Fleshed out slides for lab 2

_freeze/materials/slides_2b/execute-results/html.json

@@ -1,10 +1,8 @@
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-    "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Lab 2 -- Version Control\"\nengine: knitr\nformat: \n  revealjs: \n    slide-number: c\n    scrollable: false\n    code-overflow: wrap\n    code-line-numbers: false\n    code-copy: hover\n    theme: [night, slides.scss]\n    reference-location: document\n    footer: \"[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-biologists/)\"\n---\n\n\n## A Guide to Your Process\n\n### [Scheduling]{.blue}\n\n### [Learning Objectives]{.purple}\n\n### [Practice]{.pink}\n\n### [Supporting Information]{.orange}\n\n### [Class Discussion]{.gold}\n\n## [Today's Plan]{.blue}\n\n- Y\n\n## [Today's Learning Objectives]{.purple}\n\nAfter today's session you will be able to:\n\n. . .\n\n- X\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n<p align=\"center\">\n<img src=\"comics/debugging.png\" alt=\"Comic-style graph depicting someone's emotional state as they debug code (from initial struggle and defeat to eventual triumph)\">\n</p>\n\n\n\n## [Upcoming Due Dates]{.blue} {.smaller}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n\n### Due before lab\n\n#### (By midnight)\n\n- Muddiest Point \\#x\n\n:::\n\n:::{.column width=\"50%\"}\n\n### Due before lecture\n\n#### (By midnight)\n\n- X\n\n:::\n\n::::\n\n",
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+    "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Lab 2 -- Version Control\"\nengine: knitr\nformat: \n  revealjs: \n    slide-number: c\n    scrollable: false\n    code-overflow: wrap\n    code-line-numbers: false\n    code-copy: hover\n    theme: [night, slides.scss]\n    reference-location: document\n    footer: \"[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-biologists/)\"\n---\n\n\n## A Guide to Your Process\n\n### [Scheduling]{.blue}\n\n### [Learning Objectives]{.purple}\n\n### [Practice]{.pink}\n\n### [Supporting Information]{.orange}\n\n### [Class Discussion]{.gold}\n\n## [Today's Plan]{.blue}\n\n- Core Content\n    - Muddiest Point Review\n    - Version Control Background\n    - Navigating GitHub\n\n\\\n\n- Time Permitting\n    - Git / GitHub Setup\n    - RStudio + Git / GitHub\n\n## [Today's Learning Objectives]{.purple}\n\nAfter today's session you will be able to:\n\n. . .\n\n- Explain the difference(s) between Git and GitHub\n- Define fundamental version control vocabulary\n\n\\\n\n### Time Permitting\n\n- Integrate Git and GitHub with RStudio on your computer\n\n## [Muddiest Point Review]{.gold}\n\n- Recurring topics from most recent MPs:\n    - TBD\n\n\\\n\n. . .\n\n- What other topic(s) would you like to review?\n\n## [Version Control Background]{.orange}\n\n- \"Version control\" is a set of tools for tracking changes to a code file\n\n\\\n\n- Version control lets you work only in a single file but still preserves the history\n    - No comments you'd have to resolve (like MS Word / etc.)\n    - No need to \"Save As\" and retain many different files for each draft\n\n## [Version Control Rationale]{.orange} {.smaller}\n\nWhy use version control?\n\n\\\n\n::::{.columns}\n:::{.column width=\"33.33%\"}\n\n##### Collaboration `<svg aria-label=\"Handshake\" role=\"img\" viewBox=\"0 0 640 512\" style=\"height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;\"><title>Handshake</title><path d=\"M272.2 64.6l-51.1 51.1c-15.3 4.2-29.5 11.9-41.5 22.5L153 161.9C142.8 171 129.5 176 115.8 176H96V304c20.4 .6 39.8 8.9 54.3 23.4l35.6 35.6 7 7 0 0L219.9 397c6.2 6.2 16.4 6.2 22.6 0c1.7-1.7 3-3.7 3.7-5.8c2.8-7.7 9.3-13.5 17.3-15.3s16.4 .6 22.2 6.5L296.5 393c11.6 11.6 30.4 11.6 41.9 0c5.4-5.4 8.3-12.3 8.6-19.4c.4-8.8 5.6-16.6 13.6-20.4s17.3-3 24.4 2.1c9.4 6.7 22.5 5.8 30.9-2.6c9.4-9.4 9.4-24.6 0-33.9L340.1 243l-35.8 33c-27.3 25.2-69.2 25.6-97 .9c-31.7-28.2-32.4-77.4-1.6-106.5l70.1-66.2C303.2 78.4 339.4 64 377.1 64c36.1 0 71 13.3 97.9 37.2L505.1 128H544h40 40c8.8 0 16 7.2 16 16V352c0 17.7-14.3 32-32 32H576c-11.8 0-22.2-6.4-27.7-16H463.4c-3.4 6.7-7.9 13.1-13.5 18.7c-17.1 17.1-40.8 23.8-63 20.1c-3.6 7.3-8.5 14.1-14.6 20.2c-27.3 27.3-70 30-100.4 8.1c-25.1 20.8-62.5 19.5-86-4.1L159 404l-7-7-35.6-35.6c-5.5-5.5-12.7-8.7-20.4-9.3C96 369.7 81.6 384 64 384H32c-17.7 0-32-14.3-32-32V144c0-8.8 7.2-16 16-16H56 96h19.8c2 0 3.9-.7 5.3-2l26.5-23.6C175.5 77.7 211.4 64 248.7 64H259c4.4 0 8.9 .2 13.2 .6zM544 320V176H496c-5.9 0-11.6-2.2-15.9-6.1l-36.9-32.8c-18.2-16.2-41.7-25.1-66.1-25.1c-25.4 0-49.8 9.7-68.3 27.1l-70.1 66.2c-10.3 9.8-10.1 26.3 .5 35.7c9.3 8.3 23.4 8.1 32.5-.3l71.9-66.4c9.7-9 24.9-8.4 33.9 1.4s8.4 24.9-1.4 33.9l-.8 .8 74.4 74.4c10 10 16.5 22.3 19.4 35.1H544zM64 336a16 16 0 1 0 -32 0 16 16 0 1 0 32 0zm528 16a16 16 0 1 0 0-32 16 16 0 1 0 0 32z\"/></svg>`{=html}\n\n\\\n\nEasily share & work together on files\n\n:::\n\n:::{.column width=\"33.33%\"}\n\n##### Reproducibility `<svg aria-label=\"Arrows Left Right\" role=\"img\" viewBox=\"0 0 512 512\" style=\"height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;\"><title>Arrows Left Right</title><path d=\"M406.6 374.6l96-96c12.5-12.5 12.5-32.8 0-45.3l-96-96c-12.5-12.5-32.8-12.5-45.3 0s-12.5 32.8 0 45.3L402.7 224l-293.5 0 41.4-41.4c12.5-12.5 12.5-32.8 0-45.3s-32.8-12.5-45.3 0l-96 96c-12.5 12.5-12.5 32.8 0 45.3l96 96c12.5 12.5 32.8 12.5 45.3 0s12.5-32.8 0-45.3L109.3 288l293.5 0-41.4 41.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0z\"/></svg>`{=html}\n\n\\\n\nFully document your progress and end results\n\n::: \n\n\n:::{.column width=\"33.33%\"}\n\n##### Portfolio `<svg aria-label=\"Book\" role=\"img\" viewBox=\"0 0 448 512\" style=\"height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;\"><title>Book</title><path d=\"M96 0C43 0 0 43 0 96V416c0 53 43 96 96 96H384h32c17.7 0 32-14.3 32-32s-14.3-32-32-32V384c17.7 0 32-14.3 32-32V32c0-17.7-14.3-32-32-32H384 96zm0 384H352v64H96c-17.7 0-32-14.3-32-32s14.3-32 32-32zm32-240c0-8.8 7.2-16 16-16H336c8.8 0 16 7.2 16 16s-7.2 16-16 16H144c-8.8 0-16-7.2-16-16zm16 48H336c8.8 0 16 7.2 16 16s-7.2 16-16 16H144c-8.8 0-16-7.2-16-16s7.2-16 16-16z\"/></svg>`{=html}\n\n\\\n\nDemonstrate your skills to others with coding know-how\n\n:::\n::::\n\n## [Git Versus GitHub]{.orange} {.smaller}\n\n![](images/logo-git.png){.absolute left=-120 top=60 width=\"9%\"}\n![](images/logo-github.png){.absolute left=1000 top=20 width=\"15%\"}\n\n::::{.columns}\n:::{.column width=\"50%\"}\n\n### Git\n\n- Actual version control software\n\n\\\n\n- Does the tracking of changes\n\n\\\n\n- Works locally on your computer\n\n\\\n\n- Not something others can interact with\n\n:::\n\n:::{.column width=\"50%\"}\n\n### GitHub\n\n- <u>G</u>raphical <u>u</u>ser <u>i</u>nterface (GUI) for Git\n\n\\\n\n- Allows _viewing_ of Git-tracked changes\n    - Not actually doing version control itself\n\n\\\n\n- Other users can see your content\n    - Depending on your settings\n\n:::\n::::\n\n## [Create a Github Profile]{.gold}\n\n- On your computer, go to [github.com](https://github.com/)\n\n\\\n\n- Create a profile\n\n\\\n\n- Let me know if you run into any issues!\n\n## [Navigating GitHub]{.orange} {.smaller}\n\n- We'll work through part of an established GitHub workshop for this section\n\n\\\n\n- [nceas.github.io/scicomp-workshop-collaborative-coding/github](https://nceas.github.io/scicomp-workshop-collaborative-coding/github.html)\n\n## [Practice: Create a Repository]{.pink} {.smaller}\n\n- To practice what we've just covered, you all will make a practice repository!\n\n\\\n\n. . .\n\n- This is a test repository so:\n    - Set it to \"Private\"\n    - Create the repo with both a README and a .gitignore\n\n\\\n\n. . .\n\n- As you go through this process, take notes for 'future you'\n    - This course will require you to make two more repositories \n    - So you'll want to have a good resource to remind yourself with down the line\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n<p align=\"center\">\n<img src=\"comics/debugging.png\" alt=\"Comic-style graph depicting someone's emotional state as they debug code (from initial struggle and defeat to eventual triumph)\">\n</p>\n\n## [Upcoming Due Dates]{.blue} {.smaller}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n\n### Due before lecture\n\n#### (By midnight)\n\n- Homework \\#2\n- Read the British Ecological Society's [Reproducible Code Guide](https://www.britishecologicalsociety.org/wp-content/uploads/2017/12/guide-to-reproducible-code.pdf) (p.20-25)\n\n\n:::\n:::{.column width=\"50%\"}\n\n### Due before lab\n\n#### (By midnight)\n\n- Muddiest Point \\#3\n\n:::\n::::\n\n",
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materials/slides_2b.qmd

@@ -28,15 +28,176 @@ format:
 
 ## [Today's Plan]{.blue}
 
-- Y
+- Core Content
+    - Muddiest Point Review
+    - Version Control Background
+    - Navigating GitHub
+
+\
+
+- Time Permitting
+    - Git / GitHub Setup
+    - RStudio + Git / GitHub
 
 ## [Today's Learning Objectives]{.purple}
 
 After today's session you will be able to:
 
 . . .
 
-- X
+- Explain the difference(s) between Git and GitHub
+- Define fundamental version control vocabulary
+
+\
+
+### Time Permitting
+
+- Integrate Git and GitHub with RStudio on your computer
+
+## [Muddiest Point Review]{.gold}
+
+- Recurring topics from most recent MPs:
+    - TBD
+
+\
+
+. . .
+
+- What other topic(s) would you like to review?
+
+## [Version Control Background]{.orange}
+
+- "Version control" is a set of tools for tracking changes to a code file
+
+\
+
+- Version control lets you work only in a single file but still preserves the history
+    - No comments you'd have to resolve (like MS Word / etc.)
+    - No need to "Save As" and retain many different files for each draft
+
+## [Version Control Rationale]{.orange} {.smaller}
+
+Why use version control?
+
+\
+
+::::{.columns}
+:::{.column width="33.33%"}
+
+##### Collaboration `r fontawesome::fa(name = "handshake", a11y = "sem")`
+
+\
+
+Easily share & work together on files
+
+:::
+
+:::{.column width="33.33%"}
+
+##### Reproducibility `r fontawesome::fa(name = "arrows-left-right", a11y = "sem")`
+
+\
+
+Fully document your progress and end results
+
+::: 
+
+
+:::{.column width="33.33%"}
+
+##### Portfolio `r fontawesome::fa(name = "book", a11y = "sem")`
+
+\
+
+Demonstrate your skills to others with coding know-how
+
+:::
+::::
+
+## [Git Versus GitHub]{.orange} {.smaller}
+
+![](images/logo-git.png){.absolute left=-120 top=60 width="9%"}
+![](images/logo-github.png){.absolute left=1000 top=20 width="15%"}
+
+::::{.columns}
+:::{.column width="50%"}
+
+### Git
+
+- Actual version control software
+
+\
+
+- Does the tracking of changes
+
+\
+
+- Works locally on your computer
+
+\
+
+- Not something others can interact with
+
+:::
+
+:::{.column width="50%"}
+
+### GitHub
+
+- <u>G</u>raphical <u>u</u>ser <u>i</u>nterface (GUI) for Git
+
+\
+
+- Allows _viewing_ of Git-tracked changes
+    - Not actually doing version control itself
+
+\
+
+- Other users can see your content
+    - Depending on your settings
+
+:::
+::::
+
+## [Create a Github Profile]{.gold}
+
+- On your computer, go to [github.com](https://github.com/)
+
+\
+
+- Create a profile
+
+\
+
+- Let me know if you run into any issues!
+
+## [Navigating GitHub]{.orange} {.smaller}
+
+- We'll work through part of an established GitHub workshop for this section
+
+\
+
+- [nceas.github.io/scicomp-workshop-collaborative-coding/github](https://nceas.github.io/scicomp-workshop-collaborative-coding/github.html)
+
+## [Practice: Create a Repository]{.pink} {.smaller}
+
+- To practice what we've just covered, you all will make a practice repository!
+
+\
+
+. . .
+
+- This is a test repository so:
+    - Set it to "Private"
+    - Create the repo with both a README and a .gitignore
+
+\
+
+. . .
+
+- As you go through this process, take notes for 'future you'
+    - This course will require you to make two more repositories 
+    - So you'll want to have a good resource to remind yourself with down the line
 
 ## [Temperature Check]{.purple}
 
@@ -46,31 +207,29 @@ After today's session you will be able to:
 <img src="comics/debugging.png" alt="Comic-style graph depicting someone's emotional state as they debug code (from initial struggle and defeat to eventual triumph)">
 </p>
 
-
-
 ## [Upcoming Due Dates]{.blue} {.smaller}
 
 ::::{.columns}
 
 :::{.column width="50%"}
 
-### Due before lab
+### Due before lecture
 
 #### (By midnight)
 
-- Muddiest Point \#x
+- Homework \#2
+- Read the British Ecological Society's [Reproducible Code Guide](https://www.britishecologicalsociety.org/wp-content/uploads/2017/12/guide-to-reproducible-code.pdf) (p.20-25)
 
-:::
 
+:::
 :::{.column width="50%"}
 
-### Due before lecture
+### Due before lab
 
 #### (By midnight)
 
-- X
+- Muddiest Point \#3
 
 :::
-
 ::::