Lab Meetings
For the Spring 2023 Semester, we will meet on Thursdays 8:00-8:50am
in room 350 Moore.
Goals
- 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
- Attending: Rick, Andrea, Yiming, Oriana, Cecilia, Belle, Madison,
Belle, Molly
- Excused: Kayla, Kavya, Melody
- Absent: Ysa
- Discuss:
- Protocols Project
- Homework:
- Belle - complete evaluation of Annual Compliance Training began
evaluation
- Project Teams:
- Bowen, Madison, Belle: Annual Compliance Training
- Oriana, Yiming, Cecilia, Molly: CITI Training
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
2/23/2023
- 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
2/16/2023
Attending: Rick, Andrea, Molly, Kayla, Madison, Belle, Cecilia,
Bowen, Oriana
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
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
2/9/2023
- Attending: Rick, Andrea, Molly, Kayla, Madison, Belle, Cecilia,
Bowen, Oriana, Yiming, Melody
- 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:
README.md: 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}
package::command(paramaters)
- Homework:
- Complete any training assigned via Asana
- What theme do we want for bookdown? bookdown:: bs4_book is used
currently
2/2/2023
- Attending: Molly, Kayla, Belle, Madison, Cecilia, Oriana, Yiming,
Rick, Andrea, Melody, Bowen
- Discuss:
- Homework: Complete any outstanding Training. Check Asana!
1/26/2023
- 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
1/19/2023
- Attending: Rick, Andrea, Yiming, Molly, Bowen, Kayla, Ysa, Belle,
Cecilia, Oriana, Madison
- 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.