Lab Meetings

For the Spring 2023 Semester, we will meet on Thursdays 8:00-8:50am in room 350 Moore.

Previous meeting notes

Notes from previous semesters


  • Data science
    • Learn R on Datacamp
    • Begin by creating or updating your a brief biography for the Who we are page on the lab website.
  • Start preparing for presentations in the Spring
    • Train on poster template for R posterdown
    • Train how to use Databrary API
  • Data Processing/Analysis projects
    • Databrary Tagging
    • Databrary User Guide
    • Open Science Survey Data
    • Datavyu Coding of infant locomotion??
  • Submit abstracts for poster presentation:
  • Future readings:
    • Yiming’s PhD paper and paper reviews

Psych 494 Syllabus

Spring 2023

5/4/2023 Lab Breakfast @ Waffle Shop

4/27/2023 350 Moore

  • Attending: Rick, Andrea, Cecelia, Belle, Madison, Oriana, Yiming
    • Excused: Kayla
    • Absent: Molly, Bowen, Ysa
  • Discuss
    • How relevant is Rmarkdown in other classes? not so much, but maybe in the future

    • protocols book

      • Create instructions for: Github, data camp, rstudio and some other missing sections
      • fix image size and box formatting
    • should we switch to outlook calendar or stay with google calendar

    • most don’t use teams so stay with Discord

    • look at Play Project Surveys

  • To Do:
    • ARS - create Datacamp plan for lab next semester and add to lab meeting agendas

4/20/2023 NO MEETING

4/13/2023 350 Moore

  • Attending: Rick, Andrea, Kayla, Bowen, Cecelia, Belle, Madison, Oriana, Yiming, Ysa
    • Excused: Kavya, Melody
    • Absent: Molly
  • Discuss:
    • How to create a new project on Git and clone repository in RStudio
    • Next Project is Visual Acuity - Teller Acuity Cards
    • Work on setting up Bookdown for Visual Acuity project
    • easier to copy from another repository and alter them for new project
      • need files: _bookdown.yml, _output.yml, and index.Rmd
      • set up files and directories in visual-acuity-project folder
      • generate book
      • set up webpage

4/6/2023 350 Moore

  • Attending: Rick, Andrea, Yiming, Kayla, Bowen, Alex
    • Excused: Molly, Oriana, Madison, Kavya, Belle, Cecelia, Melody
    • Absent: Ysa
  • Discuss:
    • Ham Radio Book
      • Alex tested some of the activities in chapter 3 Hands on Hamming.
    • Motion Sensitivity Paper Study
      • What is development of infants visual acuity - Teller Acuity Cards
      • Create database/metaanalysis/data aggregation of Teller Acuity Card results over time
    • Open Science Bootcamp 2023 Book
  • Homework:
    • ARS: Find Teller Acuity Card info for Gilmore Lab
    • ARS: Schedule final meeting
    • Look up “Teller Acuity Cards” if you have time.
  • Next Week:
    • Live literature search
    • work on protocol

3/30/2023 350 Moore

3/23/2023 350 Moore

  • Attending: Rick, Andrea, Kayla, Madison, Belle, Cecilia, Melody, Bowen, Yiming
    • Excused: Oriana, Kavya, Ysa
    • Absent: Molly
  • Discuss:
    • Best way to merge work from multiple people - we think push to master
    • how to show a code chunk without running code
  • Homework:
    • ARS - add link to location in book down that shows how to show code chunk

    • change global options for saving -ARS emailed ROG

    • Everyone keep working on sections for protocols. Push changes to master branch

3/16/2023 350 Moore

  • Attending: Rick, Madison, Oriana, Kayla, Belle, Cecilia

    • Absent: Ysa, Kavya
    • Excused: Andrea, Yiming, Bowen
  • Discuss:

  • Homework:

3/9/2023 Spring Break

3/2/2023 CANCELLED


  • Attending: Rick, Andrea, Yiming, Oriana, Madison, Bowen, Cecilia
    • Absent: Molly, Ysa, Kavya
    • Excused: Belle
  • Discuss:
    • Does everyone have R and R Studio Installed? YES :)
    • Edit: Protocols repository in R Studio
      • take off numbering of headers by adding {-} at the end of each header
      • function takes an input and produces an output. Anything that is given to the function is in parentheses () while things that we are looking at are in square brackets [].
  • Homework:
    • Everyone pull the protocols repo locally to your R Studio.
    • Think about and update (if possible) pages with screenshots and descriptive text/links
      • CITI training: Oriana, Cecilia, Yiming
      • Yearly Compliance Training: Madison, Kayla, Bowen


  • Attending: Rick, Andrea, Molly, Kayla, Madison, Belle, Cecilia, Bowen, Oriana

    • Absent Ysa, Kavya
  • Discuss:

    • all but 1 have R and R Studio Installed
    • Everyone has GitHub Accounts
    • issue with syncing with GitHub error: “Support for password authentication was removed. Please use a personal access token instead.”
  • Install Github

  • Connect R with GitHub

  • Clone Repository

    • go to github website
  • In RStudio

    • Make Changes
    • render the book using command > bookdown::render_book()
    • Save
    • commit
    • Push once synchronization or R and Git is working
  • Homework:

    • create documentation for synchronization R and Git ARS/Rick/Melody
    • Outstanding Training on Asana: Molly and Kayla


  • Attending: Rick, Andrea, Molly, Kayla, Madison, Belle, Cecilia, Bowen, Oriana, Yiming, Melody
    • Absent: Ysa, Kavya
  • Discuss:
    • Work session: bookdown site for all lab protocols
      • Anatomy of using Bookdown files
        • .gitignore: don’t keep track of the files in this file
        • protocols.Rproj: this file has information project information specific to your computer
        • .Rhistory: history of your files that you have run recently
        • folders for resources
          • imgs/ (eg. jpg, )
          • pdfs/
          • docs/ rendered documents index.Rmd:
        • this a descriptive file for how to use this repository anything within a back tick (`) will appear like this .yml YAML (yet another markup language)
        • renv.lock explains the files required to run in the renv/ folder
      • render book:
      • chunk of code is in between three back ticks (```)

{whatLanguage chunkLabel, paramaters}

  • Homework:
    • Complete any training assigned via Asana
    • What theme do we want for bookdown? bookdown:: bs4_book is used currently


  • Attending: Molly, Kayla, Belle, Madison, Cecilia, Oriana, Yiming, Rick, Andrea, Melody, Bowen
    • Absent: Ysa, Kavya
  • Discuss:
  • Homework: Complete any outstanding Training. Check Asana!


  • Attending: Rick, Andrea, Bowen, Kayla, Belle, Cecilia, Madison, Oriana, Yiming
    • Excused: Ysa, Molly
    • Kavya
  • Discuss:
  • Homework:
  • Next Week:
    • Begin to create a bookdown site for all lab protocols
    • review syllabus and goals above
    • Research ethics
    • Databrary and reproducibility crisis


  • Attending: Rick, Andrea, Yiming, Molly, Bowen, Kayla, Ysa, Belle, Cecilia, Oriana, Madison
    • Excused: Kavya
  • Discuss:
    • Introductions
    • Yiming - present 15 min job talk
      • provide feedback on slides and talk
  • Homework:
    • Work on any training assigned via Asana. We will discuss next week if there are any problems.