Release of v0.4.0

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "lsamson@gcp-service.com", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),
-    person("Aaron", "Clark", , "aclark02@arcusbio.com", role = "ctb",
+    person("Aaron", "Clark", , "aclark02@arcusbio.com", role = "aut",
            comment = c(ORCID = "0000-0002-0123-0970")),
-    person("Jeff", "Thompson", , "jthompson@arcusbio.com", role = "ctb",
+    person("Jeff", "Thompson", , "jthompson@arcusbio.com", role = "aut",
            comment = c(ORCID = "0009-0007-3640-1075")),
     person("GCP-Service International Ltd.& Co. KG", role = "fnd")
   )
@@ -49,6 +49,7 @@ Imports:
 Suggests: 
     base64enc,
     chromote,
+    jsonlite,
     kableExtra,
     knitr,
     pkgload,

NEWS.md

@@ -1,3 +1,37 @@
+# clinsight 0.4.0
+
+## Changed
+
+- Implemented a `line-clamp` on table column names that wrap to more than 6 lines (#253). 
+- Added a toggle to switch data transformation (#110, #261). 
+- Added functionality to show data transformed to standard values so that all are shown in the same unit (#110, #261).
+- Figures now also show patient-specific lab limits in the figures when data is not transformed (if available) (#249).
+- Improved the time-series on-hover label so that limits and significance are also shown (#249).
+- Added a toggle to enable/disable background patterns in figures (#249).
+- Added a toggle to enable hover labels of background patterns in the figures (#249).
+- Added additional navigation buttons next to more easily navigate between between common forms and study forms (#255).
+- Added a toggle to enable text wrapping in tables (#252). 
+- Added a toggle to show laboratory limits in the tables (#110).  
+- The timeline is now available in all forms and can be toggled on or off (#258).
+- Visually updated table and figure switches to native `bslib` switches and added icons to them (#268).
+
+## Bug fixes 
+
+- [fix_multiple_choice_vars()] now also fixes long-format multiple choice variables that end with a number (#247).
+- Added date origin to `as.Date()` in `get_timeline_data()` that Posit Connect couldn't handle without (#269).
+- Switched to server-side table downloads to ensure that always all data is included in the table (#240, #241, #250).
+- Data from before baseline events (which is counted as day zero) are now also shown in figures. Now the baseline event can for example be set on the first treatment day, and the screening data will show as a negative day in the figures (#242).
+
+## Developer notes
+
+- Updated role of long-term contributors to co-authors in Description field (#246).
+- Refactored some functions so that it is no longer needed to create an `apptables` object when starting the application, improving start up efficiency (#251).
+- Refactored function to retrieve summary data to improve efficiency (#263).
+- Replaced `dplyr::case_when()` with `ifelse()` in the row review status calculation for efficiency (#243).
+- `ClinSight` now also looks for a `clinsight-config.yml` file in the current working directory and uses it as custom configuration (#256).
+- Added better control of role privileges - `allowed_to_review` and `allowed_to_query` can now be set per role in the `config.yml` file (#17, #256).
+- Several test snapshots are now much smaller, with better focus on the feature being tested so that they are easier to maintain (#259). 
+
 # clinsight 0.3.0
 
 ## Developer notes

R/app_server.R

@@ -25,10 +25,6 @@ app_server <- function(
 
   app_data <- get_appdata(merged_data, meta = meta)
   app_vars <- get_meta_vars(data = app_data, meta = meta)
-  app_tables <- lapply(
-    setNames(names(app_data), names(app_data)), \(x){
-      create_table(app_data[[x]], expected_columns = names(app_vars$items[[x]]))
-    })
   check_appdata(app_data, meta)
 
   session$userData$pending_review_records <- reactiveValues()
@@ -45,8 +41,6 @@ app_server <- function(
   # For query item selector drop-down menus:
   available_data <- get_available_data(
     data = app_data,
-    tables = app_tables,
-    all_forms = app_vars$all_forms,
     form_repeat_name = with(
       meta[["table_names"]], 
       table_name[raw_name == "form_repeat"]
@@ -57,17 +51,25 @@ app_server <- function(
   # For summary review data:
   static_overview_data <- get_static_overview_data(
     data = app_data,
+    available_data = available_data,
     expected_general_columns = unique(
       with(meta$items_expanded, item_name[item_group == "General"])
     )
   )
+
+  # For timeline data
+  timeline_data <-get_timeline_data(
+    app_data,
+    available_data = available_data,
+    treatment_label = meta$settings$treatment_label %||% "\U1F48A T\U2093"
+  )
+
   # think of using the pool package, but functions such as row_update are not yet supported.
   r <- reactiveValues(
     review_data       = do.call(reactiveValues, split_review_data(user_db, forms = app_vars$all_forms$form)),
     query_data        = collect_query_data(user_db),
     filtered_subjects = app_vars$subject_id,
     filtered_data     = app_data,
-    filtered_tables   = app_tables,
     subject_id        = app_vars$subject_id[1]
   )
 
@@ -84,27 +86,25 @@ app_server <- function(
       user_error("No valid user name provided. ")
     } 
     if(r$user_role == ""){
-      user_error(paste0(user_error(), "No valid user role provided. "))
+      user_error(paste0(user_error(), "No user role assigned. "))
     }
     if(!is.null(user_error())){
       user_error(
         paste0(
           user_error(), 
           "Functionality is limited. ",
-          "Please contact the administrator to resolve this issue."
+          "If this is unexpected, please contact the administrator."
         )
       )
     }
   })
 
-  forms_to_review_data <- app_vars$form_level_data[c("item_group", "review_required")] 
-
   observeEvent(user_error(), {
     showNotification(
       user_error(), 
       id = "user_error", 
-      type = "error",  
-      duration = NULL
+      type = "warning",  
+      duration = 5
     )
   })
 
@@ -116,34 +116,30 @@ app_server <- function(
   observeEvent(rev_sites(), {
     req(!all(rev_sites() %in% app_vars$Sites$site_code))
     r <- filter_data(r, rev_sites(), subject_ids = app_vars$subject_id,
-                     appdata = app_data, apptables = app_tables)
+                     appdata = app_data)
   })
 
   navinfo <- reactiveValues(
     active_form       = app_vars$all_forms$form[1],
     active_tab        = "Start",
-    trigger_page_change = 1
+    trigger_page_change = 1,
+    cf_toggle_timeline = reactive({input$cf_toggle_timeline}),
+    sf_toggle_timeline = reactive({input$sf_toggle_timeline})
   )
 
+  start_page_summary_vars <- c("subject_status", "WHO.classification", "Age", "Sex", "event_name")
+  forms_to_review <- with(app_vars$form_level_data, item_group[review_required])
   rev_data <- reactiveValues(
     summary = reactive({
-      req(forms_to_review_data)
-      r$review_data |>
-        reactiveValuesToList() |> 
-        do.call(what = rbind) |> 
-        dplyr::left_join(forms_to_review_data, by = "item_group") |> 
-        dplyr::filter(
-          reviewed != "Yes",
-          review_required,
-          subject_id %in% r$filtered_subjects
-        ) |>
-        summarize_review_data() |>
-        dplyr::select(subject_id, "Form" = item_group, "Event" = event_name,
-                      "Edit date" = edit_date_time, status, reviewed)
+      req(forms_to_review)
+      reactiveValuesToList(r$review_data)[forms_to_review] |> 
+        dplyr::bind_rows() |> 
+        subset(reviewed != "Yes" & subject_id %in% r$filtered_subjects) |> 
+        summarize_review_data()
     }),
     overview = reactive({
-      static_overview_data |>
-        dplyr::filter(subject_id %in% r$filtered_subjects) |>
+      with(static_overview_data, static_overview_data[subject_id %in% r$filtered_subjects, ]) |>
+        dplyr::select(tidyr::all_of("subject_id"), tidyr::any_of(start_page_summary_vars)) |> 
         dplyr::mutate(
           needs_review = subject_id %in% unique(rev_data$summary()$subject_id)
         ) |> 
@@ -206,14 +202,6 @@ app_server <- function(
     identical(session$userData$review_type(), "form")
   })
   outputOptions(output, "form_level_review", suspendWhenHidden = FALSE)
-
-  timeline_data <- reactive({
-    get_timeline_data(
-      r$filtered_data, 
-      r$filtered_tables, 
-      treatment_label = meta$settings$treatment_label %||% "\U1F48A T\U2093"
-    )
-  })
 
   ###### Load common form tabs in UI and server:
   common_forms <- with(app_vars$all_forms, form[main_tab == "Common events"])
@@ -224,6 +212,10 @@ app_server <- function(
       select = (i == common_forms[1])
     )
   })
+  bslib::nav_insert(
+    id = "common_data_tabs", 
+    nav = bslib::nav_item(actionLink("go_to_study_data", ">", class="nav-link px-3"))
+  )
   lapply(common_forms, \(x){
     mod_common_forms_server(
       id = paste0("cf_", simplify_string(x)), 
@@ -232,14 +224,17 @@ app_server <- function(
       form_review_data = reactive(r$review_data[[x]]), 
       form_items = app_vars$items[[x]], 
       active_subject = reactive(r$subject_id),
-      table_names = app_vars$table_names, 
-      timeline_data = timeline_data
+      table_names = app_vars$table_names
     ) 
   }) |>
     unlist(recursive = FALSE)
 
   ###### Load study form tabs in UI and server:
   study_forms <- with(app_vars$all_forms, form[main_tab == "Study data"])
+  bslib::nav_insert(
+    id = "study_data_tabs", 
+    nav = bslib::nav_item(actionLink("go_to_common_events", "<", class="nav-link px-3"))
+  )
   lapply(study_forms, \(i){
     bslib::nav_insert(
       id = "study_data_tabs",
@@ -248,6 +243,7 @@ app_server <- function(
       select = (i == study_forms[1])
     )
   })
+
   lapply(study_forms, \(x){
     mod_study_forms_server(
       id = paste0("sf_", simplify_string(x)), 
@@ -262,16 +258,59 @@ app_server <- function(
   }) |>
     unlist(recursive = FALSE)
 
+  bslib::nav_insert(
+    id = "common_data_tabs",
+    bslib::nav_item(
+      class = "ms-auto mb-0",
+      bslib::input_switch(
+        id = "cf_toggle_timeline",
+        label = span(icon("timeline"), "Timeline"),
+        value = TRUE,
+        width = "auto"
+      ) |> 
+        htmltools::tagAppendAttributes(class = "mb-0")
+    )
+  )
+
+  bslib::nav_insert(
+    id = "study_data_tabs",
+    bslib::nav_item(
+      class = "ms-auto",
+      bslib::input_switch(
+        id = "sf_toggle_timeline",
+        label = span(icon("timeline"), "Timeline"),
+        value = FALSE,
+        width = "auto"
+      ) |> 
+        htmltools::tagAppendAttributes(class = "mb-0")
+    )
+  )
+
+  observeEvent(session$userData$review_type(), {
+    subject_level_review <- identical(session$userData$review_type(), "subject")
+    shinyjs::toggleElement("cf_toggle_timeline", subject_level_review)
+    shinyjs::toggleElement("sf_toggle_timeline", subject_level_review)
+  })
+
+
+  observeEvent(input$go_to_study_data, {
+    bslib::nav_select(id = "main_tabs", selected = "Study data")
+  })
+  observeEvent(input$go_to_common_events, {
+    bslib::nav_select(id = "main_tabs", selected = "Common events")
+  })
+
   mod_start_page_server("start_page_1", r, rev_data, navinfo, app_vars$all_forms,
                         app_vars$table_names)
   mod_header_widgets_server(
     id = "header_widgets_1", 
     r = r, 
     rev_data = rev_data, 
-    navinfo = navinfo
+    navinfo = navinfo,
+    timeline_data = timeline_data,
+    available_data = available_data
   )
 
-
   # Only initiate the sidebar after successful login, because it contains a
   # modal that pops up if data is out of synch. Modals interfere with shinymanager.
   observeEvent(r$user_name, {
@@ -298,26 +337,16 @@ app_server <- function(
       id = "main_sidebar_1",
       r = r,
       app_data = app_data,
-      app_tables = app_tables,
       app_vars = app_vars,
       navinfo,
       forms_to_review = reactive({
-        with(rev_data$summary(), Form[subject_id == r$subject_id])
+        with(rev_data$summary(), item_group[subject_id == r$subject_id])
       }),
       db_path = user_db,
       available_data = available_data
     )
   })
 
-  mod_review_config_server(
-    "review_config_1",
-    r = r,
-    app_data = app_data,
-    app_tables = app_tables,
-    sites = app_vars$Sites,
-    subject_ids = app_vars$subject_id
-  )
-
   mod_queries_server(
     "queries_1",
     r = r,
@@ -329,7 +358,11 @@ app_server <- function(
   mod_report_server("report_1", r = r, rev_data, db_path = user_db,
                     table_names = app_vars$table_names)
 
-  mod_navigate_participants_server("navigate_participants_1", r)
+  mod_navigate_participants_server(
+    "navigate_participants_1", 
+    r,
+    static_overview_data
+  )
 
   mod_navigate_review_server(
     "navigate_review_1",

R/app_ui.R

@@ -37,7 +37,7 @@ app_ui <- function(request){
       ),
       bslib::nav_panel(
         title = "Common events",
-        bslib::navset_tab(id = "common_data_tabs") 
+        bslib::navset_tab(id = "common_data_tabs")
       ),
       bslib::nav_panel(
         "Study data",