delta science week 1

[hdolinh]

Questions:

• This markdown syntax was new for participants, what's the use case?
  • Reference Style Links and Images Links: A [linked phrase][id].
  • At the bottom of the document: [id]: http://example.com/ "Title"
• Can you specify which reference style to use in Quarto?
• What kind of manuscripts can you create using Quarto?
  • Answer: mention the gallery on the quarto website
• Using quarto to create pdf documents
• How are EML or other computer generated standards published? Do you have to submit your data to a source?
• When you are working on a synthesis project - should you include all data tables or data sets in the package? Or just cite where you sourced the data?
• Why use CARE Principles?

[hdolinh]

Issues:

• [x] Links to quarto resources are broken @camilavargasp to fix
• [ ] Data modeling lesson: Multiple observations section, make sure it's clear there are 3 observations (sp1height, sp2height, and altitude of site), not just 2 @carmengg to fix
  • [ ] more discussion may be needed btwn instructors
• [x] Data modeling lesson section 9.3.4 natural key is incorrect @carmengg to fix

[hdolinh]

@carmengg instructor observations and notes from running the activity

• Exercise 2: Assess Normalization

  • It is hard to identify if Site Table is truly denormalized and how to normalize it
    • May be helpful to add more observations so that it's easier to identify what observations are unique and what are not unique, and therefore how to parse the tables

• Overall: consider removing site_id from bird data table to remove confusion about redundancies

[carmengg]

I updated the lesson and the slides to correct section 9.3.4 (natural key issue). There's a pull request open to integrate these changes: https://github.com/NCEAS/nceas-training/pull/289

The slides are in this separate repo: https://github.com/carmengg/data-modeling-essentials-slides

[camilavargasp]

git and GitHub Lessons

• Question about Lisences:
  • How do you know which one to use?
  • Is there any talk about renaming the Apache license name? Because of it's cultural appropriation
• Are we going to talk about the differences between fork and branching?
• Why commit Rproj? Or why not?
• What are the different symbols in the git pane in RStudio. Maybe create a table explaining each of them

[carmengg]

Git & GitHub lesson

Questions that came up:

• should you commit the .Rproj file? (Rproj are specific to R studio)
• what do the different colors+letters for the squares in the RStudio Git tab mean? [did a quick search and couldn't find a sort of key]
• verify PAT is discovered/set at the beginning of lesson
• some confusion between difference between console and terminal

[carmengg]

Data Wrangling Lesson

• link it more with the Data Modeling session. For example, talk about how group_by uses keys to make groups.
• Add intro examples to slides to motivate the code-along + slide about the data we will be using.
• DO NOT jump to another made-up data frame to talk about unite() and separate(). Integrate it with the data frame used in example.

[hdolinh]

Cleaning & Wrangling Practice

• Add a note that getting the same answer through different codes is possible and okay. The code answer provided is not the only way
• Wording in Exercise 3 is somewhat confusing, consider rewording. Need to include both data frames

[carmengg]

Cleaning & Wrangling Practice

• Setup instructions: clarify whether to Push .Rproj or not. It might also be a nice to have a call-out note in the git/GitHub lesson based on the conversation we had during the lecture: it's ok to push the .Rproj file, but it might not be useful for everyone (non RSudio users).
• Remove sub-section numbers so we can only refer to Exercise #

[camilavargasp]

• Think about Runiverse and how we can have a deeper conversation on how to set it up for Delta

[hdolinh]

Git & GitHub Lesson

• Consider setting up SSH keys instead of PATs to avoid potentially losing credentials after server reboots
• Managing GitHub credentials from R, difficulty level linux blog post by Danielle Navarro

[carmengg]

General

I've heard a lot of discussion about ADA compliance (alt text for images and images accessible to color-blind people, for example).

• Maybe incorporate some of these accessibility items to the Learning Hub's materials?

[hdolinh]

Reproducibility & Provenance Lesson:

• Not all server accounts were able to successfully render their PDF doc due to error ! sh: pdflatex: command not found
• tinytex is not found in R dirs in user accounts. Reach out to Nick when he's back from vacation and ask if he can compare Halina & Matt's R environments