Merge pull request #313 from SafetyGraphics/dev-v1.0

dev-v1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: safetyGraphics
 Title: Create Interactive Graphics Related to Clinical Trial Safety
-Version: 0.11.0
+Version: 1.0.0
 Authors@R: c(
 	person("Jeremy", "Wildfire", email = "jeremy_wildfire@rhoworld.com", role = c("cre","aut")),
 	person("Becca", "Krouse", role="aut"),

NAMESPACE

@@ -28,6 +28,7 @@ importFrom(purrr,map_lgl)
 importFrom(rlang,.data)
 importFrom(rlang,parse_expr)
 importFrom(shiny,runApp)
+importFrom(shiny,shinyOptions)
 importFrom(shinyWidgets,materialSwitch)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_split)

NEWS.md

@@ -1,5 +1,9 @@
+# safetyGraphics v1.0.0
+
+The first production release of safetyGraphics includes many inprovements including the addition of 5 new interactive graphics and an embedded help page with a detailed clinical workflow for using the tool. 
+
 # safetyGraphics v0.7.3
 
 Initial CRAN release for safetyGraphics. The safetyGraphics package provides framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
 
-See the [github release tracker](https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/releases) for additional release documentation and links to issues. 
+See the [GitHub release tracker](https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/releases) for additional release documentation and links to issues. 

R/adlbc.R

@@ -1,6 +1,6 @@
 #' Safety measures sample data
 #'
-#' A dataset containing anonymized lab data from a clinical trial in the CDISC ADaM format. The structure is 1 record per measure per visit per participant. See a full description of the ADaM data standard \href{https://www.cdisc.org/sites/default/files/members/standard/foundational/adam/adam_implementation_guide_v1.0.pdf}{here}.
+#' A dataset containing anonymized lab data from a clinical trial in the CDISC ADaM format. The structure is 1 record per measure per visit per participant. See a full description of the ADaM data standard \href{https://www.cdisc.org/standards/foundational/adam/adam-implementation-guide-v11}{here}.
 #'
 #' @format A data frame with 10288 rows and 46 variables.
 #' \describe{

R/detectStandard.R

@@ -2,7 +2,7 @@
 #'
 #' This function attempts to detect the clinical data standard used in a given R data frame.
 #'
-#' This function compares the columns in the provided \code{"data"} with the required columns for a given data standard/domain combination. The function is designed to work with the SDTM and AdAM CDISC(<https://www.cdisc.org/>) standards for clinical trial data by default. Additional standards can be added by modifying the \code{"standardMetadata"} data set included as part of this package. Currently, "labs" is the only domain supported.
+#' This function compares the columns in the provided \code{"data"} with the required columns for a given data standard/domain combination. The function is designed to work with the SDTM and ADaM CDISC(<https://www.cdisc.org/>) standards for clinical trial data by default. Additional standards can be added by modifying the \code{"standardMetadata"} data set included as part of this package. Currently, "labs" is the only domain supported.
 #'
 #' @param data A data frame in which to detect the data standard
 #' @param includeFields specifies whether to check the data set for field level data in addition to columns.  Default: \code{TRUE}.

R/evaluateStandard.R

@@ -37,7 +37,7 @@ evaluateStandard <- function(data, standard, includeFields=TRUE, domain="labs"){
   # Get metadata for settings using the specified standard and see if required data elements are found
   standardChecks <- getSettingsMetadata(cols=c("text_key", "column_mapping", "field_mapping", "field_column_key", "setting_required","standard_val",standard)) %>%
   rename("standard_val"=standard) %>%
-  filter(.data$column_mapping == TRUE || .data$field_mapping ==TRUE) %>%
+  filter(.data$column_mapping == TRUE | .data$field_mapping ==TRUE) %>%
   filter(.data$setting_required==TRUE) %>%
   mutate(type = ifelse(.data$column_mapping, "column", "field")) %>% 
   rowwise %>%

R/generateSettings.R

@@ -2,14 +2,15 @@
 #'
 #' This function returns a settings object for the eDish chart based on the specified data standard.
 #'
-#' The function is designed to work with the SDTM and AdAM CDISC(<https://www.cdisc.org/>) standards for clinical trial data. Currently, eDish is the only chart supported.
+#' The function is designed to work with the SDTM and ADaM CDISC(<https://www.cdisc.org/>) standards for clinical trial data. Currently, eDish is the only chart supported.
 #'
-#' @param standard The data standard for which to create settings. Valid options are "SDTM", "AdAM" or "None". Default: \code{"None"}.
+#' @param standard The data standard for which to create settings. Valid options are "sdtm", "adam" or "none". Default: \code{"None"}.
 #' @param charts The chart or charts for which settings should be generated. Default: \code{NULL} (uses all available charts).
 #' @param useDefaults Specifies whether default values from settingsMetadata should be included in the settings object. Default: \code{TRUE}.
 #' @param partial Boolean for whether or not the standard is a partial standard. Default: \code{FALSE}.
 #' @param partial_keys Optional character vector of the matched settings if partial is TRUE. Settings should be identified using the text_key format described in ?settingsMetadata. Setting is ignored when partial is FALSE. Default: \code{NULL}.
-#' @param custom_settings a tibble with text_key and customValue columns specifiying customizations to be applied to the settings object. Default: \code{NULL}.
+#' @param custom_settings A tibble describing custom settings to be added to the settings object. Custom values overwrite default values when provided. Tibble should  have text_key and customValue columns. Default: \code{NULL}. 
+#' 
 #' @return A list containing the appropriate settings for the selected chart
 #'
 #' @examples
@@ -123,14 +124,23 @@ generateSettings <- function(standard="None", charts=NULL, useDefaults=TRUE, par
     } 
   }
 
-  #Coerce empty string to NULL
-  for (i in names(shell)){
-    if (!is.null(shell[[i]])){
-      if (shell[[i]][1]==""){
-        shell[i] <- list(NULL)
+  #Coerce empty string to NULL for data mappings
+
+  data_mappings <- safetyGraphics::getSettingsMetadata(
+    charts = charts,
+    cols="text_key",
+    filter_expr=.data$column_mapping
+  )
+  for(text_key in data_mappings){ 
+    key <- textKeysToList(text_key)[[1]]
+    current <- getSettingValue(key,shell) 
+    if (!is.null(current)){
+      if(length(current) <=1) { 
+        if(current == ""){
+          shell<-setSettingsValue(key=key, value=NULL, settings=shell)
+        } 
       }
     }
   }
-
   return(shell)
 }

R/generateShell.R

@@ -9,7 +9,7 @@
 #'
 #' @examples
 #'
-#' safetyGraphics:::generateShell(charts = "eDish")
+#' safetyGraphics:::generateShell(charts = "hepexplorer")
 #'
 #' @keywords internal
 

R/settingsMetadata.R

@@ -4,7 +4,7 @@
 #'
 #' @format A data frame with 29 rows and 17 columns
 #' \describe{
-#'    \item{chart_edish}{Flag indicating if the settings apply to the eDish Chart}
+#'    \item{chart_hepexplorer}{Flag indicating if the settings apply to the Hepatic Explorer Chart}
 #'    \item{chart_paneledoutlierexplorer}{Flag indicating if the settings apply to the Paneled Safety Outlier Explorer Chart}
 #'    \item{chart_safetyhistogram}{Flag indicating if the settings apply to the Safety Histogram Chart}
 #'    \item{chart_safetyoutlierexplorer}{Flag indicating if the settings apply to the Safety Outlier Explorer Chart}

README.md

@@ -3,9 +3,9 @@
 
 # safetyGraphics: Clinical Trial Safety Graphics with R  <img src="inst/safetyGraphicsHex/safetyGraphicsHex.png" width = "175" height = "200" align="right" />
 
-The **safetyGraphics** package provides a framework for evaluation of clinical trial safety in R. The initial release focuses on Evaluation of Drug-Induced Serious Hepatotoxicity (eDISH). A prototype of the eDish interactive graphic is available [here](https://safetygraphics.github.io/safety-eDISH/test/) and is shown below.
+The **safetyGraphics** package provides a framework for evaluation of clinical trial safety in R. It includes several safety-focused visualizations to empower clinical data monitoring. Chief among these is the Hepatic Explorer, based on the [Evaluation of the Drug-Induced Serious Hepatotoxicity (eDish)](https://www.ncbi.nlm.nih.gov/pubmed/21332248) visualization. A demo of the Hepatic Explorer interactive graphic is available [here](https://safetygraphics.github.io/hep-explorer/test-page/example1/) and is shown below.
 
-This package is being built in conjunction with the [safety-eDISH](https://github.com/safetyGraphics/safety-eDISH) javascript library. Both packages are under active development with beta testing and an initial release planned for early 2019.
+This package is being built in conjunction with the [hep-explorer](https://github.com/SafetyGraphics/hep-explorer) javascript library.
 
 ![edishgif](https://user-images.githubusercontent.com/3680095/45834450-02b3a000-bcbc-11e8-8172-324c2fe43521.gif)
 
@@ -23,7 +23,7 @@ The Shiny app provides a simple interface for:
 ```r
 devtools::install_github("SafetyGraphics/safetyGraphics")
 library("safetyGraphics")
-chartBuilderApp() #open the shiny application
+safetyGraphicsApp() #open the shiny application
 ```
 
 ### Standalone charts
@@ -33,17 +33,22 @@ Users can also initialize customized standalone charts with a few lines of code.
 ```r
 devtools::install_github("safetyGraphics/safetyGraphics")
 library("safetyGraphics")
-eDISH(data=adlbc,
-      id_col = "USUBJID",
-      value_col = "AVAL",
-      measure_col = "PARAM",
-      visit_col = "VISIT",
-      visitn_col = "VISITNUM",
-      studyday_col = "ADY",
-      normal_col_low = "A1LO",
-      normal_col_high = "A1HI",
-      measure_values = list(ALT = "Alanine Aminotransferase (U/L)",
-                            AST = "Aspartate Aminotransferase (U/L)",
-                            TB = "Bilirubin (umol/L)",
-                            ALP = "Alkaline Phosphatase (U/L)"))
+
+settings <- list(
+  id_col = "USUBJID",
+  value_col = "AVAL",
+  measure_col = "PARAM",
+  visit_col = "VISIT",
+  visitn_col = "VISITNUM",
+  studyday_col = "ADY",
+  normal_col_low = "A1LO",
+  normal_col_high = "A1HI",
+  measure_values = list(ALT = "Alanine Aminotransferase (U/L)",
+                        AST = "Aspartate Aminotransferase (U/L)",
+                        TB = "Bilirubin (umol/L)",
+                        ALP = "Alkaline Phosphatase (U/L)")
+  )
+
+chartRenderer(data=adlbc, settings=settings, chart="hepexplorer")
+
 ```

data-raw/chartsMetadata.csv

@@ -1,7 +1,7 @@
-chart,main,label,description,repo_url,settings_url,type,maxWidth
-edish,safetyedish,eDish,Interactive graphic for the Evaluation of Drug-Induced Serious Hepatotoxicity (eDISH),https://github.com/SafetyGraphics/safety-eDISH,https://github.com/SafetyGraphics/safety-eDISH/wiki/Configuration,htmlwidget,620
-safetyhistogram,safetyHistogram,Histogram,"Histogram showing distribution of lab measures, vital signs and other measures related to safety in clinical trials.",https://github.com/RhoInc/safety-histogram,https://github.com/RhoInc/safety-histogram/wiki/Configuration,htmlwidget,1000
-safetyoutlierexplorer,safetyOutlierExplorer,Outlier Explorer,"Line Chart highlighting abnormal lab measures, vital signs and other measures related to safety in clinical trials.",https://github.com/RhoInc/safety-outlier-explorer,https://github.com/RhoInc/safety-outlier-explorer/wiki/Configuration,htmlwidget,1000
-safetyshiftplot,safetyShiftPlot,Shift Plot,Shift Plot for Safety Explorer,https://github.com/RhoInc/safety-shift-plot,https://github.com/RhoInc/safety-shift-plot/wiki/Configuration,htmlwidget,620
-safetyresultsovertime,safetyResultsOverTime,Results Over Time,Population Test Results Over Time,https://github.com/RhoInc/safety-results-over-time,https://github.com/RhoInc/safety-results-over-time/wiki/Configuration,htmlwidget,1000
-paneledoutlierexplorer,paneledOutlierExplorer,Paneled Outlier Explorer,Charts showing clinical participant results for multiple measures,https://github.com/RhoIncpaneled-outlier-explorer,https://github.com/RhoInc/paneled-outlier-explorer/wiki/Configuration,htmlwidget,1000
+chart,main,label,description,repo_url,settings_url,type,maxWidth
+hepexplorer,hepexplorer,Hepatic Safety Explorer,Interactive Graphic for Exploring Liver Function Data in Clinical Trials,https://github.com/SafetyGraphics/hep-explorer,https://github.com/SafetyGraphics/hep-explorer/wiki/Configuration,htmlwidget,620
+safetyhistogram,safetyHistogram,Histogram,"Histogram showing distribution of lab measures, vital signs and other measures related to safety in clinical trials.",https://github.com/RhoInc/safety-histogram,https://github.com/RhoInc/safety-histogram/wiki/Configuration,htmlwidget,1000
+safetyoutlierexplorer,safetyOutlierExplorer,Outlier Explorer,"Line Chart highlighting abnormal lab measures, vital signs and other measures related to safety in clinical trials.",https://github.com/RhoInc/safety-outlier-explorer,https://github.com/RhoInc/safety-outlier-explorer/wiki/Configuration,htmlwidget,1000
+safetyshiftplot,safetyShiftPlot,Shift Plot,Shift Plot for Safety Explorer,https://github.com/RhoInc/safety-shift-plot,https://github.com/RhoInc/safety-shift-plot/wiki/Configuration,htmlwidget,620
+safetyresultsovertime,safetyResultsOverTime,Results Over Time,Population Test Results Over Time,https://github.com/RhoInc/safety-results-over-time,https://github.com/RhoInc/safety-results-over-time/wiki/Configuration,htmlwidget,1000
+paneledoutlierexplorer,paneledOutlierExplorer,Paneled Outlier Explorer,Charts showing clinical participant results for multiple measures,https://github.com/RhoIncpaneled-outlier-explorer,https://github.com/RhoInc/paneled-outlier-explorer/wiki/Configuration,htmlwidget,1000

data-raw/csv_to_rda.R

@@ -1,5 +1,6 @@
 library(usethis)
 library(dplyr)
+library(Hmisc)
 
 ### Prepare settingsMetadata and save to /data ###
 
@@ -29,4 +30,55 @@ usethis::use_data(chartsMetadata, overwrite = TRUE)
 ### Save sample data set to /data ###
 # This is loaded by default in the app and used for testing
 adlbc <- read.csv("data-raw/adlbc.csv", stringsAsFactors = FALSE)
+
+### Add labels to sample data set
+adlbc_labels <- c("STUDYID" = "Study Identifier", 
+                  "SUBJID" = "Subject Identifier for the Study",
+                  "USUBJID" = "Unique Subject Identifier",
+                  "TRTP" = "Planned Treatment",
+                  "TRTPN" = "Planned Treatment (N)",
+                  "TRTA" = "Actual Treatment",
+                  "TRTAN" = "Actual Treatment (N)",
+                  "TRTSDT" = "Date of First Exposure to Treatment",
+                  "TRTEDT" = "Date of Last Exposure to Treatment",
+                  "AGE" = "Age",
+                  "AGEGR1" = "Age Group",
+                  "AGEGR1N" = "Age Group (N)",
+                  "RACE" = "Race",
+                  "RACEN" = "Race (N)",
+                  "SEX" = "Sex",
+                  "COMP24FL" = "Completers Flag",
+                  "DSRAEFL" = "Discontinued due to AE?",
+                  "SAFFL" = "Safety Population Flag",
+                  "AVISIT" = "Analysis Visit",
+                  "AVISITN" = "Analysis Visit (N)",
+                  "ADY" = "Analysis Relative Day",
+                  "ADT" = "Analysis Relative Date",
+                  "VISIT" = "Visit",
+                  "VISITNUM" = "Visit (N)",
+                  "PARAM" = "Parameter",
+                  "PARAMCD" = "Parameter Code",
+                  "PARAMN" = "Parameter (N)",
+                  "PARCAT1" = "Parameter Category",
+                  "AVAL" = "Analysis Value",
+                  "BASE" = "Baseline Value",
+                  "CHG" = "Change from Baseline",
+                  "A1LO" = "Analysis Normal Range Lower Limit",
+                  "A1HI" = "Analysis Normal Range Upper Limit",
+                  "R2A1LO" = "Ratio to Low limit of Analysis Range",
+                  "R2A1HI" = "Ratio to High limit of Analysis Range",
+                  "BR2A1LO" = "Base Ratio to Analysis Range 1 Lower Lim",
+                  "BR2A1HI" = "Base Ratio to Analysis Range 1 Upper Lim",
+                  "ANL01FL" = "Analysis Population Flag",
+                  "ALBTRVAL" = "Amount Threshold Range",
+                  "ANRIND" = "Analysis Reference Range Indicator",
+                  "BNRIND" = "Baseline Reference Range Indicator",
+                  "ABLFL" = "Baseline Record Flag",
+                  "AENTMTFL" = "Analysis End Date Flag",
+                  "LBSEQ" = "Lab Sequence Number",
+                  "LBNRIND" = "Reference Range Indicator",
+                  "LBSTRESN" = "Numeric Result/Finding in Std Units")
+
+label(adlbc) = as.list(adlbc_labels[match(names(adlbc), names(adlbc_labels))])
+
 usethis::use_data(adlbc, overwrite = TRUE)

data-raw/generateSettingsMetadataDefaults.R

@@ -1,3 +1,5 @@
+library(tibble)
+
 defaults <- tribble(~text_key, ~default,
              "id_col", NULL,
              "value_col", NULL,

data-raw/settingsMetadata.csv

@@ -27,4 +27,7 @@ warningText,Warning text,"Informational text to be displayed near the top of the
 unit_col,Unit column,Unit of measure variable name,character,FALSE,TRUE,character,FALSE,,data
 start_value,Measure start value,Value of variable defined in measure_col to be rendered in the histogram when the widget loads,character,FALSE,FALSE,NA,TRUE,measure_col,data
 details,Details columns,"An optional list of specifications for details listing.  Each column to be added to details listing is a nested, named list (containing the variable name: ""value_col"" and associated label: ""label"") within the larger list.",vector,FALSE,TRUE,NA,FALSE,,data
-missingValues,Missing values,Values defining a missing value in the selected 'value' column,vector,FALSE,FALSE,NA,FALSE,,data
+missingValues,Missing values,Values defining a missing value in the selected 'value' column,vector,FALSE,FALSE,NA,FALSE,,data
+visits_without_data,Visits without data,Controls display of visits without data for the current measure,logical,FALSE,FALSE,NA,FALSE,,data
+unscheduled_visits,Unscheduled visits,Controls display of unscheduled visits,logical,FALSE,FALSE,NA,FALSE,,data
+unscheduled_visit_pattern,Unscheduled visit pattern,A regular expression that identifies unscheduled visits,character,FALSE,FALSE,NA,FALSE,,data

data-raw/settingsMetadataCharts.csv

@@ -1,4 +1,4 @@
-text_key,edish,safetyhistogram,safetyoutlierexplorer,safetyshiftplot,safetyresultsovertime,paneledoutlierexplorer
+text_key,hepexplorer,safetyhistogram,safetyoutlierexplorer,safetyshiftplot,safetyresultsovertime,paneledoutlierexplorer
 id_col,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE
 value_col,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE
 measure_col,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE
@@ -27,4 +27,7 @@ warningText,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE
 unit_col,FALSE,TRUE,TRUE,TRUE,TRUE,TRUE
 start_value,FALSE,TRUE,TRUE,TRUE,TRUE,FALSE
 details,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE
-missingValues,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE
+missingValues,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE
+visits_without_data,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE
+unscheduled_visits,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE
+unscheduled_visit_pattern,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE

data-raw/standardsMetadata.csv

@@ -27,4 +27,7 @@ warningText,,
 unit_col,STRESU,
 start_value,,
 details,,
-missingValues,,
+missingValues,,
+visits_without_data,,
+unscheduled_visits,,
+unscheduled_visit_pattern,,

inst/htmlwidgets/chartRenderer.yaml

@@ -4,17 +4,17 @@ dependencies:
     src: htmlwidgets/lib/d3-3.5.17
     script: d3.v3.min.js
   - name: webcharts
-    version: 1.11.5
-    src: htmlwidgets/lib/webcharts-1.11.5
+    version: 1.11.6
+    src: htmlwidgets/lib/webcharts-1.11.6
     script: webcharts.js
     stylesheet: webcharts.css
   - name: safety-eDish
     version: 0.17.0
-    src: htmlwidgets/lib/safety-eDISH-0.17.0
-    script: safetyedish.js
+    src: htmlwidgets/lib/hep-explorer-1.0.1
+    script: hepexplorer.js
   - name: safety-histogram
-    version: 2.3.0
-    src: htmlwidgets/lib/safety-histogram-2.3.0
+    version: 2.4.0
+    src: htmlwidgets/lib/safety-histogram-2.4.0-dev
     script: safetyHistogram.js
   - name: safety-outlier-explorer
     version: 2.5.4