Merge branch '107_heatmap_nee' of https://github.com/The-Strategy-Unit/nhp_inputs_report_app into 107_heatmap_nee

craig-parylo · craig-parylo · commit b867dc7dc693 · 2025-01-28T07:36:59.000Z
diff --git a/CODEOWNERS b/CODEOWNERS
@@ -0,0 +1,5 @@
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @primary-owner and @secondary-owner will be requested for
+# review when someone opens a pull request.
+*       @matt-dray @craig-parylo 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,6 +15,7 @@ Imports:
     AzureStor,
     bsicons,
     bslib (>= 0.7.0),
+    colourpicker,
     config (>= 0.3.1),
     data.table,
     dplyr,
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
 YEAR: 2024
-COPYRIGHT HOLDER: Golem User
+COPYRIGHT HOLDER: The Strategy Unit
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2024 Golem User
+Copyright (c) 2024 The Strategy Unit
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -615,8 +615,8 @@ app_ui <- function(request) {
                 width = 350,
                 open = TRUE,
 
-                bslib::input_switch(
-                  id = "toggle_contextual_baseline_range",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_baseline_range",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show 80% range?",
@@ -626,8 +626,8 @@ app_ui <- function(request) {
                   ),
                   value = TRUE
                 ),
-                bslib::input_switch(
-                  id = "toggle_contextual_baseline_quadrants",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_baseline_quadrants",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show quadrant lines?",
@@ -637,8 +637,8 @@ app_ui <- function(request) {
                   ),
                   value = TRUE
                 ),
-                bslib::input_switch(
-                  id = "toggle_contextual_baseline_schemecode",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_baseline_schemecode",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show scheme codes?",
@@ -693,8 +693,8 @@ app_ui <- function(request) {
                 width = 350,
                 open = TRUE,
 
-                bslib::input_switch(
-                  id = "toggle_contextual_trendline_otherschemes",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_trendline_otherschemes",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show other schemes?",
@@ -704,8 +704,8 @@ app_ui <- function(request) {
                   ),
                   value = FALSE
                 ),
-                bslib::input_switch(
-                  id = "toggle_contextual_trendline_horizon_timeline",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_trendline_horizon_timeline",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show horizon on timeline?",
@@ -715,8 +715,8 @@ app_ui <- function(request) {
                   ),
                   value = TRUE
                 ),
-                bslib::input_switch(
-                  id = "toggle_contextual_trendline_horizon_overlay",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_trendline_horizon_overlay",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show horizon as overlay?",
@@ -726,8 +726,8 @@ app_ui <- function(request) {
                   ),
                   value = FALSE
                 ),
-                bslib::input_switch(
-                  id = "toggle_contextual_trendline_average",
+                shiny::checkboxInput(
+                  inputId = "toggle_contextual_trendline_average",
                   label = bslib::tooltip(
                     trigger = list(
                       "Show pre-baseline average?",
diff --git a/README.md b/README.md
@@ -2,35 +2,50 @@
 
 <!-- badges: start -->
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
-
 <!-- badges: end -->
 
 ## Purpose
 
-An app to compare schemes' mitigator selections as part of the National Hospital Programme (NHP) modelling process. It's [deployed to Posit Connect](https://connect.strategyunitwm.nhs.uk/nhp/mitigator-comparisons/).
+An app built with [{shiny}](https://shiny.posit.co/), [{golem}](https://thinkr-open.github.io/golem/) and [{bslib}](https://rstudio.github.io/bslib/) to explore and compare schemes' mitigator selections as part of the National Hospital Programme (NHP) modelling process. 
+
+This tool is designed primarily for use by model-relationship managers (MRMs) in discussion with schemes so that the mitigator selections can be refined before being finalised.
+
+The app is [deployed to Posit Connect](https://connect.strategyunitwm.nhs.uk/nhp/mitigator-comparisons/) (login/permissions required).
 
-This tool is designed for use by model-relationship managers (MRMs) in discussion with schemes so that the mitigator selections can be refined before being finalised. Also, some of the scheme-level code here may support a standalone national-level report that's being developed separately.
+## Run the app
 
-This app replaces an original static report ([deployment](https://connect.strategyunitwm.nhs.uk/nhp/mitigators-comparison-report), [source](https://github.com/The-Strategy-Unit/nhp_peers_params)) that started to become tricky to manage and interpret without interactivity.
+### Deploy
 
-## Requirements
+You can redeploy the app to Posit Connect using the `dev/03_deploy.R` script.
+This usually happens after a new GitHub release/Git tag.
 
-Some environmental variables are needed to fetch data, for example. You will need to add a `.Renviron` file to the project directory that contains the variables named in the `.Renviron.example` file. You can ask a member of the Data Science team for the values to populate this file. Remember to restart your session after you've updated your `.Renviron` file.
+The script checks for the 'app ID' in the `rsconnect/` folder of your local project root, which is generated when you first deploy.
+Otherwise you can find the ID by opening the app from the Posit Connect 'Content' page and then looking for 'Content ID' in the Settings > Info panel of the interface.
 
-## Techincal
+### Locally
 
-### Major packages
+You can run the app locally, but some environmental variables are needed to fetch data, for example.
+You will need to add a `.Renviron` file to the project directory that contains the variables named in the `.Renviron.example` file.
+You can ask a member of the Data Science team for the values to populate this file.
+Remember to restart your session after you've updated your `.Renviron` file.
 
-The app is built with [{shiny}](https://shiny.posit.co/), the [{golem}](https://thinkr-open.github.io/golem/) Shiny-as-a-package framework and [{bslib}](https://rstudio.github.io/bslib/) for theming.
+## Data
 
-### Mitigator data
+### Mitigators
 
-The mitigators for each scheme's model scenarios are stored on Azure as large json files. One small element of these files is the 'params' item, which includes the mitigator selections.
+The mitigators for each scheme's model scenarios are stored on Azure as large json files.
+One small element of these files is the 'params' item, which includes the mitigator selections.
 
-To avoid the app having to read the entire json file for each scheme's model scenario, there is a system to pre-prepare the params alone. [A scheduled Quarto document on Posit Connect](https://connect.strategyunitwm.nhs.uk/nhp/tagged-runs-params-report/) has code to select the appropriate json file, extract the params and [save them as an RDS file to a pin](https://connect.strategyunitwm.nhs.uk/content/32c7f642-e420-448d-b888-bf655fc8fa8b/) on Posit Connect; it also saves [a CSV file to another pin](https://connect.strategyunitwm.nhs.uk/content/811dbaf9-18fe-43aa-bf8e-06b0df66004e/) that contains metadata about the model scenarios. The app then reads data from these pins using [the {pins} package](https://pins.rstudio.com/). A [blogpost by the Data Science team](https://the-strategy-unit.github.io/data_science/blogs/posts/2024-05-22-storing-data-safely/#posit-connect-pins) contains note on authenticating RStudio with Posit Connect, should you need to.
+To avoid the app having to read the entire json file for each scheme's model scenario, there is a system to pre-prepare the params alone.
+[A scheduled Quarto document on Posit Connect](https://connect.strategyunitwm.nhs.uk/nhp/tagged-runs-params-report/) has code to select the appropriate json file, extract the params and [save them as an RDS file to a pin](https://connect.strategyunitwm.nhs.uk/content/32c7f642-e420-448d-b888-bf655fc8fa8b/) on Posit Connect; it also saves [a CSV file to another pin](https://connect.strategyunitwm.nhs.uk/content/811dbaf9-18fe-43aa-bf8e-06b0df66004e/) that contains metadata about the model scenarios.
+The app then reads data from these pins using [the {pins} package](https://pins.rstudio.com/).
+A [blogpost by the Data Science team](https://the-strategy-unit.github.io/data_science/blogs/posts/2024-05-22-storing-data-safely/#posit-connect-pins) contains note on authenticating RStudio with Posit Connect, should you need to.
 
-Schemes run many scenarios, but the app only displays data from a single json. The correct file is read because the MRMs tell the Data Science team which particular scenario should be labelled on Azure with a 'run stage' of 'initial', 'intermediate' or 'final'. There's [a handy lookup table](https://connect.strategyunitwm.nhs.uk/nhp/tagged_runs/nhp-tagged-runs.html) where you can see which files have been labelled for each scheme.
+Schemes run many scenarios, but the app only displays data from a single json.
+The correct file is read because the MRMs tell the Data Science team which particular scenario should be labelled on Azure with a 'run stage' of 'final' (the default) 'intermediate' or 'initial'.
+There's [a handy lookup table](https://connect.strategyunitwm.nhs.uk/nhp/tagged_runs/nhp-tagged-runs.html) (login/permissions required) where you can see which files have been labelled for each scheme.
 
-### Supporting data
+### Supporting
 
-Supporting data is fetched from Azure. This includes lookups for mitigators and schemes, as well as data from the National Elicitation Exercise (NEE).
+Supporting data is fetched from Azure.
+This includes lookups for mitigators and schemes, as well as data from the National Elicitation Exercise (NEE).
diff --git a/dev/03_deploy.R b/dev/03_deploy.R
@@ -53,7 +53,7 @@ rsconnect::deployApp(
     "DESCRIPTION",
     "app.R"
   ),
-  appId = rsconnect::deployments(".")$appID,  # 298
+  appId = rsconnect::deployments(".")$appID,
   lint = FALSE,
   forceUpdate = TRUE
 )

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`YEAR: 2024`
`2`		`-COPYRIGHT HOLDER: Golem User`
	`2`	`+COPYRIGHT HOLDER: The Strategy Unit`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@ rsconnect::deployApp(`
`53`	`53`	`"DESCRIPTION",`
`54`	`54`	`"app.R"`
`55`	`55`	`),`
`56`		`- appId = rsconnect::deployments(".")$appID, # 298`
	`56`	`+ appId = rsconnect::deployments(".")$appID,`
`57`	`57`	`lint = FALSE,`
`58`	`58`	`forceUpdate = TRUE`
`59`	`59`	`)`