V2 release prep

.github/workflows/R-CMD-check-main.yaml

@@ -0,0 +1,46 @@
+# Run R CMD Check on PR to dev
+
+on:
+  pull_request:
+    branches:
+      - main
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Find PhantomJS path
+        id: phantomjs
+        run: |
+          echo "::set-output name=path::$(Rscript -e 'cat(shinytest:::phantom_paths()[[1]])')"
+      - name: Cache PhantomJS
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.phantomjs.outputs.path }}
+          key: ${{ matrix.config.os }}-phantomjs
+          restore-keys: ${{ matrix.config.os }}-phantomjs
+      - name: Install PhantomJS
+        shell: Rscript {0}
+        run: |
+          options(install.packages.check.source = "no")
+          if (!shinytest::dependenciesInstalled()) shinytest::installDependencies()
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

.github/workflows/R-CMD-check.yaml

@@ -38,7 +38,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
       - name: Show testthat output
         if: always()

DESCRIPTION

@@ -8,50 +8,42 @@ Authors@R: c(
 	person("Xiao","Ni", role = "aut"),
 	person("James","Buchanan", role="aut"),
 	person("Susan","Duke", role="aut"))
-Maintainer: Jeremy Wildfire <jeremy_wildfire@gmail.com>
+Maintainer: Jeremy Wildfire <jwildfire@gmail.com>
 Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
 URL: https://github.com/SafetyGraphics/safetyGraphics
 BugReports: https://github.com/SafetyGraphics/safetyGraphics/issues
 Depends: R (>= 3.5)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests:
-    fs, 
-    ggplot2,
-    knitr,
-    plotly,
-    rmarkdown,
-    markdown,
-    rstudioapi,
-    rprojroot,
-    shinydashboard,
-    shinyFiles,
-    shinytest,
-    testthat,
-    usethis
+    ggplot2 (>= 3.3.0),
+    knitr (>= 1.34),
+    rmarkdown (>= 2.10),
+    shinydashboard (>= 0.7.1),
+    shinytest (>= 1.5.0),
+    testthat (>= 3.0.4),
+    usethis (>= 2.0.1),
+    listviewer (>= 3.0.0),
+    shinybusy (>= 0.2.2),
+    shinyWidgets (>= 0.6.1)
 Imports:
-    dplyr,
-    DT,
-    datamods,
-    htmlwidgets,
-    jsonlite,
-    listviewer,
-    magrittr,
-    pharmaRTF,
-    purrr,
-    rclipboard,
-    rlang,
-    safetyData,
-    safetyCharts,
-    shiny,
-    shinyjs,
-    shinyWidgets,
-    sortable,
-    stringr,
-    yaml,
-    shinybusy
-Remotes: safetyGraphics/safetyCharts
+    dplyr (>= 1.0.0),
+    DT (>= 0.19),
+    datamods (>= 1.1.5),
+    htmlwidgets (>= 1.5.0),
+    jsonlite (>= 1.7.0),
+    magrittr (>= 2.0.0),
+    purrr (>= 0.3.0),
+    rclipboard (>= 0.1.3),
+    rlang (>= 0.4.11),
+    safetyData (>= 1.0.0),
+    safetyCharts (>= 0.2),
+    shiny (>= 1.6.0),
+    shinyjs (>= 2.0.0),
+    sortable (>= 0.4.4),
+    stringr (>= 1.4.0),
+    yaml (>= 2.2.1)
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -52,18 +52,12 @@ import(safetyData)
 import(shiny)
 import(yaml)
 importFrom(DT,renderDT)
-importFrom(listviewer,jsonedit)
-importFrom(listviewer,jsoneditOutput)
-importFrom(listviewer,renderJsonedit)
 importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(rlang,.data)
 importFrom(shiny,dataTableOutput)
 importFrom(shiny,renderDataTable)
-importFrom(shinyWidgets,progressBar)
-importFrom(shinyWidgets,updateProgressBar)
-importFrom(shinybusy,add_busy_spinner)
 importFrom(shinyjs,addClass)
 importFrom(shinyjs,delay)
 importFrom(shinyjs,disable)

NEWS.md

@@ -10,4 +10,4 @@ The first production release of safetyGraphics includes many improvements includ
 
 Initial CRAN release for safetyGraphics. The safetyGraphics package provides framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
 
-See the [GitHub release tracker](https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/releases) for additional release documentation and links to issues. 
+See the [GitHub release tracker](https://github.com/safetyGraphics/safetyGraphics/releases) for additional release documentation and links to issues. 

R/app_startup.R

@@ -8,7 +8,7 @@
 #' @param mapping list specifying the initial mapping values for each data mapping for each domain (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')). 
 #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
 #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. 
-#' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have itialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
+#' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
 #'
 #' 
 #' @return List of elements for used to initialize the shiny app with the following parameters

R/makeChartExport.R

@@ -3,7 +3,7 @@
 #' Creates R code that allows chart to be exported
 #' 
 #' @param chart chart object like the one generated by makeChartConfig().
-#' @param mapping mapping object like the one generatedf by makeMapping().
+#' @param mapping mapping object like the one generated by makeMapping().
 #' 
 #' @import purrr
 #' @importFrom yaml as.yaml

R/mod_filterTab.R

@@ -9,7 +9,13 @@
 
 filterTabUI <- function(id){  
     ns <- NS(id)
-
+    if(isNamespaceLoaded("shinyWidgets")){
+        countObj<-  shinyWidgets::progressBar(
+            id = ns("pbar"), value = 100, 
+            total = 100, display_pct = TRUE
+        )
+    }
+
     filter_ui<-list(
         h1(paste("Participant Selector")),
         span("This page dynamically filters participants across all data domains. Only the selected participants are included in charts."),
@@ -20,10 +26,7 @@ filterTabUI <- function(id){
             ),
             column(
                 width = 9,
-                progressBar(
-                    id = ns("pbar"), value = 100, 
-                    total = 100, display_pct = TRUE
-                ),
+                countObj,
                 DT::dataTableOutput(outputId = ns("table")),
                 tags$p("Code dplyr:"),
                 verbatimTextOutput(outputId = ns("code_dplyr")),
@@ -52,7 +55,6 @@ filterTabUI <- function(id){
 #' @return filtered data set
 #'
 #' @import datamods
-#' @importFrom shinyWidgets progressBar updateProgressBar
 #' @importFrom shinyjs show hide
 #' @importFrom shiny renderDataTable
 #' 
@@ -68,7 +70,6 @@ filterTab <- function(input, output, session, domainData, filterDomain, current_
         req(filterCheck())
         shinyjs::show(selector = paste0(".navbar li a[data-value=",tabID,"]"))
         shinyjs::show(selector = paste0(".navbar #population-header"))
-
         domainData[[filterDomain]]
     })
 
@@ -86,11 +87,13 @@ filterTab <- function(input, output, session, domainData, filterDomain, current_
     )  
 
     observeEvent(res_filter$filtered(), {
-        updateProgressBar(
-            session = session, 
-            id = "pbar", 
-            value = nrow(res_filter$filtered()), total = nrow(raw())
-        )
+        if(isNamespaceLoaded("shinyWidgets")){
+            shinyWidgets::updateProgressBar(
+                session = session, 
+                id = "pbar", 
+                value = nrow(res_filter$filtered()), total = nrow(raw())
+            )
+        }
 
         shinyjs::html(
             "header-count", 

R/mod_filterTabChecks.R

@@ -4,7 +4,7 @@
 #' @param filterDomain domain to use for filtering (typically "dm")
 #' @param current_mapping current data mapping (REACTIVE)
 #' 
-#' @return reactive that returns a boolean indicating whether the checks passed and filtering can be initiailized
+#' @return reactive that returns a boolean indicating whether the checks passed and filtering can be initialized
 #' 
 #' @export
 

R/mod_homeTab.R

@@ -32,16 +32,16 @@ homeTab <- function(input, output, session){
 
       <h3><i> Using the app</i></h3>
       <p>
-        Detailed instructions about using the app can be found in our <a target="_blank" href="https://cran.r-project.org/web/packages/safetyGraphics/vignettes/shinyUserGuide.html">vignette</a>.
+        Detailed instructions about using the app can be found in our <a target="_blank" href="https://github.com/SafetyGraphics/safetyGraphics/wiki/Intro">vignette</a>.
         In short, the user will initialize the app with their data, adjust settings as needed, and view the interactive charts.
         Finally, the user may export a self-contained, fully reproducible snapshot of the charts that can be easily shared with others.
       </p>
 
       <h3><i> Charts </i></h3>
       <p>
         The app is built to support a wide variety of chart types including static plots (e.g. from <a target="_blank" href="https://cran.r-project.org/web/packages/ggplot2/index.html">{ggplot2}</a>), shiny modules, <a target="_blank" href="https://cran.r-project.org/web/packages/htmlwidgets/index.html">{htmlwidgets}</a> and even static outputs like RTFs.
-        Several pre-configured charts are included in the companion <a target="_blank" href="https://www.github.com/safetyGraphics/safetyCharts">{safetyCharts}</a> R Package, and are available by default in the app.
-        Other charts can be added using the process descibed in <a target="_blank" href="https://cran.r-project.org/web/packages/safetyGraphics/vignettes/shinyUserGuide.html">this vignette</a>. 
+        Several pre-configured charts are included in the companion <a target="_blank" href="https://github.com/safetyGraphics/safetyCharts">{safetyCharts}</a> R Package, and are available by default in the app.
+        Other charts can be added using the process descibed in <a target="_blank" href="https://github.com/SafetyGraphics/safetyGraphics/wiki/ChartConfiguration">this vignette</a>. 
       </p>
 
       <p>

R/mod_safetyGraphicsUI.R

@@ -8,7 +8,6 @@
 #' @param standards a list of information regarding data standards. Each list item should use the format returned by safetyGraphics::detectStandard.
 #'
 #' @importFrom shinyjs useShinyjs
-#' @importFrom shinybusy add_busy_spinner 
 #' 
 #' @export
 
@@ -30,11 +29,16 @@ safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){
             header.append('<div id=\"population-header\" class=\"badge\" title=\"Selected Participants\" ><span id=\"header-count\"></span>/<span id=\"header-total\"></span></div>');"
         )
     )
-
+    if(isNamespaceLoaded("shinybusy")){
+        spinner<-shinybusy::add_busy_spinner(spin = "atom", position="bottom-right")
+    }else{
+        spinner<-NULL
+    }
+
     #app UI using calls to modules
     ui<-tagList(
         shinyjs::useShinyjs(),
-        add_busy_spinner(spin = "atom", position="bottom-right"),
+        spinner,
         tags$head(
             tags$style(app_css),
             tags$link(

R/mod_settingsCharts.R

@@ -2,23 +2,31 @@
 #'
 #' @param id module id
 #' 
-#' @importFrom listviewer jsoneditOutput
 #' @export
 
 settingsChartsUI <- function(id){
   ns <- NS(id)
+  if(isNamespaceLoaded("listviewer")){
+    tabs<-tabsetPanel(
+      tabPanel("List Explorer", listviewer::jsoneditOutput(ns("chartObj"), height = "800px")),
+      tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))),
+      tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) 
+    )
+  }else{
+    tabs<- tabsetPanel(
+      tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))),
+      tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) 
+    )
+  }
+
   list(
     br(),
     p(
       icon("info-circle"),
       "Full details regarding the charts are shown below. Charts specifications are saved in an R list, and can be exported for re-use on the settings/code tab. ",
       class="info"
     ),
-    tabsetPanel(
-      tabPanel("jsonedit View", listviewer::jsoneditOutput(ns("chartObj"), height = "800px") ),
-      tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))),
-      tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) 
-    )
+    tabs
   )
 }
 
@@ -29,17 +37,17 @@ settingsChartsUI <- function(id){
 #' @param session Shiny session object
 #' @param charts list data frame summarizing the charts
 #' 
-#' @importFrom listviewer renderJsonedit jsonedit 
 #' @import dplyr
 #' 
 #' @export
 
 settingsCharts <- function(input, output, session, charts){
   ns <- session$ns
-
-  output$chartObj <- listviewer::renderJsonedit({
-    listviewer::jsonedit(charts)
-  })
+  if(isNamespaceLoaded("listviewer")){
+    output$chartObj <- listviewer::renderJsonedit({
+      listviewer::jsonedit(charts)
+    })
+  }
 
   output$chartList <- renderPrint({
     print(charts)

R/prepareChart.R

@@ -1,4 +1,4 @@
-#' Prepare a chart object for safetyGraphcis
+#' Prepare a chart object for safetyGraphics
 #' 
 #' Sets default values and binds needed functions to a chart object based on chart type. 
 #' 

R/safetyGraphics.R

@@ -4,7 +4,7 @@
 #'
 #' Learn more on
 #' \href{https://CRAN.R-project.org/package=safetyGraphics}{CRAN}
-#' or \href{https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics}{GitHub}
+#' or \href{https://github.com/SafetyGraphics/safetyGraphics}{GitHub}
 #'
 #' @docType package
 #' @name SafetyGraphics

R/safetyGraphicsApp.R

@@ -6,7 +6,7 @@
 #' @param mapping list specifying the initial mapping values for each data mapping for each domain (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')). 
 #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
 #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. 
-#' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have itialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
+#' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
 #'
 #' @import shiny
 #' @import safetyData