Add a bit of content... Just some friendly notes.

Author: coatless

.gitignore

@@ -37,3 +37,9 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+
+/.quarto/
+
+/.luarc.json
+
+*_book/

README.md

@@ -1,5 +1,6 @@
-# quarto-book-template
-Template repository for creating a book powered by Quarto and Rendered by GitHub Actions onto GitHub Pages
+# r-reference
+
+The repository holds a reference book of _R_ related programming topics and ideas. This primarily serves as a way for the author to quickly catalog and store code snippets in the vein of a personal knowledge management (PKM).
 
 ## Overview
 
@@ -8,27 +9,6 @@ The repository holds:
 - [`.github/workflows/quarto-render.yml`](.github/workflows/quarto-render.yml): Install, setup, and render a Quarto book using R and Python
 - [`_quarto.yml`](_quarto.yml): Setup the properties of the book in a minimal fashion (for more options see [Quarto: Book Structure](https://quarto.org/docs/books/book-structure.html))
 - [`index.qmd`](index.qmd): Welcome page
-
-Additional files:
-
-- [`requirements.txt`](requirements.txt): List of Python Packages to install
 - [`DESCRIPTION`](DESCRIPTION): List of R Packages using the standard DESCRIPTION file to install with `pak`.
 
 ## Publishing with GitHub Actions
-
-Included in the repository is a custom GitHub Action that will automatically render and deploy the book onto GitHub Pages. 
-Before the first run of the GitHub Action, please make sure to use locally in terminal the following:
-
-```sh
-quarto publish gh-pages
-```
-
-This command [initializes the `gh-pages` branch and turns on GitHub Pages for the repository](https://quarto.org/docs/publishing/github-pages.html#source-branch).
-
-If you do not run this command before the first GitHub Action is triggered, you will likely encounter the following error message in the build log:
-
-```sh
-ERROR: No _publish.yml file available (_publish.yml specifying a destination required for non-interactive publish)
-```
-
-To avoid this issue, please make sure to run the GitHub Action locally so that GitHub can render and publish your Quarto document after every push to the repository.

_quarto.yml

@@ -3,25 +3,37 @@ project:
   output-dir: _book
 
 book:
-  title: "Title of Next Bestseller"
+  title: "R Reference"
   author: "JJB"
   description: | 
     TBA
   #cover-image: images/cover.png
-  site-url: https://tutorials.thecoatlessprofessor.com/quarto-book-template
-  repo-url: https://github.com/coatless-tutorials/quarto-book-template
+  site-url: https://textbooks.thecoatlessprofessor.com/r-reference
+  repo-url: https://github.com/coatless-textbooks/r-reference
   repo-branch: main
   repo-actions: [edit]
   sharing: [twitter, facebook, linkedin]
   chapters:
     - index.qmd
-    - part: my-first-book.qmd
+    - part: "Graphics"
       chapters: 
-        - hello-world.qmd
+        - base-r-graphics.qmd
+    - part: "Configuration"
+      chapters: 
+        - r-environment-variables.qmd
+    - part: "Parallelization"
+    - part: "Compiled Code"
   appendices:
     - appendix-notes.qmd
 
 format:
   html: 
     theme: cosmo
     code-link: true
+
+# Register Adsense plugin to appear on all pages
+adsense:
+  publisher-id: ca-pub-4979996562647159
+
+filters:
+- adsense

base-r-graphics.qmd

@@ -0,0 +1,68 @@
+# Base R Graphics
+
+
+## Customizing Plot Appearance
+
+### Adjusting Axis Labels and Titles
+
+```{r}
+# Example 1
+x <- 1:10
+y <- x^2
+plot(x, y, main = "Quadratic Function", xlab = "X", ylab = "Y")
+
+# Example 2
+df <- data.frame(Time = 1:10, Value = cumsum(rnorm(10)))
+plot(df$Time, df$Value, main = "Cumulative Sum", xlab = "Time", ylab = "Cumulative Value")
+```
+
+### Changing Line Types, Colors, and Symbols
+
+```{r}
+# Example 1
+x <- 1:5
+y1 <- x
+y2 <- 2 * x
+y3 <- 3 * x
+
+plot(x, y1, type="b", col="red", pch=16, lty=1, ylim=c(0, 15), main="Multiple Lines Example")
+points(x, y2, col="blue", pch=17, lty=2)
+lines(x, y3, col="green", lty=3)
+
+# Example 2
+set.seed(123)
+x <- rnorm(50)
+y <- x + rnorm(50, mean=2)
+plot(x, y, col="purple", pch=19, main="Scatter Plot with Customized Symbols", xlab="X", ylab="Y")
+```
+
+```{r}
+# Create data
+x <- 1:10
+y <- 1:10
+
+# Line Types
+par(mar=c(4, 4, 2, 2))
+plot(x, y, type="n", main="All Line Types", xlab="X", ylab="Y", ylim=c(0, 6))
+for (i in 0:5) {
+  lines(x, rep(i*.5, length(x)), lty=i, col="black", lwd=2)
+}
+
+legend("topright", legend=0:5, title="Line Types", lty=0:5, col="black", lwd=2, ncol=3)
+```
+
+```{r}
+# Colors
+par(mar=c(4, 4, 2, 2))
+plot(x, y, type="n", main="All Colors", xlab="X", ylab="Y", ylim=c(0, 9))
+for (i in 1:8) {
+  lines(x, rep(i*.5, length(x)), col=i, lwd=2)
+}
+
+legend("topright", legend=1:8, title="Colors", col=1:8, lwd=2, ncol=2)
+```
+
+```{r}
+# symbols
+# todo
+```

hello-world.qmd

@@ -1,23 +1,4 @@
 
-
 ## Welcome {.unnumbered}
 
-Welcome splash page! Provide an overview of the book.
-
-Sample evaluation of R and Python in a side-by-side manner:
-
-::: {layout-ncol=2}
-#### R
-
-```{r}
-my_list = list(1, 2, 3)
-typeof(my_list)
-```
-
-#### Python
-
-```{python}
-my_list = [1, 2, 3]
-type(my_list)
-```
-:::
+Hello there! You've stumbled across a reference guide that contains different useful R code and/or links. There isn't a lot of depth associated with each page if you are expecting a through walkthrough of the material.

index.qmd

@@ -0,0 +1,66 @@
+# R Environment Variables
+
+Setting up and using environment variables in R is useful for handling configuration
+details and/or suppressing private information. 
+
+## Retrieve/access environment variables:
+
+Values stored in the system environment can be retrieved using `Sys.getenv("VAR_NAME")`.
+
+```{r}
+# Example: Accessing environment variable named API_KEY
+api_key <- Sys.getenv("API_KEY")
+api_key
+```
+
+In the case where the value might not be found, make sure to specify an **unset** value that acts as a default.
+
+```{r}
+# Example: Accessing environment variable named API_KEY
+api_key <- Sys.getenv("API_KEY", unset = NA)
+api_key
+```
+
+Note, the `Sys.getenv()` function only returns a `character` value.
+
+## Set environment variables in your R environment
+
+Environment variables can be set in R by using `Sys.setenv()`.
+
+```{r}
+Sys.setenv(API_KEY = "your_api_key")
+```
+
+## Use an `.Renviron` file for configuration:
+
+Frequently using environment variables? Instead of defining them for each script, aim to store
+environment variables in a `.Renviron` file in the project directory.
+
+Variables are specified in the `.Renviron` file with the format `VAR_NAME=value`.
+
+:::callout-note
+Avoid using spaces around the `=` sign.
+:::
+
+```ini
+# Example .Renviron file
+API_KEY=your_api_key
+```
+
+## Access `.Renviron` from R using `browseURL()` or `usethis` package
+
+The `.Renviron` file may be accessed using either `browseURL("~/.Renviron")` or with `usethis::edit_r_environ()` for editing.
+
+```{r}
+#| eval: false
+# Example: Load .Renviron file with browseURL()
+utils::browseURL("~/.Renviron")
+```
+
+```{r}
+#| eval: false
+# Example: Load .Renviron file with the usethis package
+usethis::edit_r_environ()
+```
+
+### TODO: mention `dotenv` for managing environment variables?

r-environment-variables.qmd

@@ -0,0 +1,8 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}