Merge pull request #631 from SafetyGraphics/dev

v2 release

.Rbuildignore

@@ -2,7 +2,6 @@
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^packrat/
 ^\.Rprofile$
 ^cran-comments.md$
@@ -14,3 +13,5 @@
 ^doc$
 ^CRAN-RELEASE$
 ^customSettings$
+^\.github$
+^LICENSE\.md$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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-main
+
+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

@@ -0,0 +1,46 @@
+# Run R CMD Check on PR to dev
+
+on:
+  pull_request:
+    branches:
+      - dev
+
+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

.gitignore

@@ -44,4 +44,5 @@ inst/eDISH_app/tests/*-current/
 customSettings/
 
 doc
-Meta
+/Meta
+/R/Old

DESCRIPTION

@@ -1,46 +1,49 @@
 Package: safetyGraphics
-Title: Create Interactive Graphics Related to Clinical Trial Safety
-Version: 1.1.0
+Title: Interactive Graphics for Monitoring Clinical Trial Safety
+Version: 2.0.0
 Authors@R: c(
-	person("Jeremy", "Wildfire", email = "jeremy_wildfire@rhoworld.com", role = c("cre","aut")),
+	person("Jeremy", "Wildfire", email = "jwildfire@gmail.com", role = c("cre","aut")),
 	person("Becca", "Krouse", role="aut"),
 	person("Preston","Burns", role="aut"),
 	person("Xiao","Ni", role = "aut"),
 	person("James","Buchanan", role="aut"),
-	person("Susan","Duke", role="aut"),
-	person("Interactive Safety Graphics Working Group", role = "aut"),
-	person("Rho Inc.", role = "cph"))
-Maintainer: Jeremy Wildfire <jeremy_wildfire@rhoworld.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.
+	person("Susan","Duke", role="aut"))
+Maintainer: Jeremy Wildfire <jwildfire@gmail.com>
+Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application. 
 URL: https://github.com/SafetyGraphics/safetyGraphics
 BugReports: https://github.com/SafetyGraphics/safetyGraphics/issues
-Depends: R (>= 3.5)
+Depends: R (>= 4.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.2
 Suggests:
-    testthat,
-    shinytest,
-    knitr,
-    ggplot2,
-    plotly
+    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,
-    htmlwidgets,
-    purrr,
-    stringr,
-    jsonlite,
-    shiny,
-    magrittr,
-    DT,
-    shinyjs,
-    rmarkdown,
-    rlang,
-    tibble,
-    utils,
-    haven,
-    shinyWidgets,
-    tidyr,
-    shinybusy
+    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)

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2018
-COPYRIGHT HOLDER: Rho Inc.
+YEAR: 2021
+COPYRIGHT HOLDER: safetyGraphics authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2021 safetyGraphics 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.

NAMESPACE

@@ -1,43 +1,80 @@
 # Generated by roxygen2: do not edit by hand
 
-export(addChart)
-export(addSetting)
-export(chartRenderer)
+export(app_startup)
+export(chartsNav)
+export(chartsTab)
+export(chartsTabUI)
 export(detectStandard)
-export(generateSettings)
-export(getRequiredSettings)
-export(getSettingsMetadata)
-export(output_chartRenderer)
-export(removeCharts)
-export(removeSettings)
-export(render_chartRenderer)
+export(evaluateStandard)
+export(filterTab)
+export(filterTabChecks)
+export(filterTabUI)
+export(generateMappingList)
+export(homeTab)
+export(homeTabUI)
+export(loadCharts)
+export(loadChartsUI)
+export(loadData)
+export(loadDataUI)
+export(makeChartConfig)
+export(makeChartExport)
+export(makeChartParams)
+export(makeChartSummary)
+export(makeMapping)
+export(mappingColumn)
+export(mappingColumnUI)
+export(mappingDomain)
+export(mappingDomainUI)
+export(mappingSelect)
+export(mappingSelectUI)
+export(mappingTab)
+export(mappingTabUI)
+export(prepareChart)
 export(safetyGraphicsApp)
-export(trimSettings)
-export(validateSettings)
-import(DT)
+export(safetyGraphicsInit)
+export(safetyGraphicsServer)
+export(safetyGraphicsUI)
+export(settingsCharts)
+export(settingsChartsUI)
+export(settingsCode)
+export(settingsCodeUI)
+export(settingsData)
+export(settingsDataUI)
+export(settingsMapping)
+export(settingsMappingUI)
+export(settingsTab)
+export(settingsTabUI)
+import(datamods)
 import(dplyr)
-import(htmlwidgets)
-import(rmarkdown)
-import(shinyjs)
-importFrom(dplyr,"filter")
-importFrom(dplyr,filter)
-importFrom(dplyr,full_join)
-importFrom(haven,read_sas)
-importFrom(magrittr,"%>%")
+import(purrr)
+import(rclipboard)
+import(safetyData)
+import(shiny)
+import(yaml)
+importFrom(DT,renderDT)
 importFrom(purrr,keep)
 importFrom(purrr,map)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_dbl)
-importFrom(purrr,map_lgl)
-importFrom(rlang,":=")
+importFrom(purrr,map2)
 importFrom(rlang,.data)
-importFrom(rlang,parse_expr)
-importFrom(shiny,runApp)
-importFrom(shiny,shinyOptions)
-importFrom(shinyWidgets,materialSwitch)
+importFrom(shiny,dataTableOutput)
+importFrom(shiny,renderDataTable)
+importFrom(shinyjs,addClass)
+importFrom(shinyjs,delay)
+importFrom(shinyjs,disable)
+importFrom(shinyjs,disabled)
+importFrom(shinyjs,enable)
+importFrom(shinyjs,hidden)
+importFrom(shinyjs,hide)
+importFrom(shinyjs,html)
+importFrom(shinyjs,removeClass)
+importFrom(shinyjs,show)
+importFrom(shinyjs,useShinyjs)
+importFrom(sortable,add_rank_list)
+importFrom(sortable,bucket_list)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_split)
-importFrom(stringr,str_subset)
-importFrom(tibble,tibble)
-importFrom(tidyr,gather)
-importFrom(utils,globalVariables)
+importFrom(stringr,str_to_title)
+importFrom(stringr,str_to_upper)
+importFrom(utils,hasName)
+importFrom(utils,zip)
+importFrom(yaml,as.yaml)

NEWS.md

@@ -1,3 +1,16 @@
+# safetyGraphics v2.0.0
+
+Version 2 of {safetyGraphics} is a major update that adds the following features: 
+
+- Added support for multiple data domains 
+- Streamlined support for multiple chart types 
+- Improved chart export and newly added full-app export
+- Single filtering module for all charts
+- New "Config" tab summarizing app configuration
+- Created new `safetyGraphicsInit()` app with a simple UI that can initialize the app with custom data/charts
+
+For more details, see the fully updated vingettes.
+
 # safetyGraphics v1.1.0
 
 Allows users to preload their own charts and data sets for use in the safetyGraphics Shiny Application. See the "Custom Workflows" Vignette for details and examples. 
@@ -10,4 +23,4 @@ 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.