Move vignettes to Quarto

.Rbuildignore

@@ -25,3 +25,5 @@ tests/testthat/NMF*
 ^vignettes/articles$
 ^[\.]?air\.toml$
 ^[.]?air[.]toml$
+^vignettes/\.quarto$
+^vignettes/*_files$

.gitignore

@@ -12,3 +12,4 @@ revdep/library.noindex
 revdep/data.sqlite
 .httr-oauth
 revdep/cloud.noindex/*
+**/.quarto/

DESCRIPTION

@@ -51,10 +51,10 @@ Suggests:
     ggplot2,
     igraph,
     kernlab,
-    knitr,
     methods,
     modeldata (>= 0.1.1),
     parsnip (>= 1.2.0),
+    quarto,
     RANN,
     RcppRoll,
     rmarkdown,
@@ -65,8 +65,7 @@ Suggests:
     testthat (>= 3.0.0),
     workflows,
     xml2
-VignetteBuilder: 
-    knitr
+VignetteBuilder: quarto
 RdMacros: 
     lifecycle
 Config/Needs/website: tidyverse/tidytemplate, rmarkdown

vignettes/.gitignore

@@ -0,0 +1,3 @@
+*.html
+*.R
+*_files

vignettes/Dummies.Rmd → vignettes/Dummies.qmd

@@ -5,9 +5,14 @@ description: |
   This vignette describes different methods for encoding categorical 
   predictors, with special attention to interaction terms and contrasts.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Handling categorical predictors}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 ```{r}
@@ -18,7 +23,7 @@ knitr::opts_chunk$set(
   digits = 3,
   collapse = TRUE,
   comment = "#>"
-  )
+)
 options(digits = 3)
 library(recipes)
 ```
@@ -36,7 +41,7 @@ library(recipes)
 # make a copy for use below
 iris <- iris |> mutate(original = Species)
 
-iris_rec <- recipe( ~ ., data = iris)
+iris_rec <- recipe(~., data = iris)
 summary(iris_rec)
 ```
 
@@ -46,8 +51,8 @@ The default approach is to create dummy variables using the "reference cell" par
 
 ```{r}
 #| label: iris-ref-cell
-ref_cell <- 
-  iris_rec |> 
+ref_cell <-
+  iris_rec |>
   step_dummy(Species) |>
   prep(training = iris)
 summary(ref_cell)
@@ -69,8 +74,8 @@ To get this encoding you can use the `contrasts` argument like so:, the global o
 ```{r}
 #| label: iris-helmert
 # now make dummy variables with new parameterization
-helmert <- 
-  iris_rec |> 
+helmert <-
+  iris_rec |>
   step_dummy(Species, contrasts = "contr.helmert") |>
   prep(training = iris)
 summary(helmert)
@@ -90,9 +95,9 @@ Creating interactions with recipes requires the use of a model formula, such as
 
 ```{r}
 #| label: iris-2int
-iris_int <- 
+iris_int <-
   iris_rec |>
-  step_interact( ~ Sepal.Width:Sepal.Length) |>
+  step_interact(~ Sepal.Width:Sepal.Length) |>
   prep(training = iris)
 summary(iris_int)
 ```
@@ -105,10 +110,10 @@ For example, if you were to use the standard formula interface, the creation of
 
 ```{r}
 #| label: mm-int
-model.matrix(~ Species*Sepal.Length, data = iris) |> 
-  as.data.frame() |> 
+model.matrix(~ Species * Sepal.Length, data = iris) |>
+  as.data.frame() |>
   # show a few specific rows
-  slice(c(1, 51, 101)) |> 
+  slice(c(1, 51, 101)) |>
   as.data.frame()
 ```
 
@@ -119,8 +124,10 @@ With recipes, you create them sequentially. This raises an issue: do I have to t
 #| eval: false
 # Must I do this?
 iris_rec |>
-  step_interact( ~ Species_versicolor:Sepal.Length + 
-                   Species_virginica:Sepal.Length) 
+  step_interact(
+    ~ Species_versicolor:Sepal.Length +
+      Species_virginica:Sepal.Length
+  )
 ```
 
 Not only is this a pain, but it may not be obvious what dummy variables are available (especially when [`step_other`](https://recipes.tidymodels.org/reference/step_other.html) is used). 
@@ -129,10 +136,10 @@ The solution is to use a selector:
 
 ```{r}
 #| label: iris-sel
-iris_int <- 
-  iris_rec |> 
+iris_int <-
+  iris_rec |>
   step_dummy(Species) |>
-  step_interact( ~ starts_with("Species"):Sepal.Length) |>
+  step_interact(~ starts_with("Species"):Sepal.Length) |>
   prep(training = iris)
 summary(iris_int)
 ```
@@ -168,9 +175,9 @@ Would it work if I didn't convert species to a factor and used the interactions
 
 ```{r}
 #| label: iris-dont
-iris_int <- 
-  iris_rec |> 
-  step_interact( ~ Species:Sepal.Length) |>
+iris_int <-
+  iris_rec |>
+  step_interact(~ Species:Sepal.Length) |>
   prep(training = iris)
 summary(iris_int)
 ```
@@ -188,7 +195,7 @@ There are models (e.g. `glmnet` and others) that can avoid this issue so you mig
 
 ```{r}
 #| label: one-hot
-iris_rec |> 
+iris_rec |>
   step_dummy(Species, one_hot = TRUE) |>
   prep(training = iris) |>
   bake(original, new_data = NULL, starts_with("Species")) |>
@@ -203,17 +210,17 @@ This will give you the full set of indicators and, when you use the typical cont
 
 ```{r}
 #| label: one-hot-two
-hot_reference <- 
-  iris_rec |> 
+hot_reference <-
+  iris_rec |>
   step_dummy(Species, one_hot = TRUE) |>
   prep(training = iris) |>
   bake(original, new_data = NULL, starts_with("Species")) |>
   distinct()
 
 hot_reference
 
-hot_helmert <- 
-  iris_rec |> 
+hot_helmert <-
+  iris_rec |>
   step_dummy(Species, one_hot = TRUE, contrasts = "contr.helmert") |>
   prep(training = iris) |>
   bake(original, new_data = NULL, starts_with("Species")) |>

vignettes/Ordering.Rmd → vignettes/Ordering.qmd

@@ -5,9 +5,14 @@ description: |
   The order in which recipe steps are specified matters, and this vignette gives
   some general suggestions that you should consider.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Ordering of steps}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 In the recipes package, there are no constraints on the order in which steps are added to the recipe; you as a user are free to apply steps in the order appropriate to your data preprocessing needs. However, the **order of steps matters** and there are some general suggestions that you should consider.

vignettes/Roles.Rmd → vignettes/Roles.qmd

@@ -4,9 +4,14 @@ output: rmarkdown::html_vignette
 description: |
   In recipes, roles provide a way to select variables for different steps.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Roles in recipes}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 ```{r}

vignettes/Selecting_Variables.Rmd → vignettes/Selecting_Variables.qmd

@@ -5,9 +5,14 @@ description: |
   You can select which variables or features should be used in recipes. This 
   vignette goes over the basics of using selection functions.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Selecting variables}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 ```{r}

vignettes/Skipping.Rmd → vignettes/Skipping.qmd

@@ -6,9 +6,14 @@ description: |
   However, in some situations we only want to only apply a step to the training 
   data and we want to skip that step on testing data.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{On skipping steps}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 ```{r}
@@ -19,7 +24,7 @@ knitr::opts_chunk$set(
   digits = 3,
   collapse = TRUE,
   comment = "#>"
-  )
+)
 options(digits = 3)
 library(recipes)
 ```
@@ -81,7 +86,7 @@ car_recipe <- recipe(mpg ~ ., data = mtcars) |>
   prep(training = mtcars)
 
 # These *should* produce the same results (as they do for `hp`)
-bake(car_recipe, new_data = NULL)   |> head() |> select(disp, hp)
+bake(car_recipe, new_data = NULL) |> head() |> select(disp, hp)
 bake(car_recipe, new_data = mtcars) |> head() |> select(disp, hp)
 ```
 

vignettes/recipes.Rmd → vignettes/recipes.qmd

@@ -5,9 +5,14 @@ description: |
   Start here if this is your first time using recipes! You will learn about 
   basic usage, steps, selectors, and checks.
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Introduction to recipes}
   %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
 ---
 
 ```{r}