From a5db26bb30998b788c7dbd1fa477aa34a5f10d18 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Tue, 14 Sep 2021 11:04:01 -0400 Subject: [PATCH 01/17] fix link --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From f5beccce3699f60bc6f3270652905b6154439c62 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Tue, 14 Sep 2021 12:04:47 -0400 Subject: [PATCH 02/17] remove safetyCharts remote. reduce vignette file sizes --- DESCRIPTION | 1 - man/meta.Rd | 2 +- vignettes/TechnicalFAQ.Rmd | 4 ++-- vignettes/chartConfiguration.Rmd | 6 +++--- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d15e10ff..153ca1cd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,6 +52,5 @@ Imports: stringr, yaml, shinybusy -Remotes: safetyGraphics/safetyCharts VignetteBuilder: knitr Roxygen: list(markdown = TRUE) diff --git a/man/meta.Rd b/man/meta.Rd index 801bfebe..d38e7f71 100644 --- a/man/meta.Rd +++ b/man/meta.Rd @@ -3,7 +3,7 @@ \docType{data} \name{meta} \alias{meta} -\title{meta} +\title{Metadata data frame containing information about the data mapping used to configure safetyGraphics charts. One record per unique data mapping} \format{ A data frame with 31 rows and 7 columns \describe{ diff --git a/vignettes/TechnicalFAQ.Rmd b/vignettes/TechnicalFAQ.Rmd index e60f0b73..f249c87a 100644 --- a/vignettes/TechnicalFAQ.Rmd +++ b/vignettes/TechnicalFAQ.Rmd @@ -1,10 +1,10 @@ --- -title: "Cookbook" +title: "Technical FAQ" author: "Jeremy Wildfire" date: "`r Sys.Date()`" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Cookbook} + %\VignetteIndexEntry{Technical FAQ} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- diff --git a/vignettes/chartConfiguration.Rmd b/vignettes/chartConfiguration.Rmd index 72aba17f..130a5c7c 100644 --- a/vignettes/chartConfiguration.Rmd +++ b/vignettes/chartConfiguration.Rmd @@ -120,7 +120,7 @@ spaghettiPlot( 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](https://yaml.org/) file. @@ -146,7 +146,7 @@ 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: @@ -240,7 +240,7 @@ 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: - + # Example 4 - htmlwidgets and init functions From a63d5c95d8881af2da73f0adf6532162747eb255 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 16 Sep 2021 16:00:31 -0400 Subject: [PATCH 03/17] fix links --- DESCRIPTION | 68 ++++++++++++------------- R/safetyGraphics.R | 2 +- README.md | 8 +-- docs/index.html | 2 +- docs/news/index.html | 2 +- docs/reference/SafetyGraphics.html | 2 +- inst/report/safetyGraphicsReport.Rmd | 2 +- man/SafetyGraphics.Rd | 2 +- tests/testthat/test_mod_filterTab.R | 4 ++ tests/testthat/test_mod_mapping.R | 2 + tests/testthat/test_mod_mappingColumn.R | 6 +++ tests/testthat/test_mod_mappingDomain.R | 4 ++ tests/testthat/test_mod_mappingSelect.R | 3 ++ vignettes/Cookbook.Rmd | 2 +- vignettes/intro.Rmd | 2 +- 15 files changed, 65 insertions(+), 46 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 153ca1cd..5e819e94 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 @@ -18,39 +18,39 @@ Encoding: UTF-8 LazyData: true RoxygenNote: 7.1.1 Suggests: - fs, - ggplot2, - knitr, - plotly, - rmarkdown, - markdown, - rstudioapi, - rprojroot, - shinydashboard, - shinyFiles, - shinytest, - testthat, - usethis + fs (>= 1.5.0), + ggplot2 (>= 3.3.5), + knitr (>= 1.34), + plotly (>= 4.9.4.1), + rmarkdown (>= 2.10), + markdown (>= 1.1), + rstudioapi (>= 0.13), + rprojroot (>= 2.0.2), + shinydashboard (>= 0.7.1), + shinyFiles (>= 0.9.0), + shinytest (>= 1.5.0), + testthat (>= 3.0.4), + usethis (>= 2.0.1) Imports: - dplyr, - DT, - datamods, - htmlwidgets, - jsonlite, - listviewer, - magrittr, - pharmaRTF, - purrr, - rclipboard, - rlang, - safetyData, - safetyCharts, - shiny, - shinyjs, - shinyWidgets, - sortable, - stringr, - yaml, - shinybusy + dplyr (>= 1.0.0), + DT (>= 0.19), + datamods (>= 1.1.5), + htmlwidgets (>= 1.5), + jsonlite (>= 1.7.2), + listviewer (>= 3.0.0), + magrittr (>= 2.0.1), + pharmaRTF (>= 0.1.3), + purrr (>= 0.3.4), + rclipboard (>= 0.1.3), + rlang (>= 0.4.11), + safetyData (>= 1.0.0), + safetyCharts (>= 0.2), + shiny (>= 1.6.0), + shinyjs (>= 2.0.0), + shinyWidgets (>= 0.6.1), + sortable (>= 0.4.4), + stringr (>= 1.4.0), + yaml (>= 2.2.1), + shinybusy (>= 0.2.2) VignetteBuilder: knitr Roxygen: list(markdown = TRUE) 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/README.md b/README.md index 923fa06e..fa93706a 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ - [![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://github.com/SafetyGraphics/safetyGraphics/workflows/R-CMD-check/badge.svg)](https://github.com/SafetyGraphics/safetyGraphics/actions) # safetyGraphics: Clinical Trial Monitoring with R @@ -13,15 +13,15 @@ The {safetyGraphics} package provides a framework for evaluating of clinical tri 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/index.html b/docs/index.html index 6f45a499..8d3c2389 100644 --- a/docs/index.html +++ b/docs/index.html @@ -91,7 +91,7 @@
-

R build status

+

R build status

safetyGraphics: Clinical Trial Monitoring with R diff --git a/docs/news/index.html b/docs/news/index.html index 5868715f..85b0b570 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/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