Added basic schedule and website structure

_quarto.yml

@@ -3,7 +3,6 @@ project:
   render:
   - "*.qmd"
   - "*.md"
-  - "!/slides/"
 
 website:
   title: "ETC4500/ETC5450 Advanced R Programming"
@@ -14,6 +13,21 @@ website:
       - href: index.qmd
         text: Home
         icon: house-fill
+      - text: Schedule
+        icon: calendar2-fill
+        menu:
+          - week1/index.qmd
+          - week2/index.qmd
+          - week3/index.qmd
+          - week4/index.qmd
+          - week5/index.qmd
+          - week6/index.qmd
+          - week7/index.qmd
+          - week8/index.qmd
+          - week9/index.qmd
+          - week10/index.qmd
+          - week11/index.qmd
+          - week12/index.qmd
       - text: Discussion
         icon: chat-fill
         href: "https://learning.monash.edu/mod/forum/view.php?id=2034181"
@@ -30,7 +44,6 @@ format:
   html:
     theme: [cosmo, numbat.scss]
     highlight: textmate
-    css: styles.css
     toc: true
     mainfont: "Fira Sans"
     html-math-method: katex

assignments.csv

@@ -0,0 +1,5 @@
+Assignment, Due, Moodle, File, Marks
+Assignment 1, 2024-03-22, ????, "A1.qmd", 25
+Assignment 2, 2024-04-05, ????, "A2.qmd", 25
+Assignment 3, 2024-05-03, ????, "A3.qmd", 20
+Assignment 4, 2024-06-01, ????, "A4.qmd", 30

assignments/A1.qmd

@@ -0,0 +1,11 @@
+---
+title: Assignment 1 (25%)
+---
+
+> Create package skeleton. Include a basic function from set of options
+
+```{r}
+#| output: asis
+source(here::here("course_info.R"))
+submit(schedule, "Assignment 1")
+```

assignments/A2.qmd

@@ -0,0 +1,11 @@
+---
+title: Assignment 2 (25%)
+---
+
+> Give bad broken complicated function for their package, fix it thanks Write tests and docs Explain why it doesn’t work and is now better
+
+```{r}
+#| output: asis
+source(here::here("course_info.R"))
+submit(schedule, "Assignment 2")
+```

assignments/A3.qmd

@@ -0,0 +1,11 @@
+---
+title: Assignment 3 (20%)
+---
+
+> Use package within larger quarto targets workflow Uses broken function from A2
+
+```{r}
+#| output: asis
+source(here::here("course_info.R"))
+submit(schedule, "Assignment 3")
+```

assignments/A4.qmd

@@ -0,0 +1,11 @@
+---
+title: Assignment 4 (30%)
+---
+
+> Extend A1 package with object-oriented Extend tidyverse with some tidy interfacesInstructions
+
+```{r}
+#| output: asis
+source(here::here("course_info.R"))
+submit(schedule, "Assignment 4")
+```

course_info.R

@@ -0,0 +1,120 @@
+######## Course info ########
+library(tidyverse)
+
+# Start of semester
+start_semester <- "2024-02-26"
+
+# Week of mid-semester break
+mid_semester_break <- "2024-04-01"
+
+# Schedule
+schedule <- tibble(
+  Week = seq(12),
+  Topic = c(
+    "Foundations of R programming",
+    "R package development",
+    "R package development",
+    "Debugging and profiling",
+    "Functional programming",
+    "Object-oriented programming",
+    "Reactive programming: shiny",
+    "Reactive programming: targets",
+    "Metaprogramming",
+    "Metaprogramming",
+    "Rewriting R code in C++",
+    "Interfacing with other languages"
+  ),
+  Reference = c(
+    "1-8. *Advanced R*",
+    "*R Packages*",
+    "*R Packages*",
+    "22-24. *Advanced R*",
+    "9-11. *Advanced R*",
+    "12-13. *Advanced R*",
+    "*Mastering Shiny*",
+    "*The {targets} R package user manual*",
+    "17-20. *Advanced R*",
+    "17-20. *Advanced R*",
+    "25. *Advanced R*",
+    "21. *Advanced R*"
+  ),
+  Reference_URL = c(
+    "https://adv-r.hadley.nz/foundations-intro.html",
+    "https://r-pkgs.org",
+    "https://r-pkgs.org",
+    "https://adv-r.hadley.nz/debugging.html",
+    "https://adv-r.hadley.nz/fp.html",
+    "https://adv-r.hadley.nz/oo.html",
+    "https://mastering-shiny.org",
+    "https://books.ropensci.org/targets/",
+    "https://adv-r.hadley.nz/metaprogramming.html",
+    "https://adv-r.hadley.nz/metaprogramming.html",
+    "https://adv-r.hadley.nz/rcpp.html",
+    "https://adv-r.hadley.nz/translation.html"
+  )
+)
+
+# Add mid-semester break
+calendar <- tibble(
+    Date = seq(as.Date(start_semester), by = "1 week", length.out = 13)
+  ) |>
+  mutate(
+    Week = row_number(),
+    Week = if_else(Date < mid_semester_break, Week, Week - 1),
+    #Week =
+  )
+
+# Add calendar to schedule
+schedule <- schedule |>
+  left_join(calendar, by = "Week") |>
+  mutate(
+    Week = if_else(Date == mid_semester_break, NA, Week),
+    Topic = if_else(Date == mid_semester_break, "Mid-semester break", Topic),
+    Reference = if_else(Date == mid_semester_break, NA, Reference),
+    Reference_URL = if_else(Date == mid_semester_break, NA, Reference_URL)
+  ) |>
+  select(Week, Date, everything())
+
+# Add assignment details
+lastmon <- function(x) {
+  7 * floor(as.numeric(x-1+4)/7) + as.Date(1-4, origin="1970-01-01")
+}
+
+assignments <- read_csv(here::here("assignments.csv")) |>
+  mutate(
+    Date = lastmon(Due),
+    Moodle = paste0("https://learning.monash.edu/mod/assign/view.php?id=", Moodle),
+    File = paste0("assignments/", File)
+  )
+
+schedule <- schedule |>
+  full_join(assignments, by = "Date") |>
+  mutate(Week = if_else(is.na(Week) & Date > "2024-05-20", 13, Week))
+
+show_assignments <- function(week) {
+  ass <- schedule |>
+    filter(
+      Week >= week & (week > Week - 3 | week > 8),
+      !is.na(Assignment),
+    ) |>
+    select(Assignment:File)
+  if(NROW(ass) > 0) {
+    cat("\n\n## Assignments\n\n")
+    for(i in seq(NROW(ass))) {
+      cat("* [", ass$Assignment[i], "](../", ass$File[i], ") is due on ",
+          format(ass$Due[i], "%A %d %B.\n"), sep="")
+    }
+  }
+}
+
+
+submit <- function(schedule, assignment) {
+  ass <- schedule  |>
+    filter(Assignment == assignment)
+  due <- format(ass$Due, "%e %B %Y") |> stringr::str_trim()
+  url <- ass$Moodle
+  button <- paste0("<br><br><hr><b>Due: ", due, "</b><br>",
+                   "<a href=",url," class = 'badge badge-large badge-blue'>",
+                   "<font size='+2'>&nbsp;&nbsp;<b>Submit</b>&nbsp;&nbsp;</font><br></a>")
+  cat(button)
+}

index.qmd

@@ -2,13 +2,67 @@
 title: "ETC4500/5450 Advanced R Programming"
 ---
 
+R is widely used as a tool for data analysis and one of the most popular programming languages. This unit delves into R from the programming aspect instead of using it as a data analysis tool. You will learn a variety of programming paradigms and delve into the foundations of R as a programming language.
+
+## Learning outcomes
+
+1. be familiar with the foundations of R programming
+2. understand a variety of programming paradigms, including functional programming and object-oriented programming
+3. utilise R’s functional and object-oriented programming systems
+4. integrate the concept of metaprogramming to evaluate and construct new functions
+
 ## Teachers
 
-* [**Rob J Hyndman**](https://robjhyndman.com). Email: [[email protected]](mailto:[email protected])
+* [**Rob J Hyndman**](https://robjhyndman.com). Chief Examiner. Email: [[email protected]](mailto:[email protected])
 * [**Mitchell O'Hara-Wild**](https://mitchelloharawild.com). Email: [[email protected]](mailto:[email protected])
+* [**Thomas Lumley**](https://profiles.auckland.ac.nz/t-lumley). (Week 6?)
+* [**Tomasz Wozniak**](https://github.com/donotdespair). (Week 11)
 
 ## References
 
-* [Advanced R, 2e](https://adv-r.hadley.nz/) by Hadley Wickham.
-* [R packages, 2e](http://r-pkgs.org/) by Hadley Wickham & Jenny Bryan.
-* [Targets user manual](https://books.ropensci.org/targets/) by Will Landau.
+* [*Advanced R*, 2e](https://adv-r.hadley.nz/) by Hadley Wickham.
+* [*R packages*, 2e](http://r-pkgs.org/) by Hadley Wickham & Jenny Bryan.
+* [*Mastering Shiny*](https://mastering-shiny.org/) by Hadley Wickham.
+* [*The {targets} R package user manual*](https://books.ropensci.org/targets/) by Will Landau.
+
+```{r}
+#| label: load_packages
+#| include: false
+#| message: false
+#| warning: false
+#| echo: false
+#| cache: false
+library(tidyverse)
+options(knitr.kable.NA = '')
+source(here::here("course_info.R"))
+week <- as.integer(1 + ((Sys.Date() - as_date(start_semester))/7))
+```
+
+## Weekly schedule
+
+* Workshop: 2 hours in class per week
+
+```{r}
+#| label: schedule2
+#| message: false
+#| warning: false
+#| echo: false
+#| output: asis
+schedule |>
+  transmute(
+    Date = format(Date+1, "%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})")),
+    Assessments = if_else(is.na(Assignment), Assignment, glue::glue("[{Assignment}]({File})"))
+  ) |>
+  select(-Show) |>
+  knitr::kable(format = "markdown")
+```
+
+## Assessments
+
+* Make an R package (25%)
+* Fix a broken function (25%)
+* Use your package within a quarto targets workflow (20%)
+* Advanced package and metaprogramming methods (30%)

numbat.scss

@@ -67,3 +67,74 @@ a {
       display: block!important;
     }
 }
+
+
+/* Badges */
+
+.badge {
+  font-family: $font-family-sans-serif;
+  font-size: 12.75px;
+  display: inline-block;
+  line-height: 1;
+  padding: 4px 7px 3px 7px;
+  text-align: center;
+  font-weight: normal;
+  text-transform: uppercase;
+  border-radius: 15px;
+  opacity: .75;
+}
+
+a.badge.badge-red {
+  color: #fff;
+}
+a.badge.badge-blue {
+  color: #fff;
+}
+a.badge.badge-green {
+  color: #fff;
+}
+
+.badge-large {
+  font-size: 18px !important;
+  text-transform: none !important;
+  padding: 5px 5px 3px 5px;
+  text-transform: none;
+  font-family: $font-family-sans-serif;
+}
+
+.badge-small {
+  font-size: 11.25px;
+  padding: 5px 5px 3px 5px;
+}
+
+.badge:hover {
+  opacity: 1;
+}
+
+.badge-black,
+.badge-blue,
+.badge-red,
+.badge-green {
+  color: #ffffff !important;
+}
+.badge-black {
+  background: #0f0f0f;
+}
+.badge-blue {
+  background: #006DAE;
+}
+.badge-red {
+  background: #BD666D;
+}
+.badge-green {
+  background: #2c9f42;
+}
+.badge-yellow {
+  background: #ffc800;
+}
+.badge-white {
+  background: #ffffff;
+}
+.badge-grey {
+  background: #cccccc;
+}