diff --git a/_freeze/materials/slides_1a/execute-results/html.json b/_freeze/materials/slides_1a/execute-results/html.json
index 2d0a5ec..b5ee572 100644
--- a/_freeze/materials/slides_1a/execute-results/html.json
+++ b/_freeze/materials/slides_1a/execute-results/html.json
@@ -1,7 +1,7 @@
{
- "hash": "1c68a0b31adaf66a0adae08a959f5b31",
+ "hash": "43f5bb0af8121eb4882c6d83dad9f5bc",
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- "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Lecture 1 -- Data Science Background\"\nengine: knitr\nformat: \n revealjs: \n slide-number: c\n scrollable: false\n theme: [night, slides.scss]\n reference-location: document\n footer: \"[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-bio/)\"\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- Introductions\n- Data Science Background\n- Why R?\n- Problem Solving Tips (for Coding)\n- Computer File Paths\n\n## [Today's Learning Objectives]{.purple}\n\nAfter today's session you will be able to:\n \n. . .\n\n- Define \"data science\"\n- Explain why the course is taught in R\n- Identify useful code problem solving techniques\n- Demonstrate comprehension of computer file paths\n\n## [Introductions]{.gold}\n\nTell me a bit about yourselves!\n\n. . .\n\n- What is your preferred name?\n\n- What year are you in school?\n\n- What's a fun fact that brings you joy?\n\n## [Introductions (Continued)]{.gold}\n\n- Why did you sign up for the course?\n\n- What skill(s) are you most excited to learn?\n\n- What previous coding / data science experience do you have?\n - Absolutely fine if this is your first foray into data science!\n\n## [My Goal for You]{.purple}\n\n
\n\n
\n\n## [Data Science Definition]{.orange} \n\n\\\n\\\n\nData science combines [_programming_]{.gold} and statistics with [_subject matter expertise_]{.purple} to identify patterns and insights hidden in data\n\n## [Why is this Course Taught in R?]{.orange}\n\nR is a programming language that is _awesome_ for environmental data scientists\n\n\\\n\n. . .\n\nBenefits of R:\n\n\\\n\n. . . \n\n| Free | Reproducible | Accessible | Popular | Versatile |\n| :---: | :---: | :---: | :---: | :---: |\n| ``{=html} | ``{=html} | ``{=html} | ``{=html} | ``{=html} |\n\n## [R's Popularity]{.orange}\n\n\n::: {.cell}\n::: {.cell-output-display}\n{width=960}\n:::\n:::\n\n\n:::{.aside}\nData from [Lai _et al._ 2019](https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.2567)\n:::\n\n## [R Data Science Value]{.orange}{.smaller}\n\n:::{.incremental}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n### ``{=html} Reproducibility \n\n- R is written in \"[scripts]{.blue}\"\n - Scripts = step-by-step instructions\n- Scripts can be run by _any_ R user\n- Allows perfect replication of process\n- Programs that require clicking buttons are not (as) reproducible\n - Would depend on accompanying written/verbal instructions\n:::\n\n:::{.column width=\"50%\"}\n### Collaboration ``{=html}\n\n- R scripts can be co-developed!\n- They can then be shared like a paper draft\n- Many tools exist to formalize sharing\n - We'll cover one in this course!\n- Unscripted programs would again require written/verbal instructions\n - Then hoping they click the right buttons in the right way \n:::\n\n::::\n\n:::\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n
\n\n
\n\n## [Problem Solving in R]{.orange}\n\n
\n\n
\n\n## [Problem Solving Methods]{.orange} {.smaller}\n\n- Problem solving is an important life skill generally\n - Also useful for data science!\n\n\\\n\n- Let's discuss some useful strategies:\n 1. 'Rubber duck' method\n 2. Google (seriously!)\n 3. Teamwork\n 4. Take a break\n 5. Whatever methods _you_ use!\n\n## [Method 1: Rubber Duck]{.orange} {.smaller}\n\n{.absolute top=50 left=800 width=\"250\" height=\"250\"}\n- Get rubber duck / small object\n\n. . . \n\n- Explain each line of your code to the duck\n - Go into as much detail as possible\n - Re-read lines _carefully_ as you explain\n\n. . .\n\n- You'll catch typos/errors that you had missed!\n\n. . .\n\n- Why \"rubber duck\" instead of \"friend\"?\n - Because it would likely be a dull experience for your friend ``{=html}\n\n## [Method 2: Google]{.orange} {.smaller}\n\n{.absolute top=50 left=750 width=\"400\" height=\"140\"}\n\n- This is a serious suggestion!\n - Google is truly an _amazing_ resource for this\n\n\\\n\n- There are forums where where people discuss code issues\n - [StackOverflow](https://stackoverflow.com/), [GitHub Discussions](https://github.com/orgs/community/discussions/categories/programming-help), etc.\n\n\\\n\n- If you get an error:\n 1. Copy the entire error message\n 2. Paste it into Google\n 3. Check the first few links to see how others solved that issue\n\n## [Google Tips]{.orange}\n\n- Use a plus sign (`+`) between search terms\n - E.g., \"R + \\\n\n\\\n\n- When specific wording matters, use quotes!\n - E.g., \"I want results with exactly this phrase\"\n\n## [Method 3: Team Up!]{.orange} {.smaller}\n\n- Group work is a classic method of problem solving\n\n\\\n\n- Email/text classmates about errors you're encountering\n - Set up a weekly time to meet and work together\n\n\\\n\n- Group work & assignments\n - I really encourage you to work together to [solve problems]{.blue}\n - _BUT_ assignments should be produced by you alone\n - There are **no group assignments** in this course!\n\n## [Method 4: Take a Break]{.orange}\n\n
\n\n
\n\n## [Method 4: Take a Break]{.orange} {.smaller}\n\n- Coding issue can be super frustrating\n - Totally **normal** to feel this way\n\n\\\n\n. . .\n\n- If you are struggling to solve a problem, take a few minutes to step re-set\n - Physically step away and do something active\n - Do one of your hobbies for a few minutes\n - Work on something else\n\n\\\n\n. . .\n\n- Return to the problem an hour or so later and try again!\n\n## [Method 5: Yours!]{.gold}\n\n- As students, you're experienced problem solvers already!\n\n\\\n\n. . . \n\n- Code problems can likely be solved by the strategies you already use!\n\n\\\n\n. . . \n\n- How do you solve problems you encounter in other courses or at work?\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n
\n\n
\n\n## [Computer File Paths]{.orange} {.smaller}\n\n- Computers store files in \"[folders]{.purple}\"\n\n\\\n\n- Folders can be _nested_ inside other folders\n\n\\\n\n- The name of all folders leading to a particular file is that file's \"[file path]{.gold}\"\n - File path starts at the biggest folder (\"top\" folder) and ends at the file\n - Each folder name is separated by slashes (`\\` or `/`)\n\n\n\\\n\n- For example: _[\\~]{.blue} [/]{.orange} Downloads [/]{.orange} BIO316 Syllabus.pdf_\n\n## [File Path Example]{.gold} {.smaller}\n\nWhat is the file path for the [notes]{.blue} document in this image?\n\n{.absolute top=175 left=250 height=\"500\" width=\"625\"}\n\n. . . \n\n_[\\~]{.blue} [/]{.orange} Documents [/]{.orange} BIO 316 [/]{.orange} BIO316-Notes-Week 1.docx_\n\n## [Practice: File Paths]{.pink} {.smaller}\n\n- Pick a file on your computer\n - _Not_ one in the \"Downloads\" folder (file paths are too short)\n\n\\\n\n. . .\n\n- What is that file's path?\n - Hint: _[\\~]{.blue} [/]{.orange} ... [/]{.orange} ... [/]{.orange} ..._\n\n\\\n\n. . .\n\n- When you have it, show me the file and tell me its path\n\n## [Upcoming Due Dates]{.blue} {.smaller}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n\n### Due before lab\n\n#### Due ASAP\n\n- Install R (see [here](https://cran.r-project.org/))\n- Install RStudio (see [here](https://posit.co/download/rstudio-desktop/))\n- Read the syllabus (esp. point values + assignment descriptions)\n\n#### Due by midnight\n\n- Muddiest Point \\#1\n\n:::\n\n:::{.column width=\"50%\"}\n\n### Due before lecture\n\n#### (By midnight)\n\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.1-12) \n\n:::\n\n::::\n",
+ "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Lecture 1 -- Data Science Background\"\nengine: knitr\nformat: \n revealjs: \n slide-number: c\n scrollable: false\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- Introductions\n- Data Science Background\n- Why R?\n- Problem Solving Tips (for Coding)\n- Computer File Paths\n\n## [Today's Learning Objectives]{.purple}\n\nAfter today's session you will be able to:\n \n. . .\n\n- Define \"data science\"\n- Explain why the course is taught in R\n- Identify useful code problem solving techniques\n- Demonstrate comprehension of computer file paths\n\n## [Introductions]{.gold}\n\nTell me a bit about yourselves!\n\n. . .\n\n- What is your preferred name?\n\n- What year are you in school?\n\n- What's a fun fact that brings you joy?\n\n## [Introductions (Continued)]{.gold}\n\n- Why did you sign up for the course?\n\n- What skill(s) are you most excited to learn?\n\n- What previous coding / data science experience do you have?\n - Absolutely fine if this is your first foray into data science!\n\n## [My Goal for You]{.purple}\n\n
\n\n
\n\n## [Data Science Definition]{.orange} \n\n\\\n\\\n\nData science combines [_programming_]{.gold} and statistics with [_subject matter expertise_]{.purple} to identify patterns and insights hidden in data\n\n## [Why is this Course Taught in R?]{.orange}\n\nR is a programming language that is _awesome_ for environmental data scientists\n\n\\\n\n. . .\n\nBenefits of R:\n\n\\\n\n. . . \n\n| Free | Reproducible | Accessible | Popular | Versatile |\n| :---: | :---: | :---: | :---: | :---: |\n| ``{=html} | ``{=html} | ``{=html} | ``{=html} | ``{=html} |\n\n## [R's Popularity]{.orange}\n\n\n::: {.cell}\n::: {.cell-output-display}\n{width=960}\n:::\n:::\n\n\n:::{.aside}\nData from [Lai _et al._ 2019](https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.2567)\n:::\n\n## [R Data Science Value]{.orange}{.smaller}\n\n:::{.incremental}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n### ``{=html} Reproducibility \n\n- R is written in \"[scripts]{.blue}\"\n - Scripts = step-by-step instructions\n- Scripts can be run by _any_ R user\n- Allows perfect replication of process\n- Programs that require clicking buttons are not (as) reproducible\n - Would depend on accompanying written/verbal instructions\n:::\n\n:::{.column width=\"50%\"}\n### Collaboration ``{=html}\n\n- R scripts can be co-developed!\n- They can then be shared like a paper draft\n- Many tools exist to formalize sharing\n - We'll cover one in this course!\n- Unscripted programs would again require written/verbal instructions\n - Then hoping they click the right buttons in the right way \n:::\n\n::::\n\n:::\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n
\n\n
\n\n## [Problem Solving in R]{.orange}\n\n
\n\n
\n\n## [Problem Solving Methods]{.orange} {.smaller}\n\n- Problem solving is an important life skill generally\n - Also useful for data science!\n\n\\\n\n- Let's discuss some useful strategies:\n 1. 'Rubber duck' method\n 2. Google (seriously!)\n 3. Teamwork\n 4. Take a break\n 5. Whatever methods _you_ use!\n\n## [Method 1: Rubber Duck]{.orange} {.smaller}\n\n{.absolute top=50 left=800 width=\"250\" height=\"250\"}\n- Get rubber duck / small object\n\n. . . \n\n- Explain each line of your code to the duck\n - Go into as much detail as possible\n - Re-read lines _carefully_ as you explain\n\n. . .\n\n- You'll catch typos/errors that you had missed!\n\n. . .\n\n- Why \"rubber duck\" instead of \"friend\"?\n - Because it would likely be a dull experience for your friend ``{=html}\n\n## [Method 2: Google]{.orange} {.smaller}\n\n{.absolute top=50 left=750 width=\"400\" height=\"140\"}\n\n- This is a serious suggestion!\n - Google is truly an _amazing_ resource for this\n\n\\\n\n- There are forums where where people discuss code issues\n - [StackOverflow](https://stackoverflow.com/), [GitHub Discussions](https://github.com/orgs/community/discussions/categories/programming-help), etc.\n\n\\\n\n- If you get an error:\n 1. Copy the entire error message\n 2. Paste it into Google\n 3. Check the first few links to see how others solved that issue\n\n## [Google Tips]{.orange}\n\n- Use a plus sign (`+`) between search terms\n - E.g., \"R + \\\n\n\\\n\n- When specific wording matters, use quotes!\n - E.g., \"I want results with exactly this phrase\"\n\n## [Method 3: Team Up!]{.orange} {.smaller}\n\n- Group work is a classic method of problem solving\n\n\\\n\n- Email/text classmates about errors you're encountering\n - Set up a weekly time to meet and work together\n\n\\\n\n- Group work & assignments\n - I really encourage you to work together to [solve problems]{.blue}\n - _BUT_ assignments should be produced by you alone\n - There are **no group assignments** in this course!\n\n## [Method 4: Take a Break]{.orange}\n\n
\n\n
\n\n## [Method 4: Take a Break]{.orange} {.smaller}\n\n- Coding issue can be super frustrating\n - Totally **normal** to feel this way\n\n\\\n\n. . .\n\n- If you are struggling to solve a problem, take a few minutes to step re-set\n - Physically step away and do something active\n - Do one of your hobbies for a few minutes\n - Work on something else\n\n\\\n\n. . .\n\n- Return to the problem an hour or so later and try again!\n\n## [Method 5: Yours!]{.gold}\n\n- As students, you're experienced problem solvers already!\n\n\\\n\n. . . \n\n- Code problems can likely be solved by the strategies you already use!\n\n\\\n\n. . . \n\n- How do you solve problems you encounter in other courses or at work?\n\n## [Temperature Check]{.purple}\n\n#### How are you Feeling?\n\n
\n\n
\n\n## [Computer File Paths]{.orange} {.smaller}\n\n- Computers store files in \"[folders]{.purple}\"\n\n\\\n\n- Folders can be _nested_ inside other folders\n\n\\\n\n- The name of all folders leading to a particular file is that file's \"[file path]{.gold}\"\n - File path starts at the biggest folder (\"top\" folder) and ends at the file\n - Each folder name is separated by slashes (`\\` or `/`)\n\n\n\\\n\n- For example: _[\\~]{.blue} [/]{.orange} Downloads [/]{.orange} BIO316 Syllabus.pdf_\n\n## [File Path Example]{.gold} {.smaller}\n\nWhat is the file path for the [notes]{.blue} document in this image?\n\n{.absolute top=175 left=250 height=\"500\" width=\"625\"}\n\n. . . \n\n_[\\~]{.blue} [/]{.orange} Documents [/]{.orange} BIO 316 [/]{.orange} BIO316-Notes-Week 1.docx_\n\n## [Practice: File Paths]{.pink} {.smaller}\n\n- Pick a file on your computer\n - _Not_ one in the \"Downloads\" folder (file paths are too short)\n\n\\\n\n. . .\n\n- What is that file's path?\n - Hint: _[\\~]{.blue} [/]{.orange} ... [/]{.orange} ... [/]{.orange} ..._\n\n\\\n\n. . .\n\n- When you have it, show me the file and tell me its path\n\n## [Upcoming Due Dates]{.blue} {.smaller}\n\n::::{.columns}\n\n:::{.column width=\"50%\"}\n\n### Due before lab\n\n#### Due ASAP\n\n- Install R (see [here](https://cran.r-project.org/))\n- Install RStudio (see [here](https://posit.co/download/rstudio-desktop/))\n- Read the syllabus (esp. point values + assignment descriptions)\n\n#### Due by midnight\n\n- Muddiest Point \\#1\n\n:::\n\n:::{.column width=\"50%\"}\n\n### Due before lecture\n\n#### (By midnight)\n\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.1-12) \n\n:::\n\n::::\n",
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diff --git a/_freeze/materials/slides_1a/figure-revealjs/popularity-ggplot-1.png b/_freeze/materials/slides_1a/figure-revealjs/popularity-ggplot-1.png
new file mode 100644
index 0000000..1b125d4
Binary files /dev/null and b/_freeze/materials/slides_1a/figure-revealjs/popularity-ggplot-1.png differ
diff --git a/_freeze/materials/slides_template/execute-results/html.json b/_freeze/materials/slides_template/execute-results/html.json
index b8fb61e..020579b 100644
--- a/_freeze/materials/slides_template/execute-results/html.json
+++ b/_freeze/materials/slides_template/execute-results/html.json
@@ -1,8 +1,10 @@
{
- "hash": "31edf729b7ef64e17262035526024ca3",
+ "hash": "3a108990dc49417ab5b5eec979797fe9",
"result": {
- "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Nick J Lyon\"\nengine: knitr\nformat: \n revealjs: \n slide-number: c\n scrollable: false\n theme: [night, slides.scss]\n reference-location: document\n footer: \"[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-bio/)\"\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
\n\n
\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",
- "supporting": [],
+ "markdown": "---\ntitle: \"Intro to Data Science\"\nauthor: \"Nick J Lyon\"\nengine: knitr\nformat: \n revealjs: \n slide-number: c\n scrollable: false\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
\n\n
\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",
+ "supporting": [
+ "slides_template_files"
+ ],
"filters": [
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diff --git a/materials/slides_1a.qmd b/materials/slides_1a.qmd
index 0a5f7dc..d28fdf9 100644
--- a/materials/slides_1a.qmd
+++ b/materials/slides_1a.qmd
@@ -8,7 +8,7 @@ format:
scrollable: false
theme: [night, slides.scss]
reference-location: document
- footer: "[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-bio/)"
+ footer: "[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-biologists/)"
---
## A Guide to Your Process
@@ -96,7 +96,7 @@ Benefits of R:
## [R's Popularity]{.orange}
-```{r}
+```{r popularity-ggplot}
#| echo: false
# Read in data
diff --git a/materials/slides_template.qmd b/materials/slides_template.qmd
index 11beb77..cfe9c8c 100644
--- a/materials/slides_template.qmd
+++ b/materials/slides_template.qmd
@@ -8,7 +8,7 @@ format:
scrollable: false
theme: [night, slides.scss]
reference-location: document
- footer: "[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-bio/)"
+ footer: "[Programming in R for Biologists](https://njlyon0.github.io/teach_r-for-biologists/)"
---
## A Guide to Your Process
diff --git a/materials/slides_template_files/figure-revealjs/unnamed-chunk-2-1.png b/materials/slides_template_files/figure-revealjs/unnamed-chunk-2-1.png
deleted file mode 100644
index 67c2dd5..0000000
Binary files a/materials/slides_template_files/figure-revealjs/unnamed-chunk-2-1.png and /dev/null differ
![\"Comic-style](\"comics/r-knowledge.png\")
\n![\"Comic-style](\"comics/debugging.png\")
\n![\"Small](\"comics/issue-source.png\")
\n![\"Creature](\"comics/need-a-min.png\")
\n