From 3bd09aaf09b2a675891a16abd0260c1372282b98 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Mon, 30 Sep 2024 14:50:32 +0100
Subject: [PATCH 1/3] Update shinyDiagnostics.R

---
 R/shinyDiagnostics.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/shinyDiagnostics.R b/R/shinyDiagnostics.R
index cff1b38..5993d9a 100644
--- a/R/shinyDiagnostics.R
+++ b/R/shinyDiagnostics.R
@@ -14,6 +14,11 @@ shinyDiagnostics <- function(result,
   rlang::check_installed("omopViewer")
 
   result |>
-    omopViewer::exportStaticApp(directory = directory)
-
+    omopViewer::exportStaticApp(
+      directory = directory,
+      background = c(
+        "header" = "phenotypeR diagnostics",
+        "body" = "This Shiny App contains results generated by the (phenotypeR)[https://ohdsi.github.io/phenotypeR/] package (version {as.character(utils::packageVersion('CohortCharacteristics'))}) to support the assessment of cohorts in the OMOP CDM." |> glue::glue()
+      )
+    )
 }

From 4c340a1479c1429e5a5c4cae9eeb6683989380a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:44:03 +0100
Subject: [PATCH 2/3] add phenotypeR background

---
 R/shinyDiagnostics.R | 73 +++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 69 insertions(+), 4 deletions(-)

diff --git a/R/shinyDiagnostics.R b/R/shinyDiagnostics.R
index 5993d9a..da1ed6c 100644
--- a/R/shinyDiagnostics.R
+++ b/R/shinyDiagnostics.R
@@ -16,9 +16,74 @@ shinyDiagnostics <- function(result,
   result |>
     omopViewer::exportStaticApp(
       directory = directory,
-      background = c(
-        "header" = "phenotypeR diagnostics",
-        "body" = "This Shiny App contains results generated by the (phenotypeR)[https://ohdsi.github.io/phenotypeR/] package (version {as.character(utils::packageVersion('CohortCharacteristics'))}) to support the assessment of cohorts in the OMOP CDM." |> glue::glue()
-      )
+      background = getBackground(result)
     )
 }
+
+getBackground <- function(results) {
+
+  cohorts <- result |>
+    visOmopResults::filterSettings(table_name == "my_cohort") |>
+    dplyr::distinct(.data$group_name, .data$group_level) |>
+    visOmopResults::splitGroup()
+
+  if ("cohort_name" %in% colnames(cohorts)) {
+    cohorts <- c(
+      "title" = "**Cohorts**",
+      "body" = "The diagnostic results cover the following cohorts: {paste0(unique(cohorts$cohort_name), collapse = ', ')}" |> glue::glue()
+    )
+  } else {
+    cohorts <- character()
+  }
+
+  codelists <- result |>
+    visOmopResults::filterSettings(result_type == "cohort_code_use") |>
+    dplyr::distinct(.data$group_name, .data$group_level) |>
+    visOmopResults::splitGroup()
+
+  if ("codelist_name" %in% colnames(codelists)) {
+    codelists <- c(
+      "title" = "**Codelists**",
+      "body" = "Diagnostics have been generated for these codelists: {paste0(unique(codelists$codelist_name), collapse = ', ')}" |> glue::glue()
+    )
+  } else {
+    codelists <- character()
+  }
+
+  databases <- result |>
+    dplyr::filter(!is.na(.data$cdm_name)) |>
+    dplyr::pull("cdm_name") |>
+    unique()
+
+  if (length(databases) > 0) {
+    databases <- c(
+      "title" = "**Databases**",
+      "body" = "The results are based on data from the following databases: {paste0(databases, collapse = ', ')}" |> glue::glue()
+    )
+  } else {
+    databases <- character()
+  }
+
+  resTypes <- settings(result) |>
+    dplyr::filter(!is.na(.data$result_type)) |>
+    dplyr::pull("result_type") |>
+    unique()
+
+  if (length(resTypes) > 0) {
+    resTypes <- c(
+      "title" = "**Results**",
+      "body" = "The following results are available: {paste0(resTypes, collapse = ', ')}" |> glue::glue()
+    )
+  } else {
+    resTypes <- character()
+  }
+
+  c(
+    "header" = "phenotypeR Diagnostics",
+    cohorts,
+    codelists,
+    databases,
+    resTypes,
+    "footer" = "This Shiny App presents results generated using the [phenotypeR](https://ohdsi.github.io/phenotypeR/) package (version {as.character(utils::packageVersion('phenotypeR'))})." |> glue::glue()
+  )
+}

From d4293d42f6639895bb4f38ea4f3ac3537e180c84 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:51:12 +0100
Subject: [PATCH 3/3] notes

---
 DESCRIPTION          | 3 ++-
 R/shinyDiagnostics.R | 6 +++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b3f8298..90f4aae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -47,7 +47,8 @@ Imports:
     rlang,
     shiny,
     vctrs,
-    visOmopResults
+    visOmopResults,
+    glue
 URL: https://oxford-pharmacoepi.github.io/phenotypeR/
 VignetteBuilder: knitr
 Remotes: 
diff --git a/R/shinyDiagnostics.R b/R/shinyDiagnostics.R
index da1ed6c..c24bba9 100644
--- a/R/shinyDiagnostics.R
+++ b/R/shinyDiagnostics.R
@@ -20,10 +20,10 @@ shinyDiagnostics <- function(result,
     )
 }
 
-getBackground <- function(results) {
+getBackground <- function(result) {
 
   cohorts <- result |>
-    visOmopResults::filterSettings(table_name == "my_cohort") |>
+    visOmopResults::filterSettings(.data$table_name == "my_cohort") |>
     dplyr::distinct(.data$group_name, .data$group_level) |>
     visOmopResults::splitGroup()
 
@@ -37,7 +37,7 @@ getBackground <- function(results) {
   }
 
   codelists <- result |>
-    visOmopResults::filterSettings(result_type == "cohort_code_use") |>
+    visOmopResults::filterSettings(.data$result_type == "cohort_code_use") |>
     dplyr::distinct(.data$group_name, .data$group_level) |>
     visOmopResults::splitGroup()