add tests

.Rbuildignore

@@ -12,3 +12,4 @@
 ^README\.md$
 ^rsconnect$
 ^tpma-explorer\.Rproj$
+^.cache$

.lintr

@@ -1,3 +1,7 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    object_length_linter(50)
+  )
 exclusions: list(
     "data-raw/la-lookups.R"
   )

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tpma.explorer
 Title: Explore TPMA Data
-Version: 0.2.0.9000
+Version: 0.3.4
 Authors@R: c(
     person("Matt", "Dray", , "matt.dray@nhs.net", role = c("aut", "cre")),
     person("Tom", "Jemmett", , "thomas.jemmett@nhs.net", role = "aut")
@@ -18,6 +18,7 @@ Imports:
     AzureStor,
     bsicons,
     bslib,
+    cachem,
     config,
     dplyr,
     forcats,
@@ -26,6 +27,7 @@ Imports:
     ggrepel,
     glue,
     gt,
+    httr2,
     jsonlite,
     markdown,
     purrr,
@@ -36,11 +38,16 @@ Imports:
     shinycssloaders,
     stringr,
     tibble,
-    tidyr,
-    tidyselect,
-    withr
+    tidyr
 Remotes:
     The-Strategy-Unit/azkit
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
+Suggests: 
+    mockery,
+    testthat (>= 3.0.0),
+    tidyselect,
+    vdiffr,
+    withr
+Config/testthat/edition: 3

NAMESPACE

@@ -1,15 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
-export(convert_md_to_html)
 export(entable_encounters)
 export(fetch_strategy_text)
 export(generate_rates_baseline_data)
 export(get_all_geo_data)
 export(get_container)
 export(get_golem_config)
+export(get_peers_lookup)
+export(get_rates_data)
+export(get_rates_trend_data)
 export(isolate_provider_peers)
 export(make_strategy_group_lookup)
 export(md_file_to_html)
+export(md_string_to_html)
 export(plot_age_sex_pyramid)
 export(plot_nee)
 export(plot_rates_box)

R/add_external_resources.R

@@ -1,17 +1,3 @@
-#' Add External Resources to the Application
-#' This function is internally used to add external resources inside the Shiny
-#' application.
-#' @noRd
-add_external_resources <- function() {
-  shiny::addResourcePath(
-    "www",
-    app_sys("app/www")
-  )
-  shiny::singleton(
-    shiny::tags$head()
-  )
-}
-
 #' Access Files in the Current App
 #' @param ... Character vectors, specifying subdirectory and file(s)
 #'     within your package. The default, none, returns the root of the app.

R/mod_plot_rates.R

@@ -35,77 +35,45 @@ mod_plot_rates_server <- function(
 ) {
   # load static data items
   strategies_config <- get_golem_config("mitigators_config")
+  strategy_group_lookup <- make_strategy_group_lookup(strategies_config)
 
   # return the shiny module
   shiny::moduleServer(id, function(input, output, session) {
     peers_lookup <- shiny::reactive({
-      filename <- switch(
-        selected_geography(),
-        "nhp" = "nhp-peers.csv",
-        "la" = "la-peers.csv"
-      )
-
-      shiny::req(filename)
-
-      readr::read_csv(
-        app_sys("app", "data", filename),
-        col_types = "c"
-      )
+      get_peers_lookup(selected_geography())
     }) |>
       shiny::bindCache(selected_geography())
 
     #  Prepare data ----
     rates_data <- shiny::reactive({
-      df <- inputs_data()[["rates"]]
-
-      national <- df |>
-        dplyr::filter(.data$provider == "national") |>
-        dplyr::select(
-          "strategy",
-          "fyear",
-          national_rate = "std_rate"
-        )
-
-      df |>
-        dplyr::filter(!.data$provider %in% c("national", "unknown")) |>
-        dplyr::inner_join(
-          national,
-          by = c("strategy", "fyear")
-        ) |>
-        dplyr::rename(rate = "std_rate") |>
-        dplyr::select(-"crude_rate")
+      strategy <- shiny::req(selected_strategy())
+
+      get_rates_data(
+        inputs_data()[["rates"]],
+        strategy
+      )
     })
 
     rates_trend_data <- shiny::reactive({
-      shiny::req(rates_data())
-      shiny::req(selected_provider())
-      shiny::req(selected_strategy())
+      df <- shiny::req(rates_data())
+      provider <- shiny::req(selected_provider())
 
-      rates_data() |>
-        dplyr::filter(
-          .data$provider == selected_provider(),
-          .data$strategy == selected_strategy()
-        ) |>
-        dplyr::arrange(.data$fyear)
+      get_rates_trend_data(df, provider)
     })
 
     rates_baseline_data <- shiny::reactive({
-      shiny::req(rates_data())
-      shiny::req(peers_lookup())
-      shiny::req(selected_provider())
-      shiny::req(selected_strategy())
-
-      provider_peers <- isolate_provider_peers(
-        selected_provider(),
-        peers_lookup()
+      df <- shiny::req(rates_data())
+      peers_lookup <- shiny::req(peers_lookup())
+      provider <- shiny::req(selected_provider())
+      strategy <- shiny::req(selected_strategy())
+      year <- shiny::req(selected_year())
+
+      generate_rates_baseline_data(
+        df,
+        provider,
+        peers_lookup,
+        year
       )
-      rates_data() |>
-        generate_rates_baseline_data(
-          selected_provider(),
-          provider_peers,
-          selected_strategy(),
-          selected_year()
-        )
     })
 
     rates_funnel_calculations <- shiny::reactive({
@@ -133,15 +101,9 @@ mod_plot_rates_server <- function(
     })
 
     strategy_config <- shiny::reactive({
-      shiny::req(strategies_config)
-      shiny::req(selected_strategy())
-
-      strategy_group_lookup <- strategies_config |> make_strategy_group_lookup()
-
-      strategy_group <- strategy_group_lookup |>
-        dplyr::filter(.data$strategy == selected_strategy()) |>
-        dplyr::pull("group")
+      strategy <- shiny::req(selected_strategy())
 
+      strategy_group <- strategy_group_lookup[[strategy]]
       strategies_config[[strategy_group]]
     })
 

R/mod_select_geography.R

@@ -6,28 +6,18 @@ mod_select_geography_ui <- function(id) {
   shiny::selectInput(
     ns("geography_select"),
     "Filter by geography:",
-    choices = NULL
+    choices = c(
+      "NHS provider trusts" = "nhp",
+      "Local authorities (LAs)" = "la"
+    )
   )
 }
 
 #' Select Geography Server
 #' @param id Internal parameter for `shiny`.
 #' @noRd
 mod_select_geography_server <- function(id) {
-  geographies <- c(
-    "NHS provider trusts" = "nhp",
-    "Local authorities (LAs)" = "la"
-  )
-
   shiny::moduleServer(id, function(input, output, session) {
-    shiny::observe({
-      shiny::req(geographies)
-      shiny::updateSelectInput(
-        session,
-        "geography_select",
-        choices = geographies
-      )
-    })
     shiny::reactive(input$geography_select)
   })
 }

R/mod_select_strategy.R

@@ -21,47 +21,53 @@ mod_select_strategy_ui <- function(id) {
   )
 }
 
-#' Select Strategy Server
-#' @param id Internal parameter for `shiny`.
+#' Get TPMAs for the drop down menu
+#'
+#' Reads the mitigators.json file and extracts the name and category (IP/OP/AE).
+#'
+#' @return A named list of data frames, where the names are the categories (IP/OP/AE)
 #' @noRd
-mod_select_strategy_server <- function(id) {
-  # load static data items
+mod_select_strategy_get_strategies <- function() {
   strategies <- jsonlite::read_json(
     app_sys("app", "data", "mitigators.json"),
     simplify_vector = TRUE
   )
 
+  strategies |>
+    unlist() |>
+    tibble::enframe("strategy", "name") |>
+    dplyr::mutate(
+      category = stringr::str_extract(
+        .data$name,
+        "(?<= \\()(IP|OP|AE)(?=-(AA|EF))" # e.g. 'IP' in 'IP-AA-001'
+      ) |>
+        stringr::str_to_lower()
+    ) |>
+    dplyr::nest_by(.data$category) |>
+    tibble::deframe()
+}
+
+#' Select Strategy Server
+#' @param id Internal parameter for `shiny`.
+#' @noRd
+mod_select_strategy_server <- function(id) {
+  # load static data items
+  strategies <- mod_select_strategy_get_strategies()
+
   # return the shiny module
   shiny::moduleServer(id, function(input, output, session) {
-    shiny::req(strategies)
-
-    select_category <- shiny::reactive({
+    selected_category <- shiny::reactive({
       shiny::req(input$strategy_category_select)
       input$strategy_category_select
     })
 
     shiny::observe({
-      shiny::req(select_category())
+      category <- shiny::req(selected_category())
 
-      category_strategies <- strategies |>
-        unlist() |>
-        tibble::enframe("strategy", "name") |>
-        dplyr::mutate(
-          category = stringr::str_extract(
-            .data$name,
-            "(?<= \\()(IP|OP|AE)(?=-(AA|EF))" # e.g. 'IP' in 'IP-AA-001'
-          ) |>
-            stringr::str_to_lower()
-        ) |>
-        dplyr::filter(.data$category == select_category()) |>
-        dplyr::select("strategy", "name") |>
+      strategy_choices <- strategies[[category]] |>
+        dplyr::select("name", "strategy") |>
         tibble::deframe()
 
-      strategy_choices <- purrr::set_names(
-        names(category_strategies),
-        category_strategies
-      )
-
       shiny::updateSelectInput(
         session,
         "strategy_select",