Moved quarto to week 9

course_info.R

@@ -18,8 +18,8 @@ schedule <- tibble(
     "Functional programming",
     "Object-oriented programming",
     "Object-oriented S3 and vctrs",
-    "Literate and reactive programming",
-    "Targets: reproducible workflows",
+    "Reactive and literate programming",
+    "Quarto and targets: efficient reproducible workflows",
     "Metaprogramming",
     "Interfacing with other languages",
     "Rewriting R code in C++"

week8/index.qmd

@@ -10,10 +10,9 @@ source(here::here("course_info.R"))
 
 ## What you will learn this week
 
+* [Shiny](https://shiny.rstudio.com)
 * [roxygen2](https://r-pkgs.org/man.html)
 * [Rmarkdown](https://bookdown.org/yihui/rmarkdown/)
-* [Quarto](https://quarto.org)
-* [Shiny](https://shiny.rstudio.com)
 
 ```{r}
 #| output: asis
@@ -24,7 +23,6 @@ show_slides(week)
 
 * [Rob's 2020 rstudio::conf talk on Rmarkdown](https://youtu.be/_D-ux3MqGug?si=LeXPIa9K3V9N1rO_)
 
-
 ```{r}
 #| output: asis
 show_assignments(week)

week8/slides.qmd

@@ -1,6 +1,6 @@
 ---
 title: ETC4500/ETC5450 Advanced R programming
-author: "Week 8: Literate and reactive programming"
+author: "Week 8: Reactive and literate programming"
 format:
   beamer:
     pdf-engine: pdflatex
@@ -217,7 +217,7 @@ With declarative code you say “Ensure there is a sandwich in the refrigerator
 
 \fontsize{13}{13}\sf
 ::: {.callout-important title="Use-less cases"}
-This paradigm is rarely needed or used in R for data analysis. 
+This paradigm is rarely needed or used in R for data analysis.
 :::
 
 ::: {.callout-tip title="Useful cases"}
@@ -290,11 +290,11 @@ Reactivity in shiny comprises of:
 
   UI inputs `input*()` and values `reactiveValues()`
 
-* Reactive **conductors** (intermediates): 
+* Reactive **conductors** (intermediates):
 
   Expressions `reactive()` and events `eventReactive()`
 
-* Reactive **endpoints** (results): 
+* Reactive **endpoints** (results):
 
   UI outputs `render*()` and side-effects `observe()`
 
@@ -408,7 +408,7 @@ Other ways reactivity might be prevented include:
 
   * `eventReactive(rnorm(input$n_samples), input$go)`
   * `observeEvent(input$go, message("Go!"))`
-  
+
 * Rate limiting
 
   * `throttle(reactive())`: limits update frequency
@@ -710,97 +710,3 @@ summarize
 #| echo: true
 names(knitr::knit_engines$get())
 ```
-
-# Quarto
-
-## 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.
-* Heavier reliance on pandoc Lua filters
-* Uses pandoc templates for extensions
-
-\centerline{\includegraphics[width = 10cm]{qmd.png}}
-
-## Choose your engine
-
-Specify the engine in the yaml header:
-
-````{verbatim}
----
-engine: knitr
----
-````
-
-````{verbatim}
----
-engine: jupyter
-jupyter: python3
----
-````
-
-
-**Default:** If any `{r}` blocks found, use `knitr` engine; otherwise use `jupyter` (with kernel determined by first block).
-
-
-## Execute options
-
-*   `execute` option in yaml header can be used instead of a `setup` chunk:
-
-    ````{verbatim}
-    execute:
-      cache: true
-      echo: false
-      warning: false
-    ````
-
-* `setup` chunk still allowed.
-
-## Chunk options
-
-Rmarkdown syntax recognized for R chunks.
-
-More consistent chunk options use the hash-pipe `#|`
-
-````{verbatim}
-```{r}
-#| label: fig-chunklabel
-#| fig-caption: My figure
-#| fig-width: 6
-#| fig-height: 4
-mtcars |>
-  ggplot(aes(x = mpg, y = wt)) +
-  geom_point()
-```
-````
-
-## Chunk options
-
-* Quarto consistently uses hyphenated options (`fig-width` rather than `fig.width`)
-* The Rmarkdown `knitr` options are recognized for backwards compatibility.
-* Options that are R expressions need to be prefaced by `!expr`
-
-  ````{verbatim}
-  ```{r}
-  #| fig-cap: !expr paste("My figure", 1+1)
-  ```
-  ````
-
-## Extensions and templates
-\fontsize{13}{17}\sf
-
-* Quarto extensions modify and extend functionality.
-* See <https://quarto.org/docs/extensions/> for a list.
-* Templates are extensions used to define new output formats.
-* Journal templates at\newline <https://quarto.org/docs/extensions/listing-journals.html>
-* Monash templates at\newline <https://robjhyndman.com/hyndsight/quarto_templates.html>
-
-## Exercise
-
-* Create a quarto document using an html format
-* Add a code chunk to generate a figure with a figure caption.
-* Reference the figure in the text using `@fig-chunklabel`.
-* Add the monash memo extension and generate a pdf output.

week9/index.qmd

@@ -1,22 +1,31 @@
 ---
-title: "Week 9: targets"
+title: "Week 9: Quarto and targets -- efficient reproducible workflows"
 ---
 
 ```{r}
 week <- 9
 source(here::here("course_info.R"))
 ```
 
-## Main reference
-
-[The {targets} R package user manual](https://books.ropensci.org/targets/)
-
 ## What you will learn this week
 
-* Using the [targets package](https://docs.ropensci.org/targets/) for efficient and reproducible data analysis
+* [Quarto](https://quarto.org)
+* [The {targets} R package user manual](https://books.ropensci.org/targets/)
+
 
 ```{r}
 #| output: asis
 show_slides(week)
+```
+
+## Other resources
+
+* [Quarto extensions](https://quarto.org/docs/extensions/)
+* [Monash quarto templates](https://robjhyndman.com/hyndsight/quarto_templates.html)
+* [targets package](https://docs.ropensci.org/targets/)
+
+
+```{r}
+#| output: asis
 show_assignments(week)
 ```

week9/slides.qmd

@@ -0,0 +1,136 @@
+---
+title: ETC4500/ETC5450 Advanced R programming
+author: "Week 8: Quarto and targets -- efficient reproducible workflows"
+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
+    colorlinks: true
+    urlcolor: MonashBlue
+    linkcolor: burntorange
+---
+
+```{r}
+#| label: setup
+#| include: false
+#| cache: false
+source(here::here("setup.R"))
+source(here::here("course_info.R"))
+```
+
+## Outline
+
+\vspace*{0.4cm}
+\tableofcontents
+
+# Assignments
+
+## Assignments 3 and 4
+
+* Assignment 3 due 10 May
+* Assignment 4 due 24 May
+
+
+# Quarto
+
+## 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.
+* Heavier reliance on pandoc Lua filters
+* Uses pandoc templates for extensions
+
+\centerline{\includegraphics[width = 10cm]{qmd.png}}
+
+## Choose your engine
+
+Specify the engine in the yaml header:
+
+````{verbatim}
+---
+engine: knitr
+---
+````
+
+````{verbatim}
+---
+engine: jupyter
+jupyter: python3
+---
+````
+
+
+**Default:** If any `{r}` blocks found, use `knitr` engine; otherwise use `jupyter` (with kernel determined by first block).
+
+
+## Execute options
+
+*   `execute` option in yaml header can be used instead of a `setup` chunk:
+
+    ````{verbatim}
+    execute:
+      cache: true
+      echo: false
+      warning: false
+    ````
+
+* `setup` chunk still allowed.
+
+## Chunk options
+
+Rmarkdown syntax recognized for R chunks.
+
+More consistent chunk options use the hash-pipe `#|`
+
+````{verbatim}
+```{r}
+#| label: fig-chunklabel
+#| fig-caption: My figure
+#| fig-width: 6
+#| fig-height: 4
+mtcars |>
+  ggplot(aes(x = mpg, y = wt)) +
+  geom_point()
+```
+````
+
+## Chunk options
+
+* Quarto consistently uses hyphenated options (`fig-width` rather than `fig.width`)
+* The Rmarkdown `knitr` options are recognized for backwards compatibility.
+* Options that are R expressions need to be prefaced by `!expr`
+
+  ````{verbatim}
+  ```{r}
+  #| fig-cap: !expr paste("My figure", 1+1)
+  ```
+  ````
+
+## Extensions and templates
+\fontsize{13}{17}\sf
+
+* Quarto extensions modify and extend functionality.
+* See <https://quarto.org/docs/extensions/> for a list.
+* Templates are extensions used to define new output formats.
+* Journal templates at\newline <https://quarto.org/docs/extensions/listing-journals.html>
+* Monash templates at\newline <https://robjhyndman.com/hyndsight/quarto_templates.html>
+
+## Exercise
+
+* Create a quarto document using an html format
+* Add a code chunk to generate a figure with a figure caption.
+* Reference the figure in the text using `@fig-chunklabel`.
+* Add the monash memo extension and generate a pdf output.
+
+# targets