diff --git a/.github/workflows/R-CMD-check-main.yaml b/.github/workflows/R-CMD-check-main.yaml new file mode 100644 index 00000000..9fe2e60d --- /dev/null +++ b/.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 diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index bd25402d..ca9bc8a9 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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() diff --git a/DESCRIPTION b/DESCRIPTION index d15e10ff..4e502d36 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,7 @@ Authors@R: c( person("Xiao","Ni", role = "aut"), person("James","Buchanan", role="aut"), person("Susan","Duke", role="aut")) -Maintainer: Jeremy Wildfire +Maintainer: Jeremy Wildfire 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 @@ -16,42 +16,34 @@ 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) diff --git a/NAMESPACE b/NAMESPACE index ba3befaa..6259b329 100644 --- a/NAMESPACE +++ b/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) diff --git a/NEWS.md b/NEWS.md index ab8a59dc..4a1bf14d 100644 --- a/NEWS.md +++ b/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. \ No newline at end of file +See the [GitHub release tracker](https://github.com/safetyGraphics/safetyGraphics/releases) for additional release documentation and links to issues. \ No newline at end of file diff --git a/R/app_startup.R b/R/app_startup.R index 818f1ceb..bf9f9d90 100644 --- a/R/app_startup.R +++ b/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 diff --git a/R/makeChartExport.R b/R/makeChartExport.R index a911decb..ef4f2d85 100644 --- a/R/makeChartExport.R +++ b/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 diff --git a/R/mod_filterTab.R b/R/mod_filterTab.R index aa31ad70..2cc6ec66 100644 --- a/R/mod_filterTab.R +++ b/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", diff --git a/R/mod_filterTabChecks.R b/R/mod_filterTabChecks.R index 5d93abbc..91bfd20f 100644 --- a/R/mod_filterTabChecks.R +++ b/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 diff --git a/R/mod_homeTab.R b/R/mod_homeTab.R index cea29776..06f83ede 100644 --- a/R/mod_homeTab.R +++ b/R/mod_homeTab.R @@ -32,7 +32,7 @@ homeTab <- function(input, output, session){

Using the app

- Detailed instructions about using the app can be found in our vignette. + Detailed instructions about using the app can be found in our vignette. 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.

@@ -40,8 +40,8 @@ homeTab <- function(input, output, session){

Charts

The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. - Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. - Other charts can be added using the process descibed in this vignette. + Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. + Other charts can be added using the process descibed in this vignette.

diff --git a/R/mod_safetyGraphicsUI.R b/R/mod_safetyGraphicsUI.R index db044db5..02f5dc6e 100644 --- a/R/mod_safetyGraphicsUI.R +++ b/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('

/
');" ) ) - + 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$link( diff --git a/R/mod_settingsCharts.R b/R/mod_settingsCharts.R index 2d69976d..98fafc9d 100644 --- a/R/mod_settingsCharts.R +++ b/R/mod_settingsCharts.R @@ -2,11 +2,23 @@ #' #' @param id module id #' -#' @importFrom listviewer jsoneditOutput #' @export settingsChartsUI <- function(id){ ns <- NS(id) + if(isNamespaceLoaded("listviewer")){ + tabs<-tabsetPanel( + tabPanel("List Explorer", listviewer::jsoneditOutput(ns("chartObj"), height = "800px")), + tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))), + tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) + ) + }else{ + tabs<- tabsetPanel( + tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))), + tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) + ) + } + list( br(), p( @@ -14,11 +26,7 @@ settingsChartsUI <- function(id){ "Full details regarding the charts are shown below. Charts specifications are saved in an R list, and can be exported for re-use on the settings/code tab. ", class="info" ), - tabsetPanel( - tabPanel("jsonedit View", listviewer::jsoneditOutput(ns("chartObj"), height = "800px") ), - tabPanel("Verbatim", verbatimTextOutput(ns("chartList"))), - tabPanel("YAML", verbatimTextOutput(ns("chartYAML"))) - ) + tabs ) } @@ -29,17 +37,17 @@ settingsChartsUI <- function(id){ #' @param session Shiny session object #' @param charts list data frame summarizing the charts #' -#' @importFrom listviewer renderJsonedit jsonedit #' @import dplyr #' #' @export settingsCharts <- function(input, output, session, charts){ ns <- session$ns - - output$chartObj <- listviewer::renderJsonedit({ - listviewer::jsonedit(charts) - }) + if(isNamespaceLoaded("listviewer")){ + output$chartObj <- listviewer::renderJsonedit({ + listviewer::jsonedit(charts) + }) + } output$chartList <- renderPrint({ print(charts) diff --git a/R/prepareChart.R b/R/prepareChart.R index e2bf72a0..7e795d9a 100644 --- a/R/prepareChart.R +++ b/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. #' diff --git a/R/safetyGraphics.R b/R/safetyGraphics.R index 3e2cd3e6..f4c5c122 100644 --- a/R/safetyGraphics.R +++ b/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 diff --git a/R/safetyGraphicsApp.R b/R/safetyGraphicsApp.R index 1b90206c..024e922c 100644 --- a/R/safetyGraphicsApp.R +++ b/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 diff --git a/README.md b/README.md index a62df0da..0253c04d 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ - [![R build status](https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/workflows/R-CMD-check/badge.svg)](https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/actions) + [![R build status](https://www.github.com/safetyGraphics/safetyGraphics/workflows/R-CMD-check-main/badge.svg)](https://github.com/SafetyGraphics/safetyGraphics/actions) # safetyGraphics: Clinical Trial Monitoring with R -The {safetyGraphics} package provides a framework for the evaluation of clinical trial safety data in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group. +The {safetyGraphics} package provides a framework for evaluating of clinical trial safety in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group. ![edishgif](https://user-images.githubusercontent.com/3680095/45834450-02b3a000-bcbc-11e8-8172-324c2fe43521.gif) @@ -13,15 +13,15 @@ The {safetyGraphics} package provides a framework for the evaluation of clinical A demo of the app using sample data is available [here](https://jwildfire.shinyapps.io/safetyGraphics/) or can be initialized as follows: ```r -devtools::install_github("SafetyGraphics/safetyGraphics") +install.packages("safetyGraphics") library("safetyGraphics") safetyGraphicsApp() #open the shiny application ``` The most common workflow is for a user to initialize the app with their data, adjust settings as needed, and view the interactive charts. Finally, the user can share any chart by exporting its source code or by generating a self-contained, fully reproducible report that can be shared with others. -Instructions for loading study data are provided in the introductory vignette and more complex customizations are provided in the cookbook vignette. +Instructions for loading study data are provided in the introductory vignette and more complex customizations are provided in the cookbook vignette. # Charts -The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. Other charts can be added using the process descibed in this vignette. +The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. Other charts can be added using the process descibed in this vignette. diff --git a/docs/articles/Cookbook.html b/docs/articles/Cookbook.html index 24121fd4..8c1cafed 100644 --- a/docs/articles/Cookbook.html +++ b/docs/articles/Cookbook.html @@ -88,13 +88,13 @@ -
+

Cookbook

Jeremy Wildfire

-

2021-09-02

+

2021-09-21

Source: vignettes/Cookbook.Rmd @@ -106,7 +106,7 @@

2021-09-02

Cookbook Vignette

-

This vignette contains a series of examples showing how to initialize the safetyGraphics Shiny app in different scenarios. For a general overview of the app see this vignette. For more details about adding custom charts, see this vignette.

+

This vignette contains a series of examples showing how to initialize the safetyGraphics Shiny app in different scenarios. For a general overview of the app see this vignette. For more details about adding custom charts, see this vignette.

Setup and installation

@@ -179,7 +179,7 @@

charts <- makeChartConfig() charts$ageDist<-ageDist_chart safetyGraphicsApp(charts=charts) -

For extensive details on adding and customizing different types of charts, see this vignette.

+

For extensive details on adding and customizing different types of charts, see this vignette.

diff --git a/docs/articles/Cookbook_files/header-attrs-2.11/header-attrs.js b/docs/articles/Cookbook_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/Cookbook_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/TechnicalFAQ.html b/docs/articles/TechnicalFAQ.html index b1191736..7fd91d2e 100644 --- a/docs/articles/TechnicalFAQ.html +++ b/docs/articles/TechnicalFAQ.html @@ -88,13 +88,13 @@ -
+

Technical FAQ

Jeremy Wildfire

-

2021-09-02

+

2021-09-21

Source: vignettes/TechnicalFAQ.Rmd @@ -140,15 +140,15 @@

Q: Do I have to use a certain data standard with safetyGraphics?

-

A: No. Any standard (or non-standard) data can be loaded as long as it meets the minimum data requirements for the selected data domain. Metadata capturing default CDISC standards are included with the app (see ?safetyGraphics::meta) so that data mappings can be automatically populated when AdAM and SDTM data are loaded. Other data standards require the user to manually complete the data mapping in the mapping tab - see the cookbook vignette for examples.

+

A: No. Any standard (or non-standard) data can be loaded as long as it meets the minimum data requirements for the selected data domain. Metadata capturing default CDISC standards are included with the app (see ?safetyGraphics::meta) so that data mappings can be automatically populated when AdAM and SDTM data are loaded. Other data standards require the user to manually complete the data mapping in the mapping tab - see the cookbook vignette for examples.

Q: What data sources does safetyGraphics support? How do I load custom data?

-

A: This topic is covered in detail in the Loading data section of the Introductory vignettesafetyGraphics is designed to support a flexible data pipeline that supports many data types. In short, data can be loaded using the the dataDomains parameter in the safetyGraphicsApp() function or via the safetyGraphicsInit() graphical user interface.

-

safetyGraphicsApp() - custom data can be loaded via the dataDomains parameter, which should be a list containing dataframes or tibbles for each clinical domain; that list can be populated by importing data from any number of sources including databases, sas files or any number of other sources. See the cookbook vignette for some basic examples of loading custom data.

+

A: This topic is covered in detail in the [Loading data section of the Introductory vignette]https://github.com/SafetyGraphics/safetyGraphics/wiki/Intro#loading-study-data)safetyGraphics is designed to support a flexible data pipeline that supports many data types. In short, data can be loaded using the the dataDomains parameter in the safetyGraphicsApp() function or via the safetyGraphicsInit() graphical user interface.

+

safetyGraphicsApp() - custom data can be loaded via the dataDomains parameter, which should be a list containing dataframes or tibbles for each clinical domain; that list can be populated by importing data from any number of sources including databases, sas files or any number of other sources. See the cookbook vignette for some basic examples of loading custom data.

safetyGraphicsInit() - allows users to load tabular data from a variety of sources using the point-and-click interface provided in the {datamods} package.

-

More detail is provided in the Loading data section of the Introductory vignette

+

More detail is provided in the Loading data section of the Introductory vignette

diff --git a/docs/articles/TechnicalFAQ_files/header-attrs-2.11/header-attrs.js b/docs/articles/TechnicalFAQ_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/TechnicalFAQ_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/chartConfiguration.html b/docs/articles/chartConfiguration.html index 82c5b574..6a8e07ee 100644 --- a/docs/articles/chartConfiguration.html +++ b/docs/articles/chartConfiguration.html @@ -88,13 +88,13 @@ -
+

Chart Configuration

Jeremy Wildfire

-

2021-09-02

+

2021-09-21

Source: vignettes/chartConfiguration.Rmd @@ -200,7 +200,7 @@

settings )

Running the code above should create a plot with 4 panels:

-

+

With minor modifications, this chart can be added to the {safetyGraphics} shiny app, which allows us to create the chart with any mappings/data combination loaded in the app. The spaghettiPlot() function above is already written to work with safetyGraphics, so we just need to create the chart configuration object. This time we’ll capture the configuration in a YAML file.

env: safetyGraphics
 label: Spaghetti Plot
@@ -217,7 +217,7 @@ 

 charts$spaghetti<-prepareChart(read_yaml('spaghetti.yaml'))
 safetyGraphicsApp(charts=charts)

Under the charts tab, you’ll see:

-

+

If you look closely at the spaghettiPlot() code above, you’ll noticed some details that make the chart work in the app:

  • The chart function is written as a function taking data and settings as inputs. This is the expected parameterization for most charts in {safetyGraphics}.
    • @@ -293,7 +293,7 @@

    links: safetyCharts: https://github.com/SafetyGraphics/safetycharts

    Initializing the app as usual by adding it to the chart list: charts$outlierMod<-prepareChart(read_yaml('outlierMod.yaml'))

    -

    Unselecting a few measures gives the following display:

    +

    Unselecting a few measures gives the following display:

diff --git a/docs/articles/chartConfiguration_files/header-attrs-2.11/header-attrs.js b/docs/articles/chartConfiguration_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/chartConfiguration_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/intro.html b/docs/articles/intro.html index ee4c805d..2e6fd1a4 100644 --- a/docs/articles/intro.html +++ b/docs/articles/intro.html @@ -88,13 +88,13 @@ -
+

Intro to Shiny App

Jeremy Wildfire

-

2021-09-02

+

2021-09-21

Source: vignettes/intro.Rmd @@ -138,7 +138,7 @@

Charts Tab

Clicking the Charts tab opens a dropdown menu containing a series of charts related to clinical trial safety. Clicking the Hepatic Safety Explorer opens this page:

-

safetyGraphics supports many different kinds of charts including web-based interactive graphics using {htmlwidgets} (like the chart shown above), static plots, plotly plots and custom shiny modules. Each chart has a header that provides details about the chart, links to chart-specific resources and buttons that allow users to download a stand-alone html report or a .R file that reproduces the chart. See the Chart Configuration Vignette for more detail about the safetyGraphics charting framework.

+

safetyGraphics supports many different kinds of charts including web-based interactive graphics using {htmlwidgets} (like the chart shown above), static plots, plotly plots and custom shiny modules. Each chart has a header that provides details about the chart, links to chart-specific resources and buttons that allow users to download a stand-alone html report or a .R file that reproduces the chart. See the Chart Configuration Vignette for more detail about the safetyGraphics charting framework.

@@ -164,7 +164,7 @@

The app dynamically determines which data sets are required for the selected charts and updates the “Data Loader” UI when the charts selection changes. Below, we’ve selected 2 charts from the labs domain - so the other data domains are automatically hidden.

-

Once you’ve picked charts, click the “Load” buttons in the “Data Loader” section to select data files for each domain. Data is loaded using the import functionality from the {datamods} package which allows you to select data loaded in your R session or load data files directly from your file system. datamods supports any file format that {rio} can handle including text files, Excel, SAS and SPSS format.

+

Once you’ve picked charts, click the “Load” buttons in the “Data Loader” section to select data files for each domain. Data is loaded using the import functionality from the {datamods} package which allows you to select data loaded in your R session or load data files directly from your file system. datamods supports any file format that {rio} can handle including text files, Excel, SAS and SPSS format.

Once you’ve loaded files for all of the active data domains, the “Run App” button will become active. Click it to initialize the app.

@@ -192,7 +192,7 @@

Additional Resources

-

Several additional vignettes are available for more advanced topics: - Chart Configuration Vignette - details about the charting process including technical specifications and step-by-step instructions - Cookbook Vignette - a series of examples showing how to initialize the safetyGraphics Shiny app in different scenarios - Technical FAQ Vignette Vignette - vignette discussing security, validation and other technical issues

+

Several additional vignettes are available for more advanced topics: - Chart Configuration Vignette - details about the charting process including technical specifications and step-by-step instructions - Cookbook Vignette - a series of examples showing how to initialize the safetyGraphics Shiny app in different scenarios - Technical FAQ Vignette Vignette - vignette discussing security, validation and other technical issues

The {safetyGraphics} app is maintained by the Interactive Safety Graphics (ISG) subteam of the ASA Biopharm-DIA Safety Working Group. You can learn more about the team and find links to recent presentations and publications at our home page.

diff --git a/docs/articles/intro_files/header-attrs-2.11/header-attrs.js b/docs/articles/intro_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/intro_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/index.html b/docs/index.html index 0426f362..fc480ccc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -91,29 +91,29 @@
-

R build status

+

R build status

safetyGraphics: Clinical Trial Monitoring with R

-

The {safetyGraphics} package provides a framework for the evaluation of clinical trial safety data in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group.

+

The {safetyGraphics} package provides a framework for evaluating of clinical trial safety in R using a flexible data pipeline. The package includes a shiny application that allows users to explore safety data using a series of interactive graphics, including the hepatic safety explorer shown below. The package has been developed as part of the Interactive Safety Graphics (ISG) workstream of the ASA Biopharm-DIA Safety Working Group.

edishgif

Using the app

A demo of the app using sample data is available here or can be initialized as follows:

-devtools::install_github("SafetyGraphics/safetyGraphics")
+install.packages("safetyGraphics")
 library("safetyGraphics")
 safetyGraphicsApp() #open the shiny application

The most common workflow is for a user to initialize the app with their data, adjust settings as needed, and view the interactive charts. Finally, the user can share any chart by exporting its source code or by generating a self-contained, fully reproducible report that can be shared with others.

-

Instructions for loading study data are provided in the introductory vignette and more complex customizations are provided in the cookbook vignette.

+

Instructions for loading study data are provided in the introductory vignette and more complex customizations are provided in the cookbook vignette.

Charts

-

The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. Other charts can be added using the process descibed in this vignette.

+

The app is built to support a wide variety of chart types including static plots (e.g. from {ggplot2}), shiny modules, {htmlwidgets} and even static outputs like RTFs. Several pre-configured charts are included in the companion {safetyCharts} R Package, and are available by default in the app. Other charts can be added using the process descibed in this vignette.

diff --git a/docs/news/index.html b/docs/news/index.html index 5868715f..f2600411 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -152,7 +152,7 @@

safetyGraphics v0.7.3 2019-02-04

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 for additional release documentation and links to issues.

+

See the GitHub release tracker for additional release documentation and links to issues.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 85efbfd2..888bace0 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.11.2 +pandoc: 2.11.4 pkgdown: 1.6.1 pkgdown_sha: ~ articles: @@ -6,7 +6,7 @@ articles: TechnicalFAQ: TechnicalFAQ.html chartConfiguration: chartConfiguration.html intro: intro.html -last_built: 2021-09-03T01:15Z +last_built: 2021-09-21T20:39Z urls: reference: https://pages.github.com/SafetyGraphics/safetyGraphics/reference article: https://pages.github.com/SafetyGraphics/safetyGraphics/articles diff --git a/docs/reference/SafetyGraphics.html b/docs/reference/SafetyGraphics.html index 4a6f339e..2b818675 100644 --- a/docs/reference/SafetyGraphics.html +++ b/docs/reference/SafetyGraphics.html @@ -147,7 +147,7 @@

Details

Learn more on CRAN -or GitHub

+or GitHub