Added some material for week 7

course_info.R

@@ -17,8 +17,8 @@ schedule <- tibble(
     "Debugging and profiling",
     "Functional programming",
     "Object-oriented programming",
-    "Reactive programming: shiny",
-    "Reactive programming: targets",
+    "Object-oriented programming and literate programming",
+    "Reactive programming: Shiny and targets",
     "Metaprogramming",
     "Metaprogramming",
     "Rewriting R code in C++",

index.qmd

@@ -54,7 +54,7 @@ schedule |>
     Date = format(Date + 2, "%d %b"),
     Show = !is.na(Week) & Week <= 12,
     Topic = if_else(!Show, Topic, glue::glue("[{Topic}](./week{Week}/index.html)")),
-    Reference = if_else(!Show, Reference, glue::glue("[{Reference}]({Reference_URL})")),
+    #Reference = if_else(!Show, Reference, glue::glue("[{Reference}]({Reference_URL})")),
     Assessments = if_else(is.na(Assignment), Assignment, glue::glue("[{Assignment}]({File})"))
   ) |>
   select(-Show) |>

week7/Qmd_example.qmd

@@ -0,0 +1,36 @@
+---
+title: "Qmd_example"
+format:
+  html
+  memo-pdf
+date: "2024-04-15"
+---
+
+```{r}
+#| label: setup
+#| include: false
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r}
+#| label: cars
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r}
+#| label: pressure
+#| echo: false
+plot(pressure)
+```
+
+Note that the `echo: false` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

week7/Rmd_example.Rmd

@@ -0,0 +1,29 @@
+---
+title: "Rmd_example"
+output: html_document
+date: "2024-04-15"
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

week7/index.qmd

@@ -1,28 +1,36 @@
 ---
-title: "Week 7: Reactive programming - Shiny"
+title: "Week 7: Object-oriented programming and literate programming"
 ---
 
 ```{r}
 week <- 7
 source(here::here("course_info.R"))
 ```
 
-## Main reference
+## Main references
+
+* [S3](https://adv-r.hadley.nz/s3.html)
+* [vctrs](https://vctrs.r-lib.org)
+* [roxygen2](https://r-pkgs.org/man.html)
+* [Rmarkdown](https://bookdown.org/yihui/rmarkdown/)
+* [Quarto](https://quarto.org)
+
+## What you will learn this week
+
+* A Q&A on any problems with [Assignment 2](/assignments/A2.qmd)
+* More on S3 and vctrs in preparation for [Assignment 4](/assignments/A4.qmd)
+* Brief overview of literate programming
 
 ```{r}
 #| output: asis
-schedule |>
-  filter(Week == week) |>
-  mutate(ref = glue::glue("[{Reference}]({Reference_URL})")) |>
-  pull(ref)
+show_slides(week)
 ```
 
-## What you will learn this week
+## Other resources
 
-Shiny
+* [Rob's 2020 rstudio::conf talk on Rmarkdown](https://youtu.be/_D-ux3MqGug?si=LeXPIa9K3V9N1rO_)
 
 ```{r}
 #| output: asis
-show_slides(week)
 show_assignments(week)
 ```

week7/slides_literate.qmd

@@ -0,0 +1,163 @@
+---
+title: ETC4500/ETC5450 Advanced R programming
+author: "Week 7: Literate Programming"
+format:
+  beamer:
+    pdf-engine: pdflatex
+    aspectratio: 169
+    fontsize: "14pt,t"
+    section-titles: false
+    knitr:
+      opts_chunk:
+        dev: "cairo_pdf"
+    fig-width: 7.5
+    fig-height: 3.5
+    include-in-header: ../header.tex
+    keep-tex: false
+---
+
+```{r}
+#| label: setup
+#| include: false
+#| cache: false
+source(here::here("setup.R"))
+source(here::here("course_info.R"))
+```
+
+## Outline
+
+\vspace*{0.4cm}
+\tableofcontents
+
+# Literate programming
+
+## Literate programming
+
+ * Due to Donald Knuth (Stanford), 1984
+ * A script or document that contains an explanation of the program logic in a natural language (e.g. English), interspersed with snippets of source code, which can be compiled and rerun.
+ * Generates two representations\newline from a source file: formatted\newline documentation and "tangled" code.
+
+\placefig{10.5}{4.6}{width = 6cm}{WEB.png}
+
+## Literate programming
+
+* As a programming approach, it never quite caught on.
+* But it has become the standard approach for reproducible documents.
+
+## Literate programming examples
+
+* WEB (combining Pascal and TeX)
+* roxygen2 comments
+  * technically documentation generation rather than literate programming
+  * documentation embedded in code, rather than code embedded in documentation
+* Sweave documents
+* Jupyter notebooks
+* Rmarkdown documents
+* Quarto documents
+
+## roxygen2
+
+* roxygen2 documentation are just comments to R.
+* roxygen2::roxygenize():
+  * generates documentation from these comments in the form of Rd files
+  * adds relevant lines to the NAMESPACE file.
+* roxygen2::roxygenize() is called by devtools::document().
+* Advantage: keeps documentation with the code. More readable, less chance for errors.
+
+## Markdown syntax
+\fontsize{14}{16}\sf
+Markdown: a "markup" language for formatting text.
+
+* Headings:
+
+    `# Heading 1`\newline
+    `## Heading 2`
+
+* **Bold**: `**bold**`.
+* *Italic*: `*italic*`.
+* Blockquotes:
+
+    `> blockquote`.
+
+## Markdown and Rmarkdown
+
+* Markdown (markup language):
+  * Extension either `.md` or `.markdown`.
+  * Used in many places on the web, in note-taking apps, etc.
+
+* Rmarkdown (markup language):
+  * an extension of markdown that allows for embedded R code chunks.
+  * Extension `.Rmd`.
+
+* Rmarkdown (package):
+  * an R package that allows for the conversion of `.Rmd` files to other formats.
+
+## Rmarkdown files
+
+* Structure:
+  1. YAML header
+  2. Markdown content
+  3. R code chunks surrounded by `` ```{r} `` and `` ``` ``
+
+* Rmarkdown documents can be compiled to HTML, PDF, Word, and other formats
+* Compile with `rmarkdown::render("file.Rmd")`
+
+## Rmarkdown, knitr and pandoc
+
+* `rmarkdown::render()`
+  * Uses `knitr` to run all code chunks, and "knit" the results into a markdown file (replacing R chunks with output).
+  * Uses `pandoc` to convert the markdown file to the desired output format.
+  * If PDF output is desired, LaTeX then converts the tex file (from pandoc output) to pdf.
+
+\centerline{\includegraphics[width = 10cm]{rmd.png}}
+
+## Some chunk options
+\fontsize{14}{16}\sf
+
+* `eval`: whether to evaluate the code chunk
+* `echo`: whether to display the code chunk
+* `include`: whether to include the code chunk in the output
+* `results = 'hide'` hides printed output.
+* `fig.show = 'hide'` hides figures.
+* `message`: whether to display messages
+* `warning`: whether to display warnings
+* `error = TRUE`: continue even if code returns an error.
+* `fig.cap`: caption for the figure
+* `fig.width`, `fig.height`: width and height of the figure
+* `cache`: whether to cache the code chunk
+
+## Global chunk options
+
+````{verbatim}
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(
+  comment = "#>",
+  collapse = TRUE,
+  echo = FALSE,
+  message = FALSE,
+  warning = FALSE
+)
+```
+````
+
+* The chunk named `setup` will be run before any other chunks.
+
+## Debugging
+
+* The Rmarkdown document is compiled in a different environment from your R console.
+* If you get an error, try running all chunks (Ctrl+Alt+R).
+* If you can't reproduce the error, check the working directory (add `getwd()` in a chunk).
+* Try setting `error = TRUE` on problem chunk to help you diagnose what happens. (But change it back!)
+* Look at the intermediate files (`.md` or `.tex`) to see what is happening.
+
+## Quarto
+\fontsize{14}{16}\sf
+
+* Generalization of Rmarkdown (not dependent on R)
+* Supports R, Python, Javascript and Julia chunks by using either `knitr`, `jupyter` or `ObservableJS` engines.
+* More consistent yaml header and chunk options.
+* Many more output formats, and many more options for customizing format.
+* Relies on pandoc for converting `md` to other formats.
+* Uses pandoc templates (with Lua) for extensions
+
+\centerline{\includegraphics[width = 10cm]{qmd.png}}