Merge pull request #5 from nhs-r-community/add-webr-detail

Add webr detail

20230613-government-toolshed/NHSRtoolshed.qmd

@@ -1,16 +1,6 @@
 ---
 title: "The NHSR Community Toolshed"
-title-slide-attributes: 
-  data-background-color: "#43464B"
 author: "Zoë Turner"
-format:
-  revealjs:
-    theme: [default, nhsr-quarto.scss]
-    logo: https://raw.githubusercontent.com/nhs-r-community/assets/main/logo/nhsr-logo.svg
-    code-link: true
-    css: nhsr-quarto.scss
-    preview-links: true
-embed-resources: true    
 execute: 
   echo: false
   eval: true

20230613-government-toolshed/housekeeping.qmd

@@ -1,16 +1,6 @@
 ---
 title: "The NHSR Community Toolshed - Housekeeping"
-title-slide-attributes: 
-  data-background-color: "#43464B"
 author: "Zoë Turner"
-format:
-  revealjs:
-    theme: [default, nhsr-quarto.scss]
-    logo: https://raw.githubusercontent.com/nhs-r-community/assets/main/logo/nhsr-logo.svg
-    code-link: true
-    css: nhsr-quarto.scss
-    preview-links: true
-embed-resources: true    
 execute: 
   echo: false
   eval: true

20240614-coffee-coding-quarto/cc-quarto.qmd

@@ -1,16 +1,6 @@
 ---
 title: "NHSR Community Coffee and Coding - Quarto"
-title-slide-attributes: 
-  data-background-color: "#43464B"
 author: "Zoë Turner"
-format:
-  revealjs:
-    theme: [default, nhsr-quarto.scss]
-    logo: https://raw.githubusercontent.com/nhs-r-community/assets/main/logo/nhsr-logo.svg
-    code-link: true
-    css: nhsr-quarto.scss
-    preview-links: true
-embed-resources: true    
 execute: 
   echo: true
   eval: false

20241017-introduce-nhsr/README.md

@@ -1,3 +1,6 @@
 # Introducing NHS-R Community
 
 [Slides](https://presentations.nhsrcommunity.com/20241017-introduce-nhsr/introduce-nhsr.html#/title-slide) to introduce what NHS-R Community is and does.
+
+This presentation includes webr to show a couple of the NHS-R Community R
+packages.

20241017-introduce-nhsr/introduce-nhsr.html

@@ -1382,7 +1382,7 @@
   };
 
   // Store cell data
-  globalThis.qwebrCellDetails = [{"id":1,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"false","fig-width":7,"label":"unnamed-chunk-1","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"interactive"},"code":"library(NHSRdatasets)\nlibrary(dplyr)\n\nsub_set <- ae_attendances |>\n  filter(org_code == \"RQM\",  # the hospital code\n         type == 1, # the type of admission\n         period < as.Date(\"2018-04-01\")) # dates before 01/04/2018\n\nsub_set"},{"id":2,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"false","fig-width":7,"label":"unnamed-chunk-2","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"interactive"},"code":"library(NHSRplotthedots)\n\nsub_set |>\n  ptd_spc(\n    value_field = breaches,\n    date_field = period,\n    improvement_direction = \"decrease\"\n  )"},{"id":3,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"true","fig-width":7,"label":"unnamed-chunk-3","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"setup"},"code":"webr::install(\"NHSRepisodes\", repos = c(\"https://nhs-r-community.r-universe.dev\"))"},{"id":4,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"false","fig-width":7,"label":"unnamed-chunk-4","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"interactive"},"code":"library(dplyr)\n\ndat <- tribble(\n  ~patient_id, ~admission, ~discharge, ~code, ~notes,\n  1L, \"2020-01-01\", \"2020-01-10\", \"t100\", NA,\n  1L, \"2020-01-12\", \"2020-01-22\", \"t600\", NA,\n  2L, \"2020-05-01\", \"2020-10-01\", \"t100\", NA,\n  2L, \"2020-10-01\", \"2020-11-01\", \"t250\", \"same day discharge and admission\"\n) |>\n  # columns must be date format to work with NHSRepisodes functions\n  mutate(across(admission:discharge, as.Date)) \n\ndat"},{"id":5,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"false","fig-width":7,"label":"unnamed-chunk-5","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"interactive"},"code":"# Add a column to your data on the episode numbers\ndat |>\n  # Rename the columns so that they are recognised by the `add_parent_interval()` function\n  select(\n    id = patient_id,\n    start = admission,\n    end = discharge,\n    ends_with(\"number\")\n  ) |>\n  NHSRepisodes::add_parent_interval()"},{"id":6,"options":{"warning":"true","out-width":"700px","fig-height":5,"editor-font-scale":"0.5","comment":"","editor-max-height":"","output":"true","fig-cap":"","results":"markup","autorun":"false","fig-width":7,"label":"unnamed-chunk-6","message":"true","editor-quick-suggestions":"false","out-height":"","dpi":72,"read-only":"false","classes":"","editor-word-wrap":"true","context":"interactive"},"code":"# Add a column to your data on the episode numbers\ndat |>\n  # Rename the columns so that they are recognised by the `add_parent_interval()` function\n  select(\n    id = patient_id,\n    start = admission,\n    end = discharge,\n    ends_with(\"number\")\n  ) |>\n  NHSRepisodes::merge_episodes()"}];
+  globalThis.qwebrCellDetails = [{"code":"library(NHSRdatasets)\nlibrary(dplyr)\n\nsub_set <- ae_attendances |>\n  filter(org_code == \"RQM\",  # the hospital code\n         type == 1, # the type of admission\n         period < as.Date(\"2018-04-01\")) # dates before 01/04/2018\n\nsub_set","options":{"editor-quick-suggestions":"false","context":"interactive","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"false","fig-cap":"","label":"unnamed-chunk-1","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":1},{"code":"library(NHSRplotthedots)\n\nsub_set |>\n  ptd_spc(\n    value_field = breaches,\n    date_field = period,\n    improvement_direction = \"decrease\"\n  )","options":{"editor-quick-suggestions":"false","context":"interactive","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"false","fig-cap":"","label":"unnamed-chunk-2","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":2},{"code":"webr::install(\"NHSRepisodes\", repos = c(\"https://nhs-r-community.r-universe.dev\"))","options":{"editor-quick-suggestions":"false","context":"setup","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"true","fig-cap":"","label":"unnamed-chunk-3","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":3},{"code":"library(dplyr)\n\ndat <- tribble(\n  ~patient_id, ~admission, ~discharge, ~code, ~notes,\n  1L, \"2020-01-01\", \"2020-01-10\", \"t100\", NA,\n  1L, \"2020-01-12\", \"2020-01-22\", \"t600\", NA,\n  2L, \"2020-05-01\", \"2020-10-01\", \"t100\", NA,\n  2L, \"2020-10-01\", \"2020-11-01\", \"t250\", \"same day discharge and admission\"\n) |>\n  # columns must be date format to work with NHSRepisodes functions\n  mutate(across(admission:discharge, as.Date)) \n\ndat","options":{"editor-quick-suggestions":"false","context":"interactive","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"false","fig-cap":"","label":"unnamed-chunk-4","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":4},{"code":"# Add a column to your data on the episode numbers\ndat |>\n  # Rename the columns so that they are recognised by the `add_parent_interval()` function\n  select(\n    id = patient_id,\n    start = admission,\n    end = discharge,\n    ends_with(\"number\")\n  ) |>\n  NHSRepisodes::add_parent_interval()","options":{"editor-quick-suggestions":"false","context":"interactive","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"false","fig-cap":"","label":"unnamed-chunk-5","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":5},{"code":"# Add a column to your data on the episode numbers\ndat |>\n  # Rename the columns so that they are recognised by the `add_parent_interval()` function\n  select(\n    id = patient_id,\n    start = admission,\n    end = discharge,\n    ends_with(\"number\")\n  ) |>\n  NHSRepisodes::merge_episodes()","options":{"editor-quick-suggestions":"false","context":"interactive","comment":"","output":"true","message":"true","editor-max-height":"","classes":"","fig-height":5,"dpi":72,"out-height":"","results":"markup","read-only":"false","autorun":"false","fig-cap":"","label":"unnamed-chunk-6","editor-word-wrap":"true","out-width":"700px","fig-width":7,"warning":"true","editor-font-scale":"0.5"},"id":6}];
 
   </script><script type="module">
   // Declare startupMessageQWebR globally

20241017-introduce-nhsr/introduce-nhsr.qmd

@@ -1,18 +1,10 @@
 ---
 title: "Introducing the NHSR Community"
-title-slide-attributes: 
-  data-background-color: "#43464B"
 author: "Zoë Turner"
-format:
-  revealjs:
-    theme: [default, nhsr-quarto.scss]
-    code-link: true
-    css: nhsr-quarto.scss
-    preview-links: true
-embed-resources: true
 execute: 
   echo: false
   eval: true
+embed-resources: true
 filters:
   - "webr"
 engine: knitr

README.md

@@ -11,5 +11,30 @@ to explain the presentation.
 
 Formats for the folder names will be `yyymmdd-name-of-presentation`
 
-For presentation slides in quarto include `embed-resources: true` in the YAML and
-for Rmarkdown `self-contained: true`.
+## Code that is applied to all slides
+
+The code `embed-resources: true` will be applied automatically to slides so that
+the html generated does not require a separate folder to be formatted. 
+This code is applied to the entire repository and subfolders as it included in 
+the `_quarto.yml`. 
+_Note that the line `embed-resources: true` is needed in the YAML where webr is 
+used as the supporting folder is generated when the Quarto code `quarto render`
+is used on the Terminal_
+
+The style for the slides is generated from the following code which is also 
+run centrally from the `_quarto.yml` file:
+
+```
+title-slide-attributes: 
+  data-background-color: "#43464B"
+format:
+  revealjs:
+    theme: [default, nhsr-quarto.scss]
+    logo: https://raw.githubusercontent.com/nhs-r-community/assets/main/logo/nhsr-logo.svg
+    code-link: true
+    css: nhsr-quarto.scss
+    preview-links: true
+```
+
+Note that although this code can be used on files in subfolders, each folder
+requires the `nhsr-quarto.scss` to be copied to each folder.

_quarto.yml

@@ -1,5 +1,14 @@
 project:
   title: "NHSRpresentations"
-
-
-
+  render: 
+    - "*.qmd"
+    - "!*.md"
+embed-resources: true
+format:
+  revealjs:
+    theme: [default, nhsr-quarto.scss]
+    code-link: true
+    css: nhsr-quarto.scss
+    preview-links: true
+title-slide-attributes: 
+  data-background-color: "#43464B"