Delta Week 1 book

[camilavargasp]

Book Prep

• [x] Create course branch
• [x] See what needs to happen in the repro-research repository to deploy the book
• [x] Update all sections to read in the correct Qmd according to the schedule
• [x] Share with instructors the github workflow to contribute to the book
• [x] make sure book renders and deployed with no issues

[camilavargasp]

Fix

• [x] Rmd lesson. An issue with calling "ratio" in text
• [x] Section 8: programmatic-data-access.qmd not working NOTE function get_citation() not working (line 280)
• [x] Section 12: r-practice-clean-wangle.qmd. lobster_abundance_all_years_20220829 missing
• [x] Check why Quarto chunk option format are not working NOTE Not sure why, but it works if I do Rmd style chunk options
• [x] insert logic model images

[camilavargasp]

Chapters

Check when ready

• [x] index.qmd # preface
  • [x] Add schedule pic
• [x] session_01.qmd # rstudio server setup + mini intro to R programming
  • [ ] Add quarto installation instructions
  • [x] Add a brief introduction to programming in R
• [x] session_02.qmd # git setup
• [x] session_03.qmd # r intro to quarto
  • [ ]Make the example of literate analysis in Quarto format
• [x] session_04.qmd # activity reproducibility LEGO
• [x] session_05.qmd # Accesing and publishing data
  • [x] Restructure lesson focusing on synthesis science
  • [x] Add: Research/data life cycle
  • [x] Documenting data: metadata
  • [x] Publishing data
  • [x] Accessing data
  • [x] Metadata interpretation
• [x] session_06.qmd # logic modeling
• [x] session_07.qmd # git and github intro
• [x] session_08.qmd # programmatic data access
  • [x] session_09.qmd # data modeling essentials
  • [ ] session_10.qmd # synthesis
  • [x] session_11.qmd # clean and wrangle data
  • [x] session_12.qmd # r practice: clean and wrangling
  • [ ] session_13.qmd # synthesis
  • [x] session_14.qmd # r functions
  • [x] session_15.qmd # r packages
• [x] session_16.qmd # FAIR and CARE
• [x] session_17.qmd # git collab
  • [ ] session_18.qmd # synthesis
  • [ ] session_19.qmd # reproducible papers

[hdolinh]

Hey @camilavargasp RE: Check why Quarto chunk option format are not working NOTE Not sure why, but it works if I do Rmd style chunk options

I looked at the commits and in materials/sections/programmatic-data-access.qmd the r chunks with the Quarto code options have a space between the start of the r code chunk and the Quarto code options. It's nitpicky, but the code options don't execute when that space is there. In the examples below, I'm using apostrophes instead of backticks so you can see the code chunk formatting.

This doesn't work: '''{r}

| label: contentid-file-load

'''

This works: '''{r}

| label: contentid-file-load

'''

[hdolinh]

@camilavargasp RE: Section 12: r-practice-clean-wangle.qmd. lobster_abundance_all_years_20220829 missing

When I made the R practice sessions, I set the yaml for each of the session_XX.qmd files to eval: false because none of the code in the practice sessions needs to run. The answers for each question are the lines of code, not the outputs of the code. So I never added the lobster data to the nceas-training repo. If I needed to access the lobster data in the book, I used the URL link and would hide the code chunk.

Also, the file paths to the data will always be different when running code in the book vs what a participant would run so the code to read in lobster_abundance_all_years_20220829 that's visible in the r-practice-clean-wangle.qmd is a reflection of what a participant would type out.

LMK if you have any questions about this - happy to answer them

[camilavargasp]

@hdolinh Thank you for the chunk option clarification! It was driving me crazy.

I still need to finalize the r-practice-clean-wrangle.qmd and adapt it so that the exercise is only for one person as opposed to being collaborative. I'll take into consideration the points you mention above, thank you! Let you know if I run into issues or have any questions.

[hdolinh]

@camilavargasp RE: R clean and wrangle practice session:

Sounds good. One more thing I'll mention is that in both the r-practice-owner-clean-wrangle.qmd and the r-practice-collaborator-clean-wrangle.qmd files there is an "Extra Questions" section at the end that might be helpful for you. When I needed to shorten the practice session, I just made the questions not visible in the book but they're still there if you're looking for more cleaning and wrangling problems.

[mbjones]

@camilavargasp I restructured the book build pretty significantly today, making it a lot faster, and got the redland and dataone packages installing properly for section 08, which is now back in the build. Lots more to do in the build to improve it, but it should be much faster now. I switched to using binary package builds from posit, and added an effective cache of the packages. So, if you need a new package, be sure its added to the DESCRIPTION file, which is what triggers a fresh install of the packages. If you don't change DESCRIPTION, then the build will use the cache. Details in issue #71, and let me know how it works for you when you push a chapter.

[camilavargasp]

Thanks @mbjones! The book is building and sooo much faster. I'll take a deep dive into GHA after the course to make sure we continue with the necessary updates. Thanks for documenting everything on an issue.