From 9c4afb5e928d14d4ddf198172e91e25e20a27536 Mon Sep 17 00:00:00 2001
From: Milan Wiedemann <milan.wiedemann@gmail.com>
Date: Tue, 19 Nov 2024 14:26:11 +0000
Subject: [PATCH] Add Shiny App as vignette

---
 .Rbuildignore                     |  4 +++-
 .gitignore                        |  3 +++
 DESCRIPTION                       |  3 +++
 README.Rmd                        |  4 +++-
 README.md                         |  8 ++++++--
 vignettes/.gitignore              |  2 ++
 vignettes/code_usage_explorer.Rmd | 28 ++++++++++++++++++++++++++++
 7 files changed, 48 insertions(+), 4 deletions(-)
 create mode 100644 vignettes/.gitignore
 create mode 100644 vignettes/code_usage_explorer.Rmd

diff --git a/.Rbuildignore b/.Rbuildignore
index 65b639f..38800f6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -8,4 +8,6 @@
 ^docs$
 ^pkgdown$
 ^app.R$
-^rsconnect$
\ No newline at end of file
+^rsconnect$
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
index 989a496..5b735cd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,6 @@
 docs
 rsconnect/
 .DS_Store
+inst/doc
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
index be3ca17..a24650d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,6 +20,8 @@ Depends:
 LazyData: true
 LazyDataCompression: bzip2
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 URL: https://github.com/ebmdatalab/codeusage, https://ebmdatalab.github.io/codeusage/
@@ -41,3 +43,4 @@ Imports:
     shiny,
     stringr,
     tibble
+VignetteBuilder: knitr
diff --git a/README.Rmd b/README.Rmd
index 72f3d23..b571bf9 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -21,7 +21,9 @@ knitr::opts_chunk$set(
 
 <!-- badges: end -->
 
-The goal of `codeusage` is to make yearly summaries of **SNOMED Code Usage in Primary Care** and **ICD-10 and OPCS Code Usage in Secondary Care** in England, published by NHS Digital, available in R for research. The original data is available from NHS Digital at:
+The goal of `codeusage` is to make yearly summaries of **SNOMED Code Usage in Primary Care** and **ICD-10 and OPCS Code Usage in Secondary Care** in England, published by NHS Digital, available in R for research.
+The interactive [Code Usage Explorer](https://milanwiedemann.shinyapps.io/codeusage/) dashboard provides different options to explore these datasets.  
+The original data is available from NHS Digital at:
 
 -   [SNOMED Code Usage in Primary Care](https://digital.nhs.uk/data-and-information/publications/statistical/mi-snomed-code-usage-in-primary-care)
 -   [ICD-10 and OPCS Code Usage in Secondary Care](https://digital.nhs.uk/data-and-information/publications/statistical/hospital-admitted-patient-care-activity)
diff --git a/README.md b/README.md
index 6f9a0c1..bcddc98 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,12 @@
 
 <!-- badges: end -->
 
-The goal of `codeusage` is to make yearly summaries of **SNOMED CodevUsage in Primary Care** and **ICD-10 and OPCS Code Usage in SecondaryvCare** in England, published by NHS Digital, available in R forvresearch.
-The interactive [Code Usage Explorer](https://milanwiedemann.shinyapps.io/codeusage/) app allows users to explore the data online.
+The goal of `codeusage` is to make yearly summaries of **SNOMED Code
+Usage in Primary Care** and **ICD-10 and OPCS Code Usage in Secondary
+Care** in England, published by NHS Digital, available in R for
+research. The interactive [Code Usage
+Explorer](https://milanwiedemann.shinyapps.io/codeusage/) dashboard
+provides different options to explore these datasets.  
 The original data is available from NHS Digital at:
 
 - [SNOMED Code Usage in Primary
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/code_usage_explorer.Rmd b/vignettes/code_usage_explorer.Rmd
new file mode 100644
index 0000000..02c570a
--- /dev/null
+++ b/vignettes/code_usage_explorer.Rmd
@@ -0,0 +1,28 @@
+---
+title: "Shiny: Code Usage Explorer"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{shiny_code_usage_explorer}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+<style>
+.shiny-app-frame {
+  position: fixed;
+  left: 0;
+  top: 50px;
+  bottom: 0;
+  right: 0;
+}
+.shiny-app-frame iframe {
+  width: 100%;
+  height: 100%;
+  border: none;
+}
+</style>
+
+<div class="shiny-app-frame"> 
+<iframe src="https://milanwiedemann.shinyapps.io/codeusage/">
+</iframe>
+</div>
\ No newline at end of file