Merge pull request #86 from rstats-wtf/callouts

rstats-wtf · Jun 11, 2023 · 50e56e5 · 50e56e5
2 parents 6eaff9b + 4fc0706
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diff --git a/_quarto.yml b/_quarto.yml
@@ -13,26 +13,26 @@ book:
     - Shannon Pileggi
     - E. David Aja
   chapters:
-    - index.Rmd
+    - index.qmd
     - part: "A holistic workflow"
       chapters:
-        - source-and-blank-slates.Rmd
-        - projects.Rmd
-        - practice-safe-paths.Rmd
-        - naming-files.Rmd
-        - api-for-an-analysis.Rmd
+        - source-and-blank-slates.qmd
+        - projects.qmd
+        - practice-safe-paths.qmd
+        - naming-files.qmd
+        - api-for-an-analysis.qmd
     - part: "Personal R Administration"
       chapters:
-        - get-to-know-your-r-installation.Rmd
+        - get-to-know-your-r-installation.qmd
         - r-startup.qmd
-        - maintaining-r.Rmd
-        - install-single-package.Rmd
+        - maintaining-r.qmd
+        - install-single-package.qmd
     - part: "All is Fail"
       chapters:
-        - debugging-r.Rmd
-        - read-source.Rmd
-        - reprexing.Rmd
-    - sessioninfo.Rmd
+        - debugging-r.qmd
+        - read-source.qmd
+        - reprexing.qmd
+    - sessioninfo.qmd
 
 bibliography: [book.bib, packages.bib]
 link-citations: true

diff --git a/api-for-an-analysis.Rmd → api-for-an-analysis.qmd b/api-for-an-analysis.Rmd → api-for-an-analysis.qmd
diff --git a/debugging-r.Rmd → debugging-r.qmd b/debugging-r.Rmd → debugging-r.qmd
@@ -149,12 +149,12 @@ When `recover()` is called it prints a list of the current calls, with a prompt
 select which you want to browse in. Then a debugging session is started at that
 location.
 
-```{block type="rmdinfo"}
+::: {.callout-note}
 [Try activity 1](https://raw.githubusercontent.com/jimhester/wtf-debugging/master/01_debugging_spartan.R) `usethis::use_course("rstd.io/wtf-debugging")`
 [Try activity 2](https://raw.githubusercontent.com/jimhester/wtf-debugging/master/02_debugging_spartan.R) `usethis::use_course("rstd.io/wtf-debugging")`
 
 to practice debugging errors using the tools described
-```
+:::
 
 ### `debug()`
 
@@ -214,11 +214,11 @@ expressions at other points in the function body. To determine the number of
 the expression to insert convert the body of the function to a list. e.g.
 `as.list(body(fun))`.
 
-```{block type="rmdinfo"}
+::: {.callout-note}
 [Try activity 3](https://raw.githubusercontent.com/jimhester/wtf-debugging/master/03_debugging_spartan.R) `usethis::use_course("rstd.io/wtf-debugging")`
 
 to explore using `trace()` with `at`.
-```
+:::
 
 ## Debugging in R Markdown documents
 
@@ -248,11 +248,11 @@ Then knit the file on the R console with `knitr::knit()` or
 `rmarkdown::render()`. The traceback will contain all of the knitr calls as
 well, so you will need to look near the end to find the calls in your code.
 
-```{block type = "rmdwarning"}
+::: {.callout-warning}
 Note you _cannot_ use the 'Knit' button in RStudio when trying to debug
 R Markdown documents in any case. The 'Knit' button opens a separate R process,
 so there is no way to use an interactive debugger in that case.
-```
+:::
 
 ### Resources
 

diff --git a/get-to-know-your-r-installation.Rmd → get-to-know-your-r-installation.qmd b/get-to-know-your-r-installation.Rmd → get-to-know-your-r-installation.qmd
diff --git a/index.Rmd → index.qmd b/index.Rmd → index.qmd
diff --git a/install-single-package.Rmd → install-single-package.qmd b/install-single-package.Rmd → install-single-package.qmd
@@ -52,8 +52,8 @@ library(beyonce, lib.loc = tmp_lib)
 unlink(tmp_lib, recursive = TRUE)
 ```
 
-```{block type="rmdinfo"}
+::: {.callout-note}
 [Try the activity](https://raw.githubusercontent.com/jimhester/wtf-source-package/master/01_source-package_spartan.R): `usethis::use_course("rstd.io/wtf-source-package")`
 
 To practice installing various types of source packages.
-```
+:::
diff --git a/maintaining-r.Rmd → maintaining-r.qmd b/maintaining-r.Rmd → maintaining-r.qmd
@@ -33,7 +33,7 @@ In addition if the given package is _not_ already installed it will install it.
 
 First if unsure what version -> [CRAN page](https://cran.r-project.org/web/packages/devtools/index.html) -> [pkgname archive](https://cran.r-project.org/src/contrib/Archive/devtools/)
 
-```r
+```{.r}
 devtools::install_version("devtools", "1.13.3")
 ```
 
@@ -47,12 +47,12 @@ packages you are currently using.
 For 'minor' version changes, the 'y' in 'x.y.z' the package interface _can_
 change, so packages need to be re-installed.
 
-```{block type="rmdwarning"}
+::: {.callout-warning}
 You may see some suggestions that you can just copy your packages even when the
 'minor' version changes. **DO NOT DO THIS**. While it may work some (even most)
 of the time, R-core does not guarantee compatibility between these versions and
 things could break (even break silently).
-```
+:::
 
 I suggest you keep the packages R comes with (base and recommended)
 packages separate from the rest of your packages. This makes it easy to
@@ -70,16 +70,16 @@ automatically expanded to the major and minor version of R, so with R 3.5.1
 this path becomes `~/R/library/3.5`. See [Renviron](#renviron) for how
 to edit your `.Renviron` file.
 
-```{block type = "rmdwarning"}
+::: {.callout-warning}
 Paths in `R_LIBS_USER` are only used if the directories they specify actually
 exist. So in addition to adding `R_LIBS_USER` to your `.Renviron` you need to
 create the directory as well.
-```
+:::
 
 Once this is setup, the process for transferring your package library becomes.
 (assumes `R_LIBS_USER` is set to `~/Library/R/3.5/library`).
 
-```r
+```{.r}
 # Install new version of R (lets say 3.5.0 in this example)
 
 # Create a new directory for the version of R

diff --git a/naming-files.Rmd → naming-files.qmd b/naming-files.Rmd → naming-files.qmd
diff --git a/packages.bib b/packages.bib
@@ -3,24 +3,23 @@ @Manual{R-base
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
-  year = {2022},
+  year = {2023},
   url = {https://www.R-project.org/},
 }
 
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
   year = {2023},
-  note = {R package version 1.42},
+  note = {R package version 1.43},
   url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-rmarkdown,
   title = {rmarkdown: Dynamic Documents for R},
   author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
   year = {2023},
-  note = {R package version 2.21},
-  url = {https://CRAN.R-project.org/package=rmarkdown},
+  note = {https://github.com/rstudio/rmarkdown},
 }
 
 @Book{knitr2015,

diff --git a/practice-safe-paths.Rmd → practice-safe-paths.qmd b/practice-safe-paths.Rmd → practice-safe-paths.qmd
diff --git a/projects.Rmd → projects.qmd b/projects.Rmd → projects.qmd
diff --git a/read-source.Rmd → read-source.qmd b/read-source.Rmd → read-source.qmd
@@ -27,11 +27,11 @@ as stats, graphics, utils and others ([`src/library/*`](https://github.com/wch/r
 the documentation included in R including Writing R extensions, R internals and
 R admin guides ([`doc/manual`](https://github.com/wch/r-source/tree/trunk/doc/manual)).
 
-```{block type="rmdinfo"}
+::: {.callout-note}
 [Try the activity](https://raw.githubusercontent.com/jimhester/wtf-read-source/master/01_read-source_spartan.R) `usethis::use_course("rstd.io/wtf-read-source")`
 
 to search the R source for code and documentation.
-```
+:::
 
 ## Where things exist in CRAN packages
 
@@ -59,8 +59,8 @@ language the compiled code is written in.
 
 Long-form documentation in the form of vignettes are stored in `vignettes/`.
 
-```{block type="rmdinfo"}
+::: {.callout-note}
 [Try the activity](https://raw.githubusercontent.com/jimhester/wtf-read-source/master/02_read-source_spartan.R) `usethis::use_course("rstd.io/wtf-read-source")`
 
 to search and find source code and documentation in CRAN packages.
-```
+:::
diff --git a/references.Rmd b/references.Rmd
diff --git a/references.qmd b/references.qmd
@@ -1,4 +1,5 @@
-# References {.unnumbered}
+# (PART) Backmatter {-} 
 
-::: {#refs}
-:::
+`r if (knitr:::is_html_output()) '
+# References {-}
+'`
diff --git a/reprexing.Rmd → reprexing.qmd b/reprexing.Rmd → reprexing.qmd
diff --git a/search.Rmd → search.qmd b/search.Rmd → search.qmd
diff --git a/sessioninfo.Rmd → sessioninfo.qmd b/sessioninfo.Rmd → sessioninfo.qmd
diff --git a/source-and-blank-slates.Rmd → source-and-blank-slates.qmd b/source-and-blank-slates.Rmd → source-and-blank-slates.qmd
diff --git a/system-prep-for-build.Rmd → system-prep-for-build.qmd b/system-prep-for-build.Rmd → system-prep-for-build.qmd