Update docs

.Rbuildignore

@@ -14,3 +14,4 @@
 ^CRAN-RELEASE$
 ^customSettings$
 ^\.github$
+^LICENSE\.md$

DESCRIPTION

@@ -2,13 +2,12 @@ Package: safetyGraphics
 Title: Create Interactive Graphics Related to 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("Susan","Duke", role="aut"))
 Maintainer: Jeremy Wildfire <jeremy_wildfire@gmail.com>
 Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
 URL: https://github.com/SafetyGraphics/safetyGraphics

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

@@ -84,5 +84,3 @@ importFrom(stringr,str_to_upper)
 importFrom(utils,hasName)
 importFrom(utils,zip)
 importFrom(yaml,as.yaml)
-importFrom(yaml,write_yaml)
-

R/meta.R

@@ -1,5 +1,3 @@
-#' meta
-#'
 #' 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

R/mod_chartsNav.R

@@ -1,4 +1,4 @@
-#' Add a navbar tab that initializes the Chart Module UI
+#' Adds a navbar tab that initializes the Chart Module UI
 #'
 #' @param chart  chart metadata 
 #' @param ns namespace

R/mod_chartsTab.R

@@ -1,8 +1,7 @@
-#' @title Charts Tab
-#' @description  Charting module
+#' @title UI for chart module, designed to be re-used for each chart generated. 
 #'
 #' @param id module id
-#' @param chart list containing chart specifications
+#' @param chart list containing chart specifications like those returned by \link{makeChartConfig}. 
 #' 
 #' @importFrom stringr str_to_title
 #' @importFrom purrr map2
@@ -17,13 +16,12 @@ chartsTabUI <- function(id, chart){
   return(list(header, chartWrap))
 }
 
-#' @title  home tab - server
-#' @description  server for the display of the chart tab  
+#' @title Server for chart module, designed to be re-used for each chart generated. 
 #'
 #' @param input Input objects from module namespace
 #' @param output Output objects from module namespace
 #' @param session An environment that can be used to access information and functionality relating to the session
-#' @param chart list containing a safetyGraphics chart object. see custom chart vignette for details. 
+#' @param chart list containing a safetyGraphics chart object like those returned by \link{makeChartConfig}.
 #' @param data named list of current data sets (Reactive).
 #' @param mapping tibble capturing the current data mappings (Reactive).
 #' 

R/mod_filterTab.R

@@ -1,5 +1,4 @@
-#' @title  filterTabUI 
-#' @description  UI that facilitates the filtering data with datamods::filter_data_ui
+#' @title UI for the filter module in datamods::filter_data_ui
 #'
 #' @param id module id
 #' 
@@ -39,8 +38,7 @@ filterTabUI <- function(id){
 }
 
 
-#' @title  filter module server
-#' @description  server function that facilitates the data filtering with the datamods::filter_data_server module
+#' @title Server for the filter module in datamods::filter_data_ui
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_filterTabChecks.R

@@ -1,5 +1,4 @@
-#' @title filter module checks
-#' @description function that checks whether the current data and settings are appropriate for the filter tab
+#' @title  Checks for whether the current data and settings support a filter tab
 #'
 #' @param domainData list of data files for each domain
 #' @param filterDomain domain to use for filtering (typically "dm")

R/mod_homeTab.R

@@ -1,5 +1,4 @@
-#' @title Home Tab
-#' @description  Home Tab - sub-module showing details for the data loaded in the app - UI
+#' @title UI for the home module
 #'
 #' @param id module id
 #' 
@@ -13,8 +12,7 @@ homeTabUI <- function(id){
   )  
 }
 
-#' @title  home tab - server
-#' @description  server for the display of the home tab  
+#' @title Server for the filter module in datamods::filter_data_ui
 #'
 #' @param input mod input
 #' @param output mod output

R/mod_loadCharts.R

@@ -1,8 +1,7 @@
-#' @title   loadChartsUI 
-#' @description  UI that helps users pick charts
+#' @title UI for the chart loading module used in safetyGraphicsInit()
 #'
 #' @param id module id
-#' @param charts list of charts
+#' @param charts list containing chart specifications like those returned by \link{makeChartConfig}. 
 #' 
 #' @importFrom purrr keep
 #' @importFrom sortable bucket_list add_rank_list
@@ -21,15 +20,15 @@ loadChartsUI <- function(id, charts=makeChartConfig()){
     ) 
 }
 
-#' @title   loadCharts
-#' @description  server that facilitates selection of charts for safetyGraphicsApp
+#' @title Server for the chart loading module used in safetyGraphicsInit()
 #'
 #' @param input Shiny input object
 #' @param output Shiny output object
 #' @param session Shiny session object
-#' @param charts Initial list of charts
-
+#' @param charts list containing chart specifications like those returned by \link{makeChartConfig}. 
+#' 
 #' @export
+
 loadCharts <- function(input, output, session, charts=makeChartConfig()) {
     ns<-session$ns
     labels<-charts%>%map(~makeChartSummary(.x,showLinks=FALSE,class="chart-sortable"))

R/mod_loadData.R

@@ -1,5 +1,4 @@
-#' @title   loadDataUI 
-#' @description  UI that facilitates the mapping of a column data domain
+#' @title UI for the data loading module used in safetyGraphicsInit()
 #'
 #' @param id module id
 #' @param domain character vector with domains to be loaded 
@@ -19,8 +18,7 @@ loadDataUI <- function(id, domain=NULL){
   )
 }
 
-#' @title   loadDataServer
-#' @description  UI that facilitates the mapping of a column data domain
+#' @title Server for the data loading module used in safetyGraphicsInit()
 #'
 #' @param domain data domain to be loaded
 #' @param input Shiny input object

R/mod_mappingColumn.R

@@ -1,5 +1,4 @@
-#' @title   mappingColumnUI 
-#' @description  UI that facilitates the mapping of a column data domain
+#' @title  UI that facilitates the mapping of a column data (and any associated fields) 
 #'
 #' @param id module id
 #' @param meta metadata for the column (and related fields)
@@ -66,8 +65,7 @@ mappingColumnUI <- function(id, meta, data, mapping=NULL){
     col_ui
 }
 
-#' @title  mappingColumn
-#' @description  server function that facilitates the mapping of a single data element (column of field) with a simple select UI
+#' @title  Server that facilitates the mapping of a column data (and any associated fields) 
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_mappingDomain.R

@@ -1,5 +1,4 @@
-#' @title   mappingDomainUI 
-#' @description  UI that facilitates the mapping of a full data domain
+#' @title  UI that facilitates the mapping of a full data domain
 #'
 #' @param id module id
 #' @param meta metadata for the domain
@@ -37,8 +36,7 @@ mappingDomainUI <- function(id, meta, data, mapping=NULL){
 }
 
 
-#' @title  mappingDomain
-#' @description  server function that facilitates the mapping of a single data domain
+#' @title  Server that facilitates the mapping of a full data domain
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_mappingSelect.R

@@ -1,7 +1,5 @@
-#' Mapping Select UI 
+#' @title UI that facilitates the mapping of a single data element (column or field) with a simple select UI
 #' 
-#' UI that facilitates the mapping of a single data element (column or field) with a simple select UI
-#'
 #' @param id unique id for the UI
 #' @param label label associated with the control  
 #' @param choices a list of options for the control
@@ -33,8 +31,7 @@ mappingSelectUI <- function(id, label, choices=NULL, default=NULL){
     )
 }
 
-#' @title  mappingSelect
-#' @description  server function that facilitates the mapping of a single data element (column of field) with a simple select UI
+#' @title Server that facilitates the mapping of a single data element (column or field) with a simple select UI
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_mappingTab.R

@@ -1,5 +1,4 @@
-#' @title   mappingTabUI 
-#' @description  UI that facilitates the mapping of all data domain
+#' @title UI for mapping tab covering of all data domains
 #' 
 #' @param id module id
 #' @param meta metadata for all domains
@@ -68,8 +67,7 @@ mappingTabUI <- function(id, meta, domainData, mappings=NULL, standards=NULL){
 }
 
 
-#' @title  mapping module server
-#' @description  server function that facilitates the mapping of a single data domain
+#' @title Server for mapping tab covering of all data domains
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_safetyGraphicsServer.R

@@ -1,4 +1,4 @@
-#' Server for the default safetyGraphics shiny app
+#' Server for core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.  
 #'
 #' This function returns a server function suitable for use in shiny::runApp()
 #' 

R/mod_safetyGraphicsUI.R

@@ -1,4 +1,5 @@
-#' UI for the default safetyGraphics shiny app
+#' UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.  
+#'
 #'
 #' @param id module ID
 #' @param meta data frame containing the metadata for use in the app. See the preloaded file (\code{?safetyGraphics::meta}) for more data specifications and details. Defaults to \code{safetyGraphics::meta}. 

R/mod_settingsCharts.R

@@ -1,5 +1,4 @@
-#' @title Settings Module - chart details
-#' @description  Settings Module - sub-module showing details for the charts loaded in the app - UI
+#' @title UI for settings tab showing details for the charts loaded in the app 
 #'
 #' @param id module id
 #' 
@@ -23,8 +22,7 @@ settingsChartsUI <- function(id){
   )
 }
 
-#' @title  Settings Module - charts details - server
-#' @description  server for the display of the charts
+#' @title Server for settings tab showing details for the charts loaded in the app 
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_settingsCode.R

@@ -1,5 +1,5 @@
-#' UI for the settings page
-#'
+#' @title UI for settings tab providing code to re-start the app with current data/settings
+#' 
 #' @param id module ID
 #'  
 #' @export
@@ -92,8 +92,8 @@ settingsCodeUI <- function(id){
 
 }
 
-#' @title  Server for the setting code page
-#'
+#' @title Server for settings tab providing code to re-start the app with current data/settings
+#' 
 #' @param input Shiny input object
 #' @param output  Shiny output object
 #' @param session Shiny session object

R/mod_settingsData.R

@@ -1,5 +1,4 @@
-#' @title Settings Module - data details
-#' @description  Settings Module - sub-module showing details for the data loaded in the app - UI
+#' @title UI for settings tab showing current data
 #' 
 #' @param id module id
 #' 
@@ -20,8 +19,7 @@ settingsDataUI <- function(id){
   )
 }
 
-#' @title  Settings Module - data details - server
-#' @description  server for the display of the loaded data  
+#' @title Server for settings tab showing current data
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_settingsMapping.R

@@ -1,6 +1,5 @@
-#' @title  Settings view of Metadata/Mapping - UI
-#' @description  UI that displays the data mapping metadata. 
-#'
+#' @title UI for settings tab showing current mapping
+#' 
 #' @param id module id
 #' 
 #' @import rclipboard
@@ -19,8 +18,7 @@ settingsMappingUI <- function(id){
   ) 
 }  
 
-#' @title  Settings view of Metadata/Mapping - server
-#' @description  server for the display of the data mapping metadata. 
+#' @title Server for settings tab showing current mapping
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/mod_settingsTab.R

@@ -1,4 +1,4 @@
-#' UI for the settings page
+#' @title UI for the settings tab
 #'
 #' @param id module ID
 #'  
@@ -16,7 +16,7 @@ settingsTabUI <- function(id){
 }
 
 
-#' @title  Server for the setting page
+#' @title Server for the setting page
 #'
 #' @param input Shiny input object
 #' @param output  Shiny output object

R/safetyGraphicsApp.R

@@ -1,4 +1,4 @@
-#' Run the interactive safety graphics app
+#' Run the core safetyGraphics App
 #'
 #' @param domainData named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
 #' @param meta data frame containing the metadata for use in the app. See the preloaded file (\code{?safetyGraphics::meta}) for more data specifications and details. Defaults to \code{safetyGraphics::meta}. 

R/safetyGraphicsInit.R

@@ -1,4 +1,4 @@
-#' Run the interactive safety graphics app
+#' App to select charts, load data and then initialize the core safetyGraphics app 
 #'
 #' @param charts chart object
 #' @param 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.