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| # SKC CI Workshop June 2024 | |
| *"Getting started with Cyberinfrastructure"* | |
| https://gitea.skc.edu/workshops | |
| ## Lessons | |
| Lessons (Day 1): | |
| * Welcome and overview | |
| * Introduction to Jupyter Notebooks, RStudio, and Git | |
| * R for Reproducible Scientific Analysis | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/01-rstudio-intro.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/04-data-structures-part1.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/05-data-structures-part2.html | |
| * Data: https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/main/episodes/data/gapminder_data.csv | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/06-data-subsetting.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/08-plot-ggplot2.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/09-vectorization.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/11-writing-data.html | |
| * https://swcarpentry.github.io/r-novice-gapminder/instructor/15-wrap-up.html | |
| Lessons (Day 2): | |
| * Welcome and overview | |
| * Sharing & collaborating with code (Github introduction) | |
| * https://swcarpentry.github.io/git-novice/01-basics.html | |
| * Motivation: https://happygitwithr.com/big-picture.html (extra background) | |
| * https://swcarpentry.github.io/git-novice/04-changes.html | |
| * https://swcarpentry.github.io/git-novice/05-history.html | |
| * https://swcarpentry.github.io/git-novice/06-ignore.html | |
| * https://swcarpentry.github.io/git-novice/08-collab.html | |
| * https://swcarpentry.github.io/git-novice/09-conflict.html (optional) | |
| * https://swcarpentry.github.io/git-novice/10-open.html | |
| * https://swcarpentry.github.io/git-novice/11-licensing.html | |
| * Technical overview of the infrastructure. | |
| Workshop Links: | |
| * CI environment (SKC-CARE): https://ci.skc.edu/ | |
| * Git environment: https://gitea.skc.edu | |
| * Workshop site: https://gitea.skc.edu/workshops/2024-June-CI-Workshop | |
| * Workshop Gitea organization: https://gitea.skc.edu/2024-June-CI-Workshop | |
| * Instructor Notes: [Notes.md](Notes.md) | |
| * Class Notes: https://gitea.skc.edu/Workshops/2024-June-CI-Workshop-In-Class | |
| ## Resources | |
| * Git and R (recommended for students and as a teaching resource): https://happygitwithr.com/ | |
| * Introduction: https://dx.doi.org/10.7287%2Fpeerj.preprints.3159v2 | |
| * R Markdown: https://bookdown.org/yihui/rmarkdown/markdown-syntax.html | |
| * R Tutorial: https://www.cyclismo.org/tutorial/R/ | |
| * ggplot2: https://ggplot2.tidyverse.org/ | |
| * ggplot2 cheat-sheet: https://www.maths.usyd.edu.au/u/UG/SM/STAT3022/r/current/Misc/data-visualization-2.1.pdf | |
| * Git book: https://git-scm.com/book/en | |
| * Git branching: | |
| * https://happygitwithr.com/git-branches (and remotes https://happygitwithr.com/git-remotes) | |
| * https://nvie.com/posts/a-successful-git-branching-model/ | |
| * https://git-scm.com/book/en/v2/Git-Branching-Branches-in-a-Nutshell | |
| * R project introduction http://cran.r-project.org/doc/manuals/R-intro.html | |
| * R Language: https://www.r-project.org/ | |
| ### Advanced Materials | |
| * Git internals: "Git for Ages 4 And Up" - https://youtu.be/1ffBJ4sVUb4 | |
| * Test Driven Development (TDD) http://www.agiledata.org/essays/tdd.html |