161 create a study configuration vignette standalone

.Rbuildignore

@@ -8,3 +8,4 @@
 ^nepExplorer\.Rcheck$
 ^nepExplorer.*\.tar\.gz$
 ^nepExplorer.*\.tgz$
+^LICENSE\.md$

.github/workflows/test-coverage.yaml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -21,9 +21,7 @@ URL: https://github.com/SafetyGraphics/nepExplorer, https://safetygraphics.githu
 BugReports: https://github.com/SafetyGraphics/nepExplorer/issues
 Depends: R (>= 4.0)
 License: MIT + file LICENSE
-Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
 Imports:
     shiny,
     dplyr,
@@ -40,4 +38,13 @@ Imports:
     shinyWidgets
 Suggests:
     safetyGraphics, 
-    safetyData
+    safetyData,
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Config/testthat/edition: 3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2020 SafetyGraphics
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2025
+COPYRIGHT HOLDER: nepExplorer authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2025 nepExplorer authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

R/creatinine_data_fcn.R

@@ -52,17 +52,16 @@ creatinine_data_fcn <- function(df, settings) {
     left_join(baseline_creat, by = settings$id_col) %>%
     filter(.data[[settings$baseline_flag]] != settings$baseline_values)
 
-
   get_highest_stage <- function(vector_of_stages) {
-    if ("Stage 3" %in% vector_of_stages) {
-      return("Stage 3")
-    } else if ("Stage 2" %in% vector_of_stages) {
-      return("Stage 2")
-    } else if ("Stage 1" %in% vector_of_stages) {
-      return("Stage 1")
-    } else {
-      "Stage 0"
+    stages <- c("Stage 3", "Stage 2", "Stage 1", "Stage 0")
+
+    for (stage in stages) {
+      if (stage %in% vector_of_stages) {
+        return(stage)
+      }
     }
+
+    "Stage 0"
   }
 
   #get highest stage by subject
@@ -74,11 +73,8 @@ creatinine_data_fcn <- function(df, settings) {
 
     )
 
-  return(
     list(
       patient_level_stages = patient_level_stages,
       creatine_level_data = processed_creatinine_data
     )
-  )
-
 }

R/creatinine_scatter_mod.R

@@ -109,7 +109,7 @@ function(el, x) {
                               animation_time_unit = animation_time_unit()) %>% onRender(update_color_js)
     })
 
-    return(processed_creatinine_data)
+    processed_creatinine_data
 
     }
   )

R/init_nepExplorer.R

@@ -33,5 +33,5 @@ init_nepExplorer <- function(data, settings) {
                      by = c(settings[["labs"]][["id_col"]],
                             settings[["labs"]][["treatment_col"]]))
 
-  return(list(data = anly, settings = settings))
+  list(data = anly, settings = settings)
 }

R/nepexplorerMod.R

@@ -68,7 +68,7 @@ nepexplorer_ui <- function(id) {
     fluid = TRUE
   )
 
-  return(ui)
+  ui
 }