Merge branch 'main' of https://github.com/rostools/r-cubed-intermediate

.github/workflows/build-website.yml

@@ -1,16 +1,16 @@
+name: Build Website
+
 on:
   push:
     branches:
       - main
 
-name: build-deploy
-
 jobs:
   build-deploy:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2

DESCRIPTION

@@ -36,11 +36,13 @@ Imports:
     stringr,
     usethis,
     vroom,
-    withr
+    withr,
+    r3admin (>= 0.0.1)
 Suggests: 
     prodigenr,
     tidyverse
-Remotes: 
-    github::rostools/r3
+Remotes:  
+    github::rostools/r3,
+    rostools/r3admin
 Encoding: UTF-8
 LazyData: true

R/pre-course-script.R

@@ -9,6 +9,7 @@ unzip(here("data-raw/mmash-data.zip"),
   exdir = here("data-raw"),
   junkpaths = TRUE
 )
+Sys.sleep(1)
 unzip(here("data-raw/MMASH.zip"),
   exdir = here("data-raw")
 )

R/scrape-physionet.R

@@ -5,8 +5,8 @@ library(stringr)
 
 mmash_page <- bow("https://physionet.org/content/mmash/1.0.0/")
 
-mmash_html <- mmash_page %>%
-  scrape() %>%
+mmash_html <- mmash_page |>
+  scrape() |>
   html_node(".col-md-8")
 
 temp_html <- tempfile(fileext = ".html")
@@ -15,8 +15,8 @@ write_html(mmash_html, temp_html)
 temp_md <- tempfile(fileext = ".md")
 pandoc_convert(temp_html, to = "markdown_strict", output = temp_md)
 
-readLines(temp_md)[-(8:76)] %>%
-  str_remove("\\\\") %>%
+readLines(temp_md)[-(8:76)] |>
+  str_remove("\\\\") |>
   writeLines(temp_md)
 
 render(

appendix/extras.qmd

@@ -77,14 +77,11 @@ map(numbers, over_five)
 
 This works great as is, but sometimes you might not need to create a new
 function to use inside of `map()`. Instead we could use an anonymous
-function with either `function()` or `~`.
+function with `\()` (or either `function()` or `~`).
 
 ```{r}
 # Anonymous function
-map(numbers, function(x) if (x > 5) TRUE else FALSE)
-
-# Anonymous function (with shortcut)
-map(numbers, ~ if (.x > 5) TRUE else FALSE)
+map(numbers, \(x) if (x > 5) TRUE else FALSE)
 ```
 
 ## Debugging functions
@@ -148,12 +145,12 @@ Here's an example where you want to use your own arguments in
 
 ```{r test-nse, error=TRUE}
 test_nse <- function(data, filter_condition) {
-  data %>%
+  data |>
     dplyr::filter(filter_condition)
 }
 
-CO2 %>%
-  tibble() %>%
+CO2 |>
+  tibble() |>
   test_nse(conc > 100)
 ```
 
@@ -179,15 +176,15 @@ with `{{}}`.
 ```{r test-nse-fixed}
 #| error: true
 test_nse <- function(data, filter_condition) {
-  data %>%
+  data |>
     dplyr::filter({{ filter_condition }})
 }
 
-CO2 %>%
-  tibble() %>%
+CO2 |>
+  tibble() |>
   test_nse(conc > 100)
 
-CO2 %>%
-  tibble() %>%
+CO2 |>
+  tibble() |>
   test_nse(uptake < 30)
 ```

includes/packages.bib

@@ -1,145 +1,166 @@
 @Manual{R-desc,
   title = {desc: Manipulate DESCRIPTION Files},
   author = {Gábor Csárdi and Kirill Müller and Jim Hester},
-  year = {2022},
-  note = {https://github.com/r-lib/desc#readme},
+  year = {2023},
+  note = {R package version 1.4.3},
+  url = {https://desc.r-lib.org/},
 }
 
 @Manual{R-downlit,
   title = {downlit: Syntax Highlighting and Automatic Linking},
   author = {Hadley Wickham},
-  year = {2022},
-  note = {https://downlit.r-lib.org/},
+  year = {2023},
+  note = {R package version 0.4.3},
+  url = {https://downlit.r-lib.org/},
 }
 
 @Manual{R-dplyr,
   title = {dplyr: A Grammar of Data Manipulation},
   author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
   year = {2023},
-  note = {https://dplyr.tidyverse.org},
+  note = {R package version 1.1.4},
+  url = {https://dplyr.tidyverse.org},
 }
 
 @Manual{R-fs,
   title = {fs: Cross-Platform File System Operations Based on libuv},
   author = {Jim Hester and Hadley Wickham and Gábor Csárdi},
   year = {2023},
-  note = {https://fs.r-lib.org, https://github.com/r-lib/fs},
+  note = {R package version 1.6.3},
+  url = {https://fs.r-lib.org},
 }
 
 @Manual{R-glue,
   title = {glue: Interpreted String Literals},
   author = {Jim Hester and Jennifer Bryan},
-  year = {2022},
-  note = {https://github.com/tidyverse/glue},
+  year = {2024},
+  note = {R package version 1.7.0},
+  url = {https://glue.tidyverse.org/},
 }
 
 @Manual{R-here,
   title = {here: A Simpler Way to Find Your Files},
   author = {Kirill Müller},
   year = {2020},
-  note = {https://here.r-lib.org/},
+  note = {R package version 1.0.1},
+  url = {https://here.r-lib.org/},
 }
 
 @Manual{R-htmltools,
   title = {htmltools: Tools for HTML},
   author = {Joe Cheng and Carson Sievert and Barret Schloerke and Winston Chang and Yihui Xie and Jeff Allen},
-  year = {2023},
-  note = {https://github.com/rstudio/htmltools},
+  year = {2024},
+  note = {R package version 0.5.8, 
+https://rstudio.github.io/htmltools/},
+  url = {https://github.com/rstudio/htmltools},
 }
 
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
   year = {2023},
-  note = {R package version 1.43},
+  note = {R package version 1.45},
   url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-magrittr,
   title = {magrittr: A Forward-Pipe Operator for R},
   author = {Stefan Milton Bache and Hadley Wickham},
   year = {2022},
-  note = {https://magrittr.tidyverse.org},
+  note = {R package version 2.0.3, 
+https://github.com/tidyverse/magrittr},
+  url = {https://magrittr.tidyverse.org},
 }
 
 @Manual{R-pak,
   title = {pak: Another Approach to Package Installation},
   author = {Gábor Csárdi and Jim Hester},
-  note = {R package version 0.5.1},
+  year = {2024},
+  note = {R package version 0.7.2},
   url = {https://pak.r-lib.org/},
-  year = {2023},
 }
 
 @Manual{R-prodigenr,
   title = {prodigenr: Research Project Directory Generator},
   author = {Luke Johnston},
   year = {2022},
-  note = {https://github.com/rostools/prodigenr},
+  note = {R package version 0.6.2, 
+https://rostools.github.io/prodigenr/},
+  url = {https://github.com/rostools/prodigenr},
 }
 
 @Manual{R-purrr,
   title = {purrr: Functional Programming Tools},
   author = {Hadley Wickham and Lionel Henry},
   year = {2023},
-  note = {https://purrr.tidyverse.org/},
+  note = {R package version 1.0.2},
+  url = {https://purrr.tidyverse.org/},
 }
 
 @Manual{R-r3,
   title = {r3: Companion Package for the R3 Courses},
   author = {Luke Johnston},
   year = {2023},
-  note = {R package version 0.2.4},
+  note = {R package version 0.2.5},
   url = {https://github.com/rostools/r3},
 }
 
 @Manual{R-snakecase,
   title = {snakecase: Convert Strings into any Case},
   author = {Malte Grosser},
-  year = {2019},
-  note = {R package version 0.11.0},
+  year = {2023},
+  note = {R package version 0.11.1},
   url = {https://github.com/Tazinho/snakecase},
 }
 
 @Manual{R-stringr,
   title = {stringr: Simple, Consistent Wrappers for Common String Operations},
   author = {Hadley Wickham},
-  year = {2022},
-  note = {https://stringr.tidyverse.org},
+  year = {2023},
+  note = {R package version 1.5.1, 
+https://github.com/tidyverse/stringr},
+  url = {https://stringr.tidyverse.org},
 }
 
 @Manual{R-styler,
   title = {styler: Non-Invasive Pretty Printing of R Code},
   author = {Kirill Müller and Lorenz Walthert},
   year = {2023},
-  note = {https://github.com/r-lib/styler},
+  note = {R package version 1.10.2},
+  url = {https://github.com/r-lib/styler},
 }
 
 @Manual{R-tidyverse,
   title = {tidyverse: Easily Install and Load the Tidyverse},
   author = {Hadley Wickham},
   year = {2023},
-  note = {https://tidyverse.tidyverse.org},
+  note = {R package version 2.0.0, 
+https://github.com/tidyverse/tidyverse},
+  url = {https://tidyverse.tidyverse.org},
 }
 
 @Manual{R-usethis,
   title = {usethis: Automate Package and Project Setup},
-  author = {Hadley Wickham and Jennifer Bryan and Malcolm Barrett},
-  year = {2022},
-  note = {https://usethis.r-lib.org},
+  author = {Hadley Wickham and Jennifer Bryan and Malcolm Barrett and Andy Teucher},
+  year = {2024},
+  note = {R package version 2.2.3},
+  url = {https://usethis.r-lib.org},
 }
 
 @Manual{R-vroom,
   title = {vroom: Read and Write Rectangular Text Data Quickly},
   author = {Jim Hester and Hadley Wickham and Jennifer Bryan},
   year = {2023},
-  note = {https://vroom.r-lib.org},
+  note = {R package version 1.6.5},
+  url = {https://vroom.r-lib.org},
 }
 
 @Manual{R-withr,
   title = {withr: Run Code With Temporarily Modified Global State},
   author = {Jim Hester and Lionel Henry and Kirill Müller and Kevin Ushey and Hadley Wickham and Winston Chang},
-  year = {2022},
-  note = {https://withr.r-lib.org},
+  year = {2024},
+  note = {R package version 3.0.0},
+  url = {https://withr.r-lib.org},
 }
 
 @Book{knitr2015,

preamble/pre-course.qmd

@@ -81,7 +81,7 @@ objectives for this page:
 #| echo: false
 #| eval: true
 #| output: asis
-r3admin::read_common("reading-website.md")
+cat(r3admin::read_common("reading-website.md"), sep = "\n")
 ```
 
 ## Installing the latest programs {#sec-install-programs}
@@ -90,7 +90,7 @@ r3admin::read_common("reading-website.md")
 #| echo: false
 #| eval: true
 #| output: asis
-r3admin::read_common("installing-programs.md")
+cat(r3admin::read_common("installing-programs.md"), sep = "\n")
 ```
 
 ## Installing the R packages {#sec-install-r-packages}
@@ -99,7 +99,7 @@ r3admin::read_common("installing-programs.md")
 #| echo: false
 #| eval: true
 #| output: asis
-r3admin::read_pkg_install("advanced")
+cat(r3admin::read_template_pkg_install("advanced"), sep = "\n")
 ```
 
 ## Setting up Git {#sec-setup-git}
@@ -357,7 +357,7 @@ is tell R to first look for the `.Rproj` file and then start looking for
 the file we actually want. This might not make sense yet, but as we go
 through the course, you will see why this is important to consider.
 
-::: callout-note
+::: {.callout-note appearance="default"}
 You don't need to run the below code. But if you want to see the
 structure and content of a directory, you can use the `dir_tree()`
 function from the `{fs}` package, which means "filesystem", by running
@@ -493,9 +493,11 @@ either `Ctrl-Shift-A` or `Code -> Reformat Code` menu item. Next, we'll
 extract the new `data-raw/MMASH.zip` file using `unzip()` again. Because
 we want to keep the folder structure inside this zip file, we won't use
 `junkpaths`. Write and execute this code in the `data-raw/mmash.R`
-script.
+script. We'll also add a `Sys.sleep(1)` to pause the script for a second
+because sometimes the unzipping can be too fast and cause problems.
 
 ```{r unzip-data-file}
+Sys.sleep(1)
 unzip(here("data-raw/MMASH.zip"),
   exdir = here("data-raw")
 )

preamble/schedule.csv

@@ -23,7 +23,5 @@ Day 3,10:15,Coffee break and snacks,mug-hot,
 Day 3,10:30,Quickly re-arranging data with pivots,laptop-code,../sessions/pivots.html
 Day 3,12:15,Lunch,utensils,
 Day 3,13:00,Hands-on exercises,briefcase,../sessions/hands-on-work.html
-Day 3,15:00,Coffee break and snacks,mug-hot,
-Day 3,15:15,Hands-on exercises,laptop-code,../sessions/hands-on-work.html
-Day 3,16:20,Closing remarks,person-chalkboard,../sessions/what-next.html
-Day 3,16:45,Short survey and farewell,comment-dots,https://docs.google.com/forms/d/e/1FAIpQLSe2gpbN9ExCXyeTfJLgu_poemF0iUtkcihnCunXl3YA4e1hHQ/viewform?usp=sf_link
+Day 3,14:20,Closing remarks,person-chalkboard,../sessions/what-next.html
+Day 3,14:45,Short survey and farewell,comment-dots,https://docs.google.com/forms/d/e/1FAIpQLSe2gpbN9ExCXyeTfJLgu_poemF0iUtkcihnCunXl3YA4e1hHQ/viewform?usp=sf_link