principles</a></li> <li><a href="https://royalsocietypublishing.org/doi/10.1098/rsos.201520" rel="nofollow">Credibility of preprints</a></li> <li><a href="https://www.biorxiv.org/content/10.1101/332783v3" rel="nofollow">The Portal Project: a long-term study of a Chihuahuan desert ecosystem</a></li> </ul> <p><strong>In-session activities</strong></p> <ol> <li><strong>Q & A / Admin</strong> (5-10 min) </li> <li> <p>Address questions </p> </li> <li> <p><strong>Lecture / Discussion</strong> (30 min)</p> </li> <li> <p>How can Open Science improve Equity, Diversity, and Inclusion </p> </li> <li> <p><strong>Hands-on activities</strong> (45 minutes)</p> </li> <li>Examples of workflows using OSF and other tools</li> <li>One example of an in-progress manuscript with <a href="https://osf.io/ujnw2/" rel="nofollow">supporting materials at OSF</a></li> <li>A slightly older example of a published paper with <a href="https://osf.io/vuhe8/" rel="nofollow">supporting materials on OSF</a></li> <li><a href="https://osf.io/nrkdt/" rel="nofollow">OSF Example student template</a></li> </ol> <hr> <h4><strong>Assignment:</strong></h4> <p><strong>Due date</strong>: October 23, Noon Pacific<br> <strong>Worth</strong>: 30%<br> <a href="https://osf.io/a2w78/" rel="nofollow"><strong>Rubric</strong></a></p> <p>Pick one article in your field of study, and: 1. Provide a brief summary of its purpose and main findings. 2. Determine whether the journal in which the article is published has any form of checklist for authors with respect to transparency and reproducibility. If yes, provide a link. 3. Evaluate the article with respect to the 10 questions in this <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41559-018-0545-z/MediaObjects/41559_2018_545_MOESM1_ESM.pdf" rel="nofollow">checklist</a>. Your answers to each question should be brief, i.e. yes / no if appropriate, or a few sentences at most.</p> <p>Use R Markdown to author your report, and include a bibliography at the end of your document (the bibliography should include at least one reference).</p> <p>Submit a rendered PDF document, and be sure to include a link to OSF or Github for access to the RMD file.</p> <h4><strong>Group project:</strong></h4> <p><strong>Due date</strong>: November 6, Noon Pacific<br> <strong>Worth</strong>: 70%<br> <a href="https://osf.io/9yfe2/" rel="nofollow"><strong>Rubric</strong></a></p> <p><strong>OPTION 1:</strong></p> <p>Collaborate to prepare and submit a pre-registration for a replication study in your field of interest. The proposed statistical methods should be demonstrated using simulated / made-up data (with properties informed by published data), with supporting figures included in the pre-registration, and associated analysis script available for download. </p> <p><strong>OPTION 2:</strong></p> <p>Using the skills you've learned, collaborate to co-author a brief, mock manuscript that uses published data to address a question of your choice. It can be exploratory or confirmatory. The study should include at least one table and one figure, a bibliography, it should be computationally reproducible, and all aspects should be accessible online.</p>
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