Merge branch 'main' into update-r-ii

_quarto.yml

@@ -1,5 +1,7 @@
 project:
   type: website
+  resources: 
+    - "robots.txt"
   render: 
     - "*.qmd"
 
@@ -12,6 +14,10 @@ website:
   repo-actions: [edit, issue]
   site-url: https://cct-datascience.github.io/repro-data-sci/
   navbar:
+    tools:
+      - icon: github
+        text: Source #shows on hover
+        href: https://github.com/cct-datascience/repro-data-sci
     left:
       - href: index.qmd
         text: Home

index.qmd

@@ -13,7 +13,7 @@ Welcome to the syllabus for the CCT Data Science fall workshop series: **Reprodu
 We'll meet on Tuesdays and Thursdays from 11 a.m.to 1 p.m.
 via Zoom (link pinned in Slack channel)
 
-<!-- Edit by editing schedule.csv. To add links, use markdown [text](url) separated by commas. This code turns that into a bulleted list. -->
+<!-- Edit by editing schedule.csv. To add links, use markdown [text](url) separated by commas. This code turns that into a bulleted list.-->
 
 ```{r}
 #| echo: false

lessons/10-get-credit/notes.qmd

@@ -8,9 +8,13 @@ bibliography: references.bib
 
 ## Objective
 
-Learn the wrap-up steps to publish/archive a research compendium with a DOI.
-Understand reproducible computational environment.
-Learn `renv` and discuss Docker (concept).
+-   Add a basic CITATION.cff file to your repo
+
+-   Practice the wrap-up steps to publish/archive a research compendium with a DOI.
+
+-   Understand concept of a reproducible computational environment.
+
+-   Learn `renv` and discuss Docker (concept).
 
 ## Lesson Outline
 
@@ -31,22 +35,21 @@ Learn `renv` and discuss Docker (concept).
 
     -   Show CITATION.cff files for this repo and maybe one for a research compendium
     -   Show "cite this" button on GitHub
-    -   Show CITATION.cff creation tool [CFFINIT](https://citation-file-format.github.io/cff-initializer-javascript/#/)
-    -   Maybe mention `cffr::cff_validate()`
+    -   Everyone use CITATION.cff creation tool [CFFINIT](https://citation-file-format.github.io/cff-initializer-javascript/#/) to create a *basic* CITATION.cff
+    -   *Maybe* mention `cffr::cff_validate()`
 
 -   Archiving
 
-    -   Most participants probably won't be ready to follow along with their own repos, but we will be there to help when they are ready
-    -   Demo archiving a repo with Zenodo using this repo
+    -   Exercise: guide everyone through archiving a repo with Zenodo using sandbox.zenodo.org
     -   Add DOI badge to readme
     -   Update CITATION.cff with DOI
 
 -   `renv`
 
     -   Discuss why
-    -   Ask students to activate `renv` for a project and inspect files it creates (have co-instructor share screen)
+    -   Ask students to activate `renv` for a project and inspect files it creates
     -   Explain how `renv` works, especially `renv::status()` , and `renv::snapshot()`
-    -   Clone co-instructor's repo with `renv` files
+    -   Clone demo repo with `renv` files
         -   Show that no packages are available initially (project is isolated)
         -   run `renv::restore()`
 
@@ -58,4 +61,4 @@ Learn `renv` and discuss Docker (concept).
 
 ## Homework
 
--   Prep for showcase session
+-   Prep for reproducibility colloquium

lessons/10-get-credit/slides.qmd

@@ -5,7 +5,7 @@ date: "2024-10-03"
 date-format: long
 format:
   uaz-revealjs:
-    reference-location: document
+    reference-location: section
     link-external-newwindow: true
     chalkboard: true
     logo: "../../logo.png"
@@ -27,7 +27,7 @@ Figure 2 from @maitner
 Figure 2: Predicted impacts of code-sharing on cumulative citations.
 Predicted values shown are for the mean Impact Factor (3.0) across the publications analyzed.
 Fully open = open code and open-access publication; fully closed = closed-access publication and no publicly available code.
-Predictions are based on estimated model coe cients (Table 2)
+Predictions are based on estimated model coeficients (Table 2)
 :::
 
 ## Getting credit for your code
@@ -43,33 +43,51 @@ Make it **easier** for people to cite your code
 ## CITATION.cff
 
 ::: incremental
--   Citation File Format are plain text files written in YAML
+-   A `CITATION.cff` file contains citation information written in YAML
 
 -   Adding a `CITATION.cff` file to your repo...
 
     -   Puts a "cite this repository" button on GitHub
 
     -   Helps code archive tools fill out metadata correctly when you archive your repo
 
--   Create a CITATION.cff file with this [helper](https://citation-file-format.github.io/cff-initializer-javascript/#/)
+-   Learn more and create your own: <https://citation-file-format.github.io/>
 
 -   See example [here](https://github.com/cct-datascience/repro-data-sci/blob/main/CITATION.cff)
 :::
 
 ## Options for archiving {.smaller}
 
-| Service   | Versioned DOIs? | Free?                              | GitHub integration? | Notes                                             |
-|--------------|--------------|--------------|--------------|----------------|
-| Zenodo    | Yes             | Yes                                | Yes                 | Backed by CERN, built with code and data in mind  |
-| Dryad     | Yes             | No, but some publishers cover cost | No                  | Intended for data, not code. Partners with Zenodo |
-| Figshare  | Yes             | Yes                                | Yes                 | Can't choose your license                         |
-| UA ReDATA | Yes             | Yes (for UA researchers)           | No                  | University of Arizona Libraries                   |
+| Service | Versioned DOIs? | Free? | GitHub integration? | Notes |
+|---------------|---------------|---------------|---------------|---------------|
+| Zenodo | Yes | Yes | Yes | Backed by CERN, built with code and data in mind |
+| Dryad | Yes | No, but some publishers cover cost | No | Intended for data, not code. Partners with Zenodo |
+| Figshare | Yes | Yes | Yes | Can't choose your license |
+| UA ReDATA | Yes | Yes (for UA researchers) | No | University of Arizona Libraries |
 
 ::: aside
 More detailed comparisons [here](https://www.agu.org/-/media/Files/Publications/Generalist-Data-Repository-Grid.pdf)
 :::
 
-# Zenodo Archiving Demo
+## Zenodo Archiving Demo
+
+1.  Log in to [sandbox.zenodo.org](https://sandbox.zenodo.org) using GitHub[^1]
+2.  In drop-down menu with your username, select "GitHub"
+3.  Find your repo in the list and flip the switch next to it
+4.  Go to your repo on GitHub and make a release
+5.  On sandbox.zenodo.org, get markdown to add a badge to README.md
+
+::: notes
+Demo archiving a repo with sandbox.zenodo.org and have everyone follow along with the repo they've been using for notes.
+:::
+
+## When to archive?
+
+No hard rules on this, but my preference:
+
+1.  Just before submitting a manuscript: release v 0.1.0
+2.  After responding to reviewers or re-submitting: increment "minor" version, e.g. v 0.2.0
+3.  After acceptance: release v 1.0.0
 
 ## Reproducible computational environments
 
@@ -113,15 +131,20 @@ To deactivate `renv`, run `renv::deactivate()`.
 To also remove all the files it created, run `renv::deactivate(clean = TRUE)` instead.
 :::
 
+::: notes
+Briefly discuss the contents of `renv.lock`, `.Rprofile`, and `renv/`.
+Point out `renv/.gitignore` — trust it about which files should go on GitHub.
+:::
+
 ## Limitations of `renv`
 
--   Only tracks R packages [^1]
+-   Only tracks R packages [^2]
 
 -   Can't reproduce operating system or system libraries
 
 -   Sometimes quite annoying to use (but it's getting better!)
 
-## Reproducible Everything with Docker
+## *More* Reproducibility with Docker
 
 Docker containers...
 
@@ -135,7 +158,7 @@ Docker containers...
 -   Can be downloaded and run from the command line
 :::
 
-## Making a Docker Container
+## Making a Docker Container <!--# skipped for 2024 --> {visibility="hidden"}
 
 A **Dockerfile** holds instructions on what to install and what code to run.
 Actually creating a Docker container is beyond the scope of this workshop, but you can [learn how](https://www.r-bloggers.com/2019/02/running-your-r-script-in-docker/)!
@@ -159,7 +182,7 @@ RUN Rscript /02_code/install_packages.R
 
 ## Hold up, what *is* reproducibility again?
 
-There is a reproducibility **tradeoff** for using `renv` and Docker---robust computational reproducibility **but** harder for novices to reproduce
+There is a reproducibility **trade-off** for using `renv` and Docker---robust computational reproducibility **but** harder for novices to reproduce
 
 . . .
 
@@ -169,17 +192,32 @@ If you use these tools, provide:
 -   Where to go for help troubleshooting
 -   Ways to access your code *without* extra layers
 
-## Drop-in Session & Showcase
+## Resources
+
+-   [`renv` website](https://rstudio.github.io/renv/articles/renv.html)
+
+-   CITATION.cff [info](https://citation-file-format.github.io/) and [creator tool](https://citation-file-format.github.io/cff-initializer-javascript/#/)
+
+-   [Zenodo-GitHub integration](https://zenodo.org/account/settings/github/)
 
--   Next week (10/10, 10/12): No workshops!
+-   [Reproducible computational environments with Docker](https://reproducibility.rocks/materials/day4/01-docker/)
 
--   Tuesday 10/17: Drop-in help session
+## Next week
 
--   Tuesday 10/24: Reproducibility show & tell
+-   Tuesday 10/18: **Drop-in co-working session**.
+
+    -   Come and work on your reproducibility colloquium project/presentation
+
+-   Thursday 10/10: **Reproducibility Colloquium!**
+
+    -   Invite your lab-mates, PI, friends!
 
 ## References
 
 ::: refs
 :::
 
-[^1]: `renv` can also be set up to track [Python dependencies](https://rstudio.github.io/renv/articles/python.html)
+[^1]: sandbox.zenodo.org is just for practice.
+    Use zenodo.org when you're ready to get a *real* DOI!
+
+[^2]: `renv` can also be set up to track [Python dependencies](https://rstudio.github.io/renv/articles/python.html)

robots.txt

@@ -0,0 +1,51 @@
+# sources: 
+# https://www.cyberciti.biz/web-developer/block-openai-bard-bing-ai-crawler-bots-using-robots-txt-file/
+# https://neil-clarke.com/block-the-bots-that-feed-ai-models-by-scraping-your-website/
+
+# Data from Common Crawl is used to train ChatGPT, Bard, etc.
+User-agent: CCBot
+Disallow: /
+
+# Stops ChatGPT users from instructing ChatGPT to access our site
+User-agent: ChatGPT-User
+Disallow: /
+
+# Don't add any content to the GPT model
+User-agent: GPTBot
+Disallow: /
+
+# Blocks Bard and VertexAI. Does not impact search indexing.
+User-agent: Google-Extended
+Disallow: /
+
+# webz.io.  They sell data for training LLMs 
+User-agent: Omgilibot
+Disallow: /
+
+User-agent: Omgili
+Disallow: /
+
+# Specific to AI.  Won't prevent previews from showing up correctly on Facebook posts
+User-agent: FacebookBot
+Disallow: /
+
+# Anthropic AI (Claude)
+User-agent: anthropic-ai
+Disallow: /
+
+User-agent: Claude-Web
+Disallow: /
+
+User-agent: ClaudeBot
+Disallow: /
+
+# ByteDance's bot for gathering LLM training data
+User-agent: Bytespider
+Disallow: /
+
+User-agent: ImagesiftBot 
+Disallow: /
+
+# Takes content and re-writes it using genAI
+User-agent: PerplexityBot
+Disallow: /

schedule.csv

@@ -8,6 +8,6 @@ Lesson,Date,Theme,Topic,Links,Notes
 7,2024-09-24,Tidy & Wrangle,Data manipulation & coding best practices,[slides](lessons/7-data-manipulation/slides.html),data carpentry R ecology episodes 2 & 3
 8,2024-09-26,Repeat & Reproduce,Intermediate R programming I,[slides](lessons/8-intermediate-r-1/slides.html),functions
 9,2024-10-01,Repeat & Reproduce,Intermediate R programming II,[slides](lessons/9-intermediate-r-2/slides.html),iteration 
-10,2024-10-03,Document & Publish,Getting credit for your hard work,,"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases"
+10,2024-10-03,Document & Publish,Getting credit for your hard work,[slides](lessons/10-get-credit/slides.html),"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases"
 11,2024-10-08,Review,Drop-in co-working,,
 12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,[guidelines](colloquium.html),