YEAR: 2021 +YEAR: 2022 COPYRIGHT HOLDER: safetyGraphics authors@@ -90,7 +90,7 @@License
diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 45f5f258..24d09f86 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ @@ -72,8 +72,7 @@MIT License
- -diff --git a/docs/articles/ChartConfiguration.html b/docs/articles/ChartConfiguration.html index 39b5bc02..e20da912 100644 --- a/docs/articles/ChartConfiguration.html +++ b/docs/articles/ChartConfiguration.html @@ -33,7 +33,7 @@ @@ -96,7 +96,7 @@Copyright (c) 2021 safetyGraphics authors
+Copyright (c) 2021-2023 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.
@@ -94,7 +93,7 @@MIT License
Chart Configuration
Jeremy Wildfire
-2022-04-08
+2022-12-14
Source:vignettes/ChartConfiguration.Rmd@@ -506,7 +506,7 @@ChartConfiguration.RmdDefault Technical workflow -
Site built with pkgdown 2.0.2.
+Site built with pkgdown 2.0.6.
diff --git a/docs/articles/Cookbook.html b/docs/articles/Cookbook.html index c6258a2b..4340e0e0 100644 --- a/docs/articles/Cookbook.html +++ b/docs/articles/Cookbook.html @@ -33,7 +33,7 @@ @@ -96,7 +96,7 @@Cookbook
Jeremy Wildfire
-2022-04-08
+2022-12-14
Source:vignettes/Cookbook.Rmd@@ -213,7 +213,7 @@Cookbook.RmdCustom ChartsExample 7 - Drop Unwanted Charts
Users can also generate a list of charts and then drop charts that they don’t want to include. For example, if you wanted to drop charts with
-typeof “htmlwidgets” you could run this code.library(purrr) +@@ -375,7 +375,7 @@library(purrr) charts <- makeChartConfig() #gets charts from safetyCharts pacakge by default notWidgets <- charts %>% purrr::keep(~.x$type != "htmlwidget") safetyGraphicsApp(charts=notWidgets)Example 13 - Create an ECG diff --git a/docs/articles/Intro.html b/docs/articles/Intro.html index df464181..b7318e91 100644 --- a/docs/articles/Intro.html +++ b/docs/articles/Intro.html @@ -33,7 +33,7 @@ @@ -96,7 +96,7 @@
Intro to Shiny App
Jeremy Wildfire
-2022-04-08
+2022-12-14
Source:vignettes/Intro.Rmd@@ -263,7 +263,7 @@Intro.RmdAppendix 2 - Minimum Data Requir diff --git a/docs/articles/TechnicalFAQ.html b/docs/articles/TechnicalFAQ.html index 881e5c95..7220fa0c 100644 --- a/docs/articles/TechnicalFAQ.html +++ b/docs/articles/TechnicalFAQ.html @@ -33,7 +33,7 @@ @@ -96,7 +96,7 @@
Technical FAQ
Jeremy Wildfire
-2022-04-08
+2022-12-14
Source:vignettes/TechnicalFAQ.Rmd@@ -200,16 +200,16 @@TechnicalFAQ.RmdQ: How can the safetyGraphic
Q: Do you recommend deploying the app to a dedicated server for internal usage?
-A: It depends a bit on your use-case and how the app is hosted. For example, analysts using the data in an exploratory fashion can probably just run it from RStudio, but if multiple medical monitors using the app for medical monitoring in active studies probably need a more robust (and possibly validated) set up using Shiny Server, RStudio Connect or something similar.
+A: It depends a bit on your use-case and how the app is hosted. For example, analysts using the data in an exploratory fashion can probably just run it from RStudio, but if multiple medical monitors using the app for medical monitoring in active studies probably need a more robust (and possibly validated) set up using Shiny Server, RStudio Connect or something similar.
Q: Can I deploy
-safetyGraphicsto shinyapps.io to explore trial data from my organization?A: We advise against loading non-authorized, private, or non-deidentified patient data outside of your organization’s firewall. Consult with your IT and QA first. There is huge risk associated with confidentiality, IP, and patient privacy. Also refer to ShinyApps.io Chapter 8 Security and Compliance.
+A: We advise against loading non-authorized, private, or non-deidentified patient data outside of your organization’s firewall. Consult with your IT and QA first. There is huge risk associated with confidentiality, IP, and patient privacy. Also refer to ShinyApps.io Chapter 8 Security and Compliance.
diff --git a/docs/articles/index.html b/docs/articles/index.html index 43fa36e1..b2873dc0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ @@ -93,7 +93,7 @@-Q: Can I deploy
safetyGraphicsto an internal RStudio Connect server? +Q: Can I deploysafetyGraphicsto an internal RStudio Connect server?A: Yes. The script below should be easy to deploy via the RStudio interface or by running
rsconnect::deployApp()and can easily be customized to support custom data and charts.# Launch the ShinyApp (Do not remove this comment) @@ -245,7 +245,7 @@-
Site built with pkgdown 2.0.2.
+Site built with pkgdown 2.0.6.
All vignettes
diff --git a/docs/authors.html b/docs/authors.html index a04e7640..22263d65 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ @@ -108,13 +108,13 @@Citation
Wildfire J, Krouse B, Burns P, Ni X, Buchanan J, Duke S (2022). safetyGraphics: Interactive Graphics for Monitoring Clinical Trial Safety. -R package version 2.1.0, https://github.com/SafetyGraphics/safetyGraphics. +R package version 2.1.1, https://github.com/SafetyGraphics/safetyGraphics.
@Manual{, title = {safetyGraphics: Interactive Graphics for Monitoring Clinical Trial Safety}, author = {Jeremy Wildfire and Becca Krouse and Preston Burns and Xiao Ni and James Buchanan and Susan Duke}, year = {2022}, - note = {R package version 2.1.0}, + note = {R package version 2.1.1}, url = {https://github.com/SafetyGraphics/safetyGraphics}, }@@ -129,7 +129,7 @@Citation
diff --git a/docs/index.html b/docs/index.html index 99eb9706..08e33b9b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ @@ -172,7 +172,7 @@Developers
diff --git a/docs/news/index.html b/docs/news/index.html index cc8e0cd7..c1fda958 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -73,7 +73,11 @@Changelog
-+safetyGraphics v2.1.0
+safetyGraphics v2.1.1
+Resolves a bug that was causing unexpected data filters on initial load.
++diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 95a887a3..1436e593 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,12 +1,12 @@ pandoc: 2.11.4 -pkgdown: 2.0.2 +pkgdown: 2.0.6 pkgdown_sha: ~ articles: ChartConfiguration: ChartConfiguration.html Cookbook: Cookbook.html Intro: Intro.html TechnicalFAQ: TechnicalFAQ.html -last_built: 2022-04-08T09:33Z +last_built: 2022-12-14T21:21Z urls: reference: https://safetygraphics.github.io/safetyGraphics/reference article: https://safetygraphics.github.io/safetyGraphics/articles diff --git a/docs/reference/SafetyGraphics.html b/docs/reference/SafetyGraphics.html index 9cef77b4..94ae2606 100644 --- a/docs/reference/SafetyGraphics.html +++ b/docs/reference/SafetyGraphics.html @@ -17,7 +17,7 @@ @@ -97,7 +97,7 @@safetyGraphics v2.1.02022-04-08
This release focuses on updates the safetyGraphics metadata framework:
- The default metadata table has been migrated to safetyCharts and modularized. In short,
safetyGraphics::metais now saved assafetyCharts::meta_aes,safetyCharts::meta_labsandsafetyCharts::meta_dm.- A new
@@ -116,7 +120,7 @@makeMetafunction has been created and integrated in to the default workflow for the Shiny app.makeMetaprovides a much more flexible framework for creating and storing metadata. See?makeMetaand the Cookbook and Chart Configuration vignettes for more details.safetyGra
Details
diff --git a/docs/reference/app_startup.html b/docs/reference/app_startup.html index 36dcea48..d693dd8b 100644 --- a/docs/reference/app_startup.html +++ b/docs/reference/app_startup.html @@ -17,7 +17,7 @@ @@ -93,22 +93,37 @@Startup code for shiny app
Arguments
- domainData
- + +
named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
- meta
- + +
data frame containing the metadata for use in the app. If no metadata is provided (default value is NULL), metatdata is generated by
makeMeta().- charts
- + +
list of charts in the format produced by safetyGraphics::makeChartConfig()
- 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')).
- autoMapping
- + +
boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the
mappingparameter overwrite automatically generated mappings when both are found. Defaults to true.- 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.- 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.
diff --git a/docs/reference/chartsNav.html b/docs/reference/chartsNav.html index 5cde768e..e9c1b961 100644 --- a/docs/reference/chartsNav.html +++ b/docs/reference/chartsNav.html @@ -17,7 +17,7 @@ @@ -85,8 +85,11 @@Value
-List of elements for used to initialize the shiny app with the following parameters
- + + +
"meta" List of configuration metadata
List of elements for used to initialize the shiny app with the following parameters
"meta" List of configuration metadata
"charts" List of charts
"domainData" List of domain level data sets
- @@ -127,7 +142,7 @@
"mapping" Initial Data Mapping
Value
Adds a navbar tab that initializes the Chart Module UI
Arguments
@@ -101,7 +104,7 @@
- chart
- + +
chart metadata
- ns
- +
namespace
Arguments
diff --git a/docs/reference/chartsTab.html b/docs/reference/chartsTab.html index f2e85631..3b71ed1d 100644 --- a/docs/reference/chartsTab.html +++ b/docs/reference/chartsTab.html @@ -17,7 +17,7 @@ @@ -85,16 +85,27 @@Server for chart module, designed to be re-used for each chart generated.Arguments
@@ -109,7 +120,7 @@
- input
- + +
Input objects from module namespace
- output
- + +
Output objects from module namespace
- session
- + +
An environment that can be used to access information and functionality relating to the session
- chart
- + +
list containing a safetyGraphics chart object like those returned by makeChartConfig.
- data
- + +
named list of current data sets (Reactive).
- mapping
- +
tibble capturing the current data mappings (Reactive).
Arguments
diff --git a/docs/reference/chartsTabUI.html b/docs/reference/chartsTabUI.html index 3419e23c..b9bf3bdd 100644 --- a/docs/reference/chartsTabUI.html +++ b/docs/reference/chartsTabUI.html @@ -17,7 +17,7 @@ @@ -85,8 +85,11 @@UI for chart module, designed to be re-used for each chart generated.
Arguments
@@ -101,7 +104,7 @@
- id
- + +
module id
- chart
- +
list containing chart specifications like those returned by makeChartConfig.
Arguments
diff --git a/docs/reference/detectStandard.html b/docs/reference/detectStandard.html index fcfe1e30..cefeb60a 100644 --- a/docs/reference/detectStandard.html +++ b/docs/reference/detectStandard.html @@ -17,7 +17,7 @@ @@ -85,14 +85,21 @@Detect the data standard used for a data set
Arguments
- data
- + +
A data frame in which to detect the data standard - required.
- domain
- + +
the domain to evaluate - should match a value of
meta$domain. Uses the first value inmeta$domainif no value is provided.- meta
- +
the metadata containing the data standards.
Value
-A data frame describing the detected standard for each
+ + +"text_key"in the provided metadata. Columns are"domain","text_key","column"and"standard".A data frame describing the detected standard for each
"text_key"in the provided metadata. Columns are"domain","text_key","column"and"standard".diff --git a/docs/reference/evaluateStandard.html b/docs/reference/evaluateStandard.html index 03daed4c..be2bea98 100644 --- a/docs/reference/evaluateStandard.html +++ b/docs/reference/evaluateStandard.html @@ -17,7 +17,7 @@ @@ -85,16 +85,25 @@Details
@@ -323,7 +330,7 @@Examples
Evaluate a data set against a data standard
Arguments
- data
- + +
A data frame in which to detect the data standard
- meta
- + +
the metadata containing the data standards.
- domain
- + +
the domain to evaluate - should match a value of
meta$domain- standard
- +
standard to evaluate
Value
-a list describing to what degree the data set matches the data standard. The "match" property describes compliance with the standard as "full", "partial" or "none". The "checks" property is a list of the data elements expected for the standard and whether they are "valid" in the given data set. "total_checks", "valid_checks" and "invalid_checks" provide counts of the specified checks. "match_percent" is calculated as valid_checks/total_checks. "mapping" is a data frame describing the detected standard for each
+ + +"text_key"in the provided metadata. Columns are"text_key","current"containing the name of the matched column or field value in the data and"match"a boolean indicating whether the data matches the standard.a list describing to what degree the data set matches the data standard. The "match" property describes compliance with the standard as "full", "partial" or "none". The "checks" property is a list of the data elements expected for the standard and whether they are "valid" in the given data set. "total_checks", "valid_checks" and "invalid_checks" provide counts of the specified checks. "match_percent" is calculated as valid_checks/total_checks. "mapping" is a data frame describing the detected standard for each
"text_key"in the provided metadata. Columns are"text_key","current"containing the name of the matched column or field value in the data and"match"a boolean indicating whether the data matches the standard.@@ -203,7 +212,7 @@diff --git a/docs/reference/filterTab.html b/docs/reference/filterTab.html index 73b1e3a9..f6f40b00 100644 --- a/docs/reference/filterTab.html +++ b/docs/reference/filterTab.html @@ -17,7 +17,7 @@ @@ -94,24 +94,41 @@Examples
Server for the filter module in datamods::filter_data_ui
Arguments
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- domainData
- + +
list of data files for each domain
- filterDomain
- + +
domain to use for filtering (typically "dm")
- current_mapping
- + +
current data mapping
- tabID
- + +
ID for the tab containing the filter UI (used for testing)
- filterVars
- +
Variables to use for filtering (used for testing)
@@ -126,7 +143,7 @@Value
-filtered data set
+ + +filtered data set
Value
diff --git a/docs/reference/filterTabChecks.html b/docs/reference/filterTabChecks.html index 1e52da30..06fe6a5f 100644 --- a/docs/reference/filterTabChecks.html +++ b/docs/reference/filterTabChecks.html @@ -17,7 +17,7 @@ @@ -85,14 +85,21 @@Checks for whether the current data and settings support a filter tab
Arguments
- domainData
- + +
list of data files for each domain
- filterDomain
- + +
domain to use for filtering (typically "dm")
- current_mapping
- +
current data mapping (REACTIVE)
@@ -107,7 +114,7 @@Value
-reactive that returns a boolean indicating whether the checks passed and filtering can be initialized
+ + +reactive that returns a boolean indicating whether the checks passed and filtering can be initialized
Value
diff --git a/docs/reference/filterTabUI.html b/docs/reference/filterTabUI.html index 37897f34..27576248 100644 --- a/docs/reference/filterTabUI.html +++ b/docs/reference/filterTabUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for the filter module in datamods::filter_data_ui
Arguments
@@ -99,7 +100,7 @@
- id
- +
module id
Arguments
diff --git a/docs/reference/generateMappingList.html b/docs/reference/generateMappingList.html index 018252f7..09dbc66e 100644 --- a/docs/reference/generateMappingList.html +++ b/docs/reference/generateMappingList.html @@ -17,7 +17,7 @@ @@ -85,10 +85,15 @@Convert mapping data.frame to a list
Arguments
@@ -103,7 +108,7 @@
- settingsDF
- + +
data frame containing current mapping
- domain
- + +
mapping domain to return (returns all domains as a named list by default)
- pull
- +
call pull() the value for each parameter - needed for testing only. default: FALSE
Arguments
diff --git a/docs/reference/hasColumn.html b/docs/reference/hasColumn.html index 9ca6b751..d79af87d 100644 --- a/docs/reference/hasColumn.html +++ b/docs/reference/hasColumn.html @@ -17,7 +17,7 @@ @@ -85,12 +85,17 @@Check whether a column is found in a data set
Arguments
- columnName
- + +
The column to look for.
- data
- +
the data.frame to search.
Value
-logical scalar. TRUE if the column is found. FALSE otherwise
+ + +logical scalar. TRUE if the column is found. FALSE otherwise
@@ -114,7 +119,7 @@diff --git a/docs/reference/hasField.html b/docs/reference/hasField.html index 5d084e10..8e5adab0 100644 --- a/docs/reference/hasField.html +++ b/docs/reference/hasField.html @@ -17,7 +17,7 @@ @@ -85,14 +85,21 @@Examples
Check whether a specified field value is found in a data set
Arguments
- fieldValue
- + +
A value to check for.
- columnName
- + +
The column to check.
- data
- +
the data.frame to search.
Value
-logical scalar. TRUE if field_value is found. FALSE otherwise
+ + +logical scalar. TRUE if field_value is found. FALSE otherwise
@@ -127,7 +134,7 @@diff --git a/docs/reference/homeTab.html b/docs/reference/homeTab.html index a27a0e9e..41a4c63f 100644 --- a/docs/reference/homeTab.html +++ b/docs/reference/homeTab.html @@ -17,7 +17,7 @@ @@ -85,10 +85,15 @@Examples
Server for the filter module in datamods::filter_data_ui
Arguments
@@ -103,7 +108,7 @@
- input
- + +
mod input
- output
- + +
mod output
- session
- +
mod session
Arguments
diff --git a/docs/reference/homeTabUI.html b/docs/reference/homeTabUI.html index 2c80837f..dc4a6204 100644 --- a/docs/reference/homeTabUI.html +++ b/docs/reference/homeTabUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for the home module
Arguments
@@ -99,7 +100,7 @@
- id
- +
module id
Arguments
diff --git a/docs/reference/index.html b/docs/reference/index.html index ac1e2a10..a909f937 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ @@ -276,7 +276,7 @@Helper Functions -
Site built with pkgdown 2.0.2.
+Site built with pkgdown 2.0.6.
diff --git a/docs/reference/loadCharts.html b/docs/reference/loadCharts.html index 9d29e774..bb4c274f 100644 --- a/docs/reference/loadCharts.html +++ b/docs/reference/loadCharts.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@Server for the chart loading module used in safetyGraphicsInit()
Arguments
@@ -105,7 +112,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- charts
- +
list containing chart specifications like those returned by makeChartConfig.
Arguments
diff --git a/docs/reference/loadChartsUI.html b/docs/reference/loadChartsUI.html index d7cc4b6e..e772b925 100644 --- a/docs/reference/loadChartsUI.html +++ b/docs/reference/loadChartsUI.html @@ -17,7 +17,7 @@ @@ -85,8 +85,11 @@UI for the chart loading module used in safetyGraphicsInit()
Arguments
@@ -101,7 +104,7 @@
- id
- + +
module id
- charts
- +
list containing chart specifications like those returned by makeChartConfig.
Arguments
diff --git a/docs/reference/loadData.html b/docs/reference/loadData.html index c0df5d66..cd97207f 100644 --- a/docs/reference/loadData.html +++ b/docs/reference/loadData.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@Server for the data loading module used in safetyGraphicsInit()
Arguments
@@ -105,7 +112,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- domain
- +
data domain to be loaded
Arguments
diff --git a/docs/reference/loadDataUI.html b/docs/reference/loadDataUI.html index a41acc85..c6beb61b 100644 --- a/docs/reference/loadDataUI.html +++ b/docs/reference/loadDataUI.html @@ -17,7 +17,7 @@ @@ -85,8 +85,11 @@UI for the data loading module used in safetyGraphicsInit()
Arguments
@@ -101,7 +104,7 @@
- id
- + +
module id
- domain
- +
character vector with domains to be loaded
Arguments
diff --git a/docs/reference/makeChartConfig.html b/docs/reference/makeChartConfig.html index 9ba48a52..c0720bb5 100644 --- a/docs/reference/makeChartConfig.html +++ b/docs/reference/makeChartConfig.html @@ -17,7 +17,7 @@ @@ -90,16 +90,25 @@Make Chart Config
Arguments
- dirs
- + +
path to one or more directories containing yaml config files (relative to working directory)
- packages
- + +
installed packages names containing yaml config files in the /inst/packageLocation folder
- packageLocation
- + +
inst folder where yaml config files (and possibly R functions referenced in yaml workflow) are located in
packages- sourceFiles
- +
boolean indicating whether to source all R files found in dirs.
diff --git a/docs/reference/makeChartExport.html b/docs/reference/makeChartExport.html index 410e4d61..55337e41 100644 --- a/docs/reference/makeChartExport.html +++ b/docs/reference/makeChartExport.html @@ -17,7 +17,7 @@ @@ -85,12 +85,17 @@Value
-returns a named list of charts derived from YAML files. Each element of the list contains information about a single chart, and has the following parameters:
- + + +
"env" Environment for the chart. Must be set to "safetyGraphics" or the chart is dropped.
returns a named list of charts derived from YAML files. Each element of the list contains information about a single chart, and has the following parameters:
"env" Environment for the chart. Must be set to "safetyGraphics" or the chart is dropped.
"name" Name of the chart. Also the name of the element in the list - e.g. charts$aeExplorer$name is "aeExplorer"
"label" Short description of the chart
- @@ -125,7 +134,7 @@
"type" Type of chart; options are: 'htmlwidget', 'module', 'plot', 'table', 'html' or 'plotly'.
Value
Make Chart Export
Arguments
- chart
- + +
chart object like the one generated by makeChartConfig().
- mapping
- +
mapping object like the one generated by makeMapping().
@@ -105,7 +110,7 @@Value
-returns a character vector that can be saved as R code.
+ + +returns a character vector that can be saved as R code.
Value
diff --git a/docs/reference/makeChartParams.html b/docs/reference/makeChartParams.html index cf4383a6..56a1703b 100644 --- a/docs/reference/makeChartParams.html +++ b/docs/reference/makeChartParams.html @@ -17,7 +17,7 @@ @@ -85,10 +85,15 @@Make Chart Parameters
Arguments
@@ -103,7 +108,7 @@
- data
- + +
list of domain-level data
- chart
- + +
list containing chart specifications
- mapping
- +
data frame with current mapping
Arguments
diff --git a/docs/reference/makeChartSummary.html b/docs/reference/makeChartSummary.html index 3380b78c..82daffb0 100644 --- a/docs/reference/makeChartSummary.html +++ b/docs/reference/makeChartSummary.html @@ -17,7 +17,7 @@ @@ -85,10 +85,15 @@html chart summary
Arguments
@@ -103,7 +108,7 @@
- chart
- + +
list containing chart specifications
- showLinks
- + +
boolean indicating whether to include links
- class
- +
character to include as class
Arguments
diff --git a/docs/reference/makeMapping.html b/docs/reference/makeMapping.html index 223b14a4..5a81014b 100644 --- a/docs/reference/makeMapping.html +++ b/docs/reference/makeMapping.html @@ -17,7 +17,7 @@ @@ -85,16 +85,25 @@Create data mapping based on data standards and user input
Arguments
- domainData
- + +
named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
- meta
- + +
data frame containing the metadata for use in the app.
- autoMapping
- + +
boolean indicating whether the app should use
safetyGraphics::detectStandard()to detect data standards and automatically generate mappings for the data provided. Values specified in thecustomMappingparameter overwrite auto-generated mappings when both are found. Defaults to true.- customMapping
- +
optional list specifying initial mapping values within each data mapping (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')).
@@ -110,7 +119,7 @@Value
-List containing data standard information and mapping
- + + +
"mapping" Initial Data Mapping
List containing data standard information and mapping
"mapping" Initial Data Mapping
"standards" List of domain level data standards (or NULL if autoMapping is false)
Value
diff --git a/docs/reference/makeMeta.html b/docs/reference/makeMeta.html index f1295474..065b321f 100644 --- a/docs/reference/makeMeta.html +++ b/docs/reference/makeMeta.html @@ -23,7 +23,7 @@ @@ -94,10 +94,13 @@Create a metadata object table for a set of charts
Arguments
- charts
- +
list of safetyGraphics chart objects for which to create metadata
diff --git a/docs/reference/mappingColumn.html b/docs/reference/mappingColumn.html index f162b3fb..00764545 100644 --- a/docs/reference/mappingColumn.html +++ b/docs/reference/mappingColumn.html @@ -17,7 +17,7 @@ @@ -85,18 +85,29 @@Value
-tibble of metadata with the following columns:
- domain
+ + +tibble of metadata with the following columns:
- domain
Data domain
- text_key
@@ -142,7 +145,7 @@Value
Server that facilitates the mapping of a column data (and any associated fie
Arguments
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- meta
- + +
metadata data frame for the object
- data
- +
current data file for the domain
@@ -111,7 +122,7 @@Value
-A reactive data.frame providing the current value for text_key associated with the selected column
+ + +A reactive data.frame providing the current value for text_key associated with the selected column
Value
diff --git a/docs/reference/mappingColumnUI.html b/docs/reference/mappingColumnUI.html index 8a75157c..1c348a0e 100644 --- a/docs/reference/mappingColumnUI.html +++ b/docs/reference/mappingColumnUI.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@UI that facilitates the mapping of a column data (and any associated fields)
Arguments
@@ -105,7 +112,7 @@
- id
- + +
module id
- meta
- + +
metadata for the column (and related fields)
- data
- + +
current data file for the domain
- mapping
- +
current data mapping for the column (and related fields)
Arguments
diff --git a/docs/reference/mappingDomain.html b/docs/reference/mappingDomain.html index 215737fe..c0cf2d71 100644 --- a/docs/reference/mappingDomain.html +++ b/docs/reference/mappingDomain.html @@ -17,7 +17,7 @@ @@ -85,18 +85,29 @@Server that facilitates the mapping of a full data domain
Arguments
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- meta
- + +
metadata for the domain
- data
- +
clinical data for the domain
@@ -111,7 +122,7 @@Value
-A reactive data frame containing the mapping for the domain
+ + +A reactive data frame containing the mapping for the domain
Value
diff --git a/docs/reference/mappingDomainUI.html b/docs/reference/mappingDomainUI.html index c622ec66..ade5dee4 100644 --- a/docs/reference/mappingDomainUI.html +++ b/docs/reference/mappingDomainUI.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@UI that facilitates the mapping of a full data domain
Arguments
@@ -105,7 +112,7 @@
- id
- + +
module id
- meta
- + +
metadata for the domain
- data
- + +
data file for the domain
- mapping
- +
current data mapping
Arguments
diff --git a/docs/reference/mappingSelect.html b/docs/reference/mappingSelect.html index e1f3438e..9eef8bce 100644 --- a/docs/reference/mappingSelect.html +++ b/docs/reference/mappingSelect.html @@ -17,7 +17,7 @@ @@ -85,14 +85,21 @@Server that facilitates the mapping of a single data element (column or fiel
Arguments
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- +
Shiny session object
@@ -107,7 +114,7 @@Value
-A reactive containing the selected column
+ + +A reactive containing the selected column
Value
diff --git a/docs/reference/mappingSelectUI.html b/docs/reference/mappingSelectUI.html index fdf6bd7e..91f2d56c 100644 --- a/docs/reference/mappingSelectUI.html +++ b/docs/reference/mappingSelectUI.html @@ -17,7 +17,7 @@ @@ -85,16 +85,25 @@UI that facilitates the mapping of a single data element (column or field) w
Arguments
- id
- + +
unique id for the UI
- label
- + +
label associated with the control
- choices
- + +
a list of options for the control
- default
- +
default value for the control
@@ -109,7 +118,7 @@Value
-returns the selected value wrapped in a
+ + +reactive().returns the selected value wrapped in a
reactive().Value
diff --git a/docs/reference/mappingTab.html b/docs/reference/mappingTab.html index 93adc97a..9e9153cd 100644 --- a/docs/reference/mappingTab.html +++ b/docs/reference/mappingTab.html @@ -17,7 +17,7 @@ @@ -85,18 +85,29 @@Server for mapping tab covering of all data domains
Arguments
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- meta
- + +
metadata for all domains
- domainData
- +
clinical data for all domains
@@ -111,7 +122,7 @@Value
-list of mappings for all domains
+ + +list of mappings for all domains
Value
diff --git a/docs/reference/mappingTabUI.html b/docs/reference/mappingTabUI.html index b10f27dd..4de66f55 100644 --- a/docs/reference/mappingTabUI.html +++ b/docs/reference/mappingTabUI.html @@ -17,7 +17,7 @@ @@ -85,14 +85,23 @@UI for mapping tab covering of all data domains
Arguments
@@ -107,7 +116,7 @@
- id
- + +
module id
- meta
- + +
metadata for all domains
- domainData
- + +
list of data files for each domain
- mappings
- + +
optional data frame containing stacked mappings for all domains
- standards
- +
optional list of data standards like the ones generated by
detectStandard()Arguments
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index 5d6d7f62..fc110263 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -17,7 +17,7 @@ @@ -94,7 +94,7 @@Pipe operator
diff --git a/docs/reference/prepareChart.html b/docs/reference/prepareChart.html index ca0a5a82..f6647d1c 100644 --- a/docs/reference/prepareChart.html +++ b/docs/reference/prepareChart.html @@ -17,7 +17,7 @@ @@ -85,10 +85,13 @@Prepare a chart object for safetyGraphics
Arguments
- chart
- +
chart object like the one generated by makeChartConfig().
@@ -103,7 +106,7 @@Value
-returns the chart object with a new functions object added.
+ + +returns the chart object with a new functions object added.
Value
diff --git a/docs/reference/safetyGraphicsApp.html b/docs/reference/safetyGraphicsApp.html index b76f1b80..c206d8ee 100644 --- a/docs/reference/safetyGraphicsApp.html +++ b/docs/reference/safetyGraphicsApp.html @@ -17,7 +17,7 @@ @@ -95,20 +95,35 @@Run the core safetyGraphics App
Arguments
@@ -123,7 +138,7 @@
- domainData
- + +
named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
- meta
- + +
data frame containing the metadata for use in the app. If no metadata is provided, metatdata is generated by
makeMeta().- charts
- + +
list of charts in the format produced by safetyGraphics::makeChartConfig()
- 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')).
- autoMapping
- + +
boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the
mappingparameter overwrite automatically generated mappings when both are found. Defaults to true.- 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.- 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.
- runNow
- +
Should the shiny app object created be run directly? Helpful when writing functions to dispatch to shinyapps, rsconnect, or shinyproxy.
Arguments
diff --git a/docs/reference/safetyGraphicsInit.html b/docs/reference/safetyGraphicsInit.html index 33cb93c7..9aa2074f 100644 --- a/docs/reference/safetyGraphicsInit.html +++ b/docs/reference/safetyGraphicsInit.html @@ -17,7 +17,7 @@ @@ -89,10 +89,15 @@App to select charts, load data and then initialize the core safetyGraphics
Arguments
@@ -107,7 +112,7 @@
- charts
- + +
chart object
- delayTime
- + +
time (in ms) between drawing app UI and starting server. Default set to 1000 (1 second), but could need to be higher on slow machine.
- maxFileSize
- +
maximum file size in MB allowed for file upload
Arguments
diff --git a/docs/reference/safetyGraphicsServer.html b/docs/reference/safetyGraphicsServer.html index e896d0d3..a7130380 100644 --- a/docs/reference/safetyGraphicsServer.html +++ b/docs/reference/safetyGraphicsServer.html @@ -17,7 +17,7 @@ @@ -94,20 +94,35 @@Server for core safetyGraphics app including Home, Mapping, Filter, Charts a
Arguments
@@ -122,7 +137,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- meta
- + +
data frame containing the metadata for use in the app.
- mapping
- + +
current mapping
- domainData
- + +
named list of data.frames to be loaded in to the app.
- charts
- + +
list of charts to include in the app
- 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.Arguments
diff --git a/docs/reference/safetyGraphicsUI.html b/docs/reference/safetyGraphicsUI.html index c7eab72f..bb19807c 100644 --- a/docs/reference/safetyGraphicsUI.html +++ b/docs/reference/safetyGraphicsUI.html @@ -17,7 +17,7 @@ @@ -85,14 +85,23 @@UI for the core safetyGraphics app including Home, Mapping, Filter, Charts a
Arguments
@@ -107,7 +116,7 @@
- id
- + +
module ID
- meta
- + +
data frame containing the metadata for use in the app.
- domainData
- + +
named list of data.frames to be loaded in to the app.
- mapping
- + +
data.frame specifying the initial values for each data mapping. If no mapping is provided, the app will attempt to generate one via
detectStandard()- standards
- +
a list of information regarding data standards. Each list item should use the format returned by safetyGraphics::detectStandard.
Arguments
diff --git a/docs/reference/setMappingListValue.html b/docs/reference/setMappingListValue.html index db126349..37e2f64a 100644 --- a/docs/reference/setMappingListValue.html +++ b/docs/reference/setMappingListValue.html @@ -17,7 +17,7 @@ @@ -85,16 +85,25 @@Set the value for a given named parameter
Arguments
- key
- + +
a list defining the position of parameter in the settings object.
- value
- + +
the value to set
- settings
- + +
The settings list used to generate a chart like
eDISH()- forceCreate
- +
Specifies whether the function should create a new list() when none exisits. This most commonly occurs when deeply nested objects.
Value
-the updated settings object
+ + +the updated settings object
@@ -122,7 +131,7 @@diff --git a/docs/reference/settingsCharts.html b/docs/reference/settingsCharts.html index 80b721fe..099bdb5a 100644 --- a/docs/reference/settingsCharts.html +++ b/docs/reference/settingsCharts.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@Examples
Server for settings tab showing details for the charts loaded in the app
Arguments@@ -105,7 +112,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- charts
- +
list data frame summarizing the charts
Arguments
diff --git a/docs/reference/settingsChartsUI.html b/docs/reference/settingsChartsUI.html index ba903493..7ecb129a 100644 --- a/docs/reference/settingsChartsUI.html +++ b/docs/reference/settingsChartsUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for settings tab showing details for the charts loaded in the app
Arguments
@@ -99,7 +100,7 @@
- id
- +
module id
Arguments
diff --git a/docs/reference/settingsCode.html b/docs/reference/settingsCode.html index 3de8f77c..fe989cd4 100644 --- a/docs/reference/settingsCode.html +++ b/docs/reference/settingsCode.html @@ -17,7 +17,7 @@ @@ -85,16 +85,27 @@Server for settings tab providing code to re-start the app with current data
Arguments
@@ -109,7 +120,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- mapping
- + +
mapping
- charts
- + +
charts
- domainData
- +
data list
Arguments
diff --git a/docs/reference/settingsCodeUI.html b/docs/reference/settingsCodeUI.html index b3bfcee6..666f53ad 100644 --- a/docs/reference/settingsCodeUI.html +++ b/docs/reference/settingsCodeUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for settings tab providing code to re-start the app with current data/set
Arguments
@@ -99,7 +100,7 @@
- id
- +
module ID
Arguments
diff --git a/docs/reference/settingsData.html b/docs/reference/settingsData.html index 13ead6d1..517d39ff 100644 --- a/docs/reference/settingsData.html +++ b/docs/reference/settingsData.html @@ -17,7 +17,7 @@ @@ -85,12 +85,19 @@Server for settings tab showing current data
Arguments
@@ -105,7 +112,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- domains
- +
named list of the data.frames for each domain
Arguments
diff --git a/docs/reference/settingsDataUI.html b/docs/reference/settingsDataUI.html index a1cde00a..92afc682 100644 --- a/docs/reference/settingsDataUI.html +++ b/docs/reference/settingsDataUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for settings tab showing current data
Arguments
@@ -99,7 +100,7 @@
- id
- +
module id
Arguments
diff --git a/docs/reference/settingsMapping.html b/docs/reference/settingsMapping.html index 846494a9..5d44f5da 100644 --- a/docs/reference/settingsMapping.html +++ b/docs/reference/settingsMapping.html @@ -17,7 +17,7 @@ @@ -85,14 +85,23 @@Server for settings tab showing current mapping
Arguments
@@ -107,7 +116,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- metadata
- + +
Data mapping metadata used for initial loading of app
- mapping
- +
reactive data frame representing the current metadata mapping. columns = "domain", "text_id" and "current"
Arguments
diff --git a/docs/reference/settingsMappingUI.html b/docs/reference/settingsMappingUI.html index d2f19e3b..cea45ad8 100644 --- a/docs/reference/settingsMappingUI.html +++ b/docs/reference/settingsMappingUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for settings tab showing current mapping
Arguments
@@ -99,7 +100,7 @@
- id
- +
module id
Arguments
diff --git a/docs/reference/settingsTab.html b/docs/reference/settingsTab.html index 08450de2..b5b68763 100644 --- a/docs/reference/settingsTab.html +++ b/docs/reference/settingsTab.html @@ -17,7 +17,7 @@ @@ -85,18 +85,31 @@Server for the setting page
Arguments
@@ -111,7 +124,7 @@
- input
- + +
Shiny input object
- output
- + +
Shiny output object
- session
- + +
Shiny session object
- domains
- + +
domains
- metadata
- + +
metadata
- mapping
- + +
mapping
- charts
- +
charts
Arguments
diff --git a/docs/reference/settingsTabUI.html b/docs/reference/settingsTabUI.html index 728f8f1b..290e377e 100644 --- a/docs/reference/settingsTabUI.html +++ b/docs/reference/settingsTabUI.html @@ -17,7 +17,7 @@ @@ -85,6 +85,7 @@UI for the settings tab
Arguments
@@ -99,7 +100,7 @@
- id
- +
module ID
Arguments
diff --git a/docs/reference/textKeysToList.html b/docs/reference/textKeysToList.html index f61b7557..43f1ca6c 100644 --- a/docs/reference/textKeysToList.html +++ b/docs/reference/textKeysToList.html @@ -17,7 +17,7 @@ @@ -85,10 +85,13 @@Helper function to convert keys from text to nested lists
Arguments
- textKeys
- +
a list (or vector) of character keys using the "--" delimiter to indicate hierarchy
Value
-A list of unnamed lists, with position in the nested list indicating hierarchy
+ + +A list of unnamed lists, with position in the nested list indicating hierarchy
@@ -131,7 +134,7 @@diff --git a/vignettes/TechnicalFAQ.Rmd b/vignettes/TechnicalFAQ.Rmd index 26f8c7fb..bbb32a02 100644 --- a/vignettes/TechnicalFAQ.Rmd +++ b/vignettes/TechnicalFAQ.Rmd @@ -104,13 +104,13 @@ Just like the discussion regarding [Validation and Quality Control](#validation- ## Q: Do you recommend deploying the app to a dedicated server for internal usage? -**A**: It depends a bit on your use-case and how the app is hosted. For example, analysts using the data in an exploratory fashion can probably just run it from RStudio, but if multiple medical monitors using the app for medical monitoring in active studies probably need a more robust (and possibly validated) set up using [Shiny Server](https://github.com/rstudio/shiny-server/blob/master/README.md), [RStudio Connect](https://www.rstudio.com/products/connect/) or something similar. +**A**: It depends a bit on your use-case and how the app is hosted. For example, analysts using the data in an exploratory fashion can probably just run it from RStudio, but if multiple medical monitors using the app for medical monitoring in active studies probably need a more robust (and possibly validated) set up using [Shiny Server](https://github.com/rstudio/shiny-server/blob/master/README.md), [RStudio Connect](https://posit.co/products/enterprise/connect/) or something similar. ## Q: Can I deploy `safetyGraphics` to shinyapps.io to explore trial data from my organization? -**A**: We advise against loading non-authorized, private, or non-deidentified patient data outside of your organization's firewall. Consult with your IT and QA first. There is huge risk associated with confidentiality, IP, and patient privacy. Also refer to [ShinyApps.io Chapter 8 Security and Compliance](https://docs.rstudio.com/shinyapps.io/security-and-compliance.html). +**A**: We advise against loading non-authorized, private, or non-deidentified patient data outside of your organization's firewall. Consult with your IT and QA first. There is huge risk associated with confidentiality, IP, and patient privacy. Also refer to [ShinyApps.io Chapter 8 Security and Compliance](https://docs.posit.co/shinyapps.io/security-and-compliance.html). -## **Q**: Can I deploy `safetyGraphics` to an internal [RStudio Connect](https://www.rstudio.com/products/connect/) server? +## **Q**: Can I deploy `safetyGraphics` to an internal [RStudio Connect](https://posit.co/products/enterprise/connect/) server? **A**: Yes. The [script below](https://github.com/SafetyGraphics/safetyGraphics/blob/dev/inst/deploy/app.R) should be easy to deploy via the RStudio interface or by running `rsconnect::deployApp()` and can easily be customized to support custom data and charts.Examples