Update RMarkdown episode to use Quarto and add section on parametrised reports

config.yaml

@@ -1,3 +1,4 @@
+---
 #------------------------------------------------------------
 # Values for this lesson.
 #------------------------------------------------------------
@@ -8,32 +9,32 @@
 # lc: Library Carpentry
 # cp: Carpentries (to use for instructor training for instance)
 # incubator: The Carpentries Incubator
-carpentry: 'swc'
+carpentry: "swc"
 
 # Overall title for pages.
-title: 'R for AMR Epidemiology'
+title: "R for AMR Epidemiology"
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: '2015-04-18'
+created: "2015-04-18"
 
 # Comma-separated list of keywords for the lesson
-keywords: 'software, data, lesson, The Carpentries'
+keywords: "software, data, lesson, The Carpentries"
 
 # Life cycle stage of the lesson
 # possible values: pre-alpha, alpha, beta, stable
-life_cycle: 'stable'
+life_cycle: "stable"
 
 # License of the lesson materials (recommended CC-BY 4.0)
-license: 'CC-BY 4.0'
+license: "CC-BY 4.0"
 
 # Link to the source repository for this lesson
-source: 'https://github.com/UCL-ARC/r-amr-epidemiology'
+source: "https://github.com/UCL-ARC/r-amr-epidemiology"
 
 # Default branch of your lesson
-branch: 'main'
+branch: "main"
 
 # Who to contact if there are any issues
-contact: '[email protected]'
+contact: "[email protected]"
 
 # Navigation ------------------------------------------------
 #
@@ -58,55 +59,54 @@ contact: '[email protected]'
 # - another-learner.md
 
 # Order of episodes in your lesson
-episodes: 
-- 01-rstudio-intro.Rmd
-- 02-project-intro.Rmd
-- 03-seeking-help.Rmd
-- 04-data-structures-part1.Rmd
-- 05-data-structures-part2.Rmd
-- 06-filedir.md
-- 07-basics.md
-- 08-setup.md
-- 09-create.md
-- 10-changes.md
-- 11-history.md
-- 12-ignore.md
-- 13-supplemental-rstudio.md
-- 14-data-subsetting.Rmd
-# - 07-control-flow.Rmd
-- 15-plot-ggplot2.Rmd
-# - 09-vectorization.Rmd
-# - 10-functions.Rmd
-- 16-writing-data.Rmd
-- 17-github.md
-- 18-collab.md
-- 19-conflict.md
-- 20-dplyr.Rmd
-- 21-tidyr.Rmd
-# basic stats
-- 22-knitr-markdown.Rmd 
-- 23-statistics.Rmd
-# 23-regression
-# 24-logregression
-# 25-broom
-# 26-r-sql
-- 27-wrap-up.Rmd
+episodes:
+  - 01-rstudio-intro.Rmd
+  - 02-project-intro.Rmd
+  - 03-seeking-help.Rmd
+  - 04-data-structures-part1.Rmd
+  - 05-data-structures-part2.Rmd
+  - 06-filedir.md
+  - 07-basics.md
+  - 08-setup.md
+  - 09-create.md
+  - 10-changes.md
+  - 11-history.md
+  - 12-ignore.md
+  - 13-supplemental-rstudio.md
+  - 14-data-subsetting.Rmd
+  # - 07-control-flow.Rmd
+  - 15-plot-ggplot2.Rmd
+  # - 09-vectorization.Rmd
+  # - 10-functions.Rmd
+  - 16-writing-data.Rmd
+  - 17-github.md
+  - 18-collab.md
+  - 19-conflict.md
+  - 20-dplyr.Rmd
+  - 21-tidyr.Rmd
+  # basic stats
+  - 22-quarto.md
+  - 23-statistics.Rmd
+  # 23-regression
+  # 24-logregression
+  # 25-broom
+  # 26-r-sql
+  - 27-wrap-up.Rmd
 
 # Information for Learners
-learners: 
+learners:
 
 # Information for Instructors
-instructors: 
+instructors:
 
 # Learner Profiles
-profiles: 
+profiles:
 
 # Customisation ---------------------------------------------
 #
 # This space below is where custom yaml items (e.g. pinning
 # sandpaper and varnish versions) should live
 
-
-url: 'https://UCL-ARC.github.io/R-AMR-Epidemiology'
+url: "https://UCL-ARC.github.io/R-AMR-Epidemiology"
 analytics: carpentries
 lang: en