Merge pull request #155 from SafetyGraphics/dev

v0.4.0

.github/workflows/R-CMD-check.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "rcmdcheck"))

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: safetyCharts
 Title: Charts for Monitoring Clinical Trial Safety
-Version: 0.3.0
+Version: 0.4.0
 Authors@R:
     person(
         given = "Jeremy",
@@ -15,16 +15,18 @@ BugReports: https://github.com/SafetyGraphics/safetyCharts/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Imports:
     dplyr,
     DT,
     forcats,
     ggplot2,
+    htmltools,
     htmlwidgets,
     huxtable,
     jsonlite, 
+    magrittr, 
     pharmaRTF,
     plotly,
     purrr,
@@ -33,6 +35,8 @@ Imports:
     shiny,
     stringr,
     Tendril,
+    tibble,
+    tidyr,
     Tplyr
 Suggests:
     testthat,

NAMESPACE

@@ -1,33 +1,50 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
 export(QT_OutlierExplorer_server)
 export(QT_OutlierExplorer_ui)
 export(QT_Outlier_Explorer)
+export(aeExplorer)
 export(demogRTF_server)
 export(demogRTF_table)
 export(demogRTF_ui)
 export(hepExplorer)
 export(init_aeExplorer)
 export(init_aeTimelines)
+export(init_cmExplorer)
+export(init_mhExplorer)
 export(init_paneledOutlierExplorer)
 export(init_safetyOutlierExplorer)
 export(init_safetyResultsOverTime)
 export(init_safetyShiftPlot)
 export(lab_distribution_server)
 export(lab_distribution_ui)
+export(paneledOutlierExplorer)
 export(render_widget)
 export(safetyOutlierExplorer_server)
 export(safetyOutlierExplorer_ui)
 export(safety_outlier_explorer)
 export(safety_results_over_time)
+export(stack_events)
+export(standardize_events)
 export(tendril_chart)
-import(Tendril)
 import(Tplyr)
 import(dplyr)
 import(ggplot2)
-import(htmlwidgets)
 import(rlang)
 import(shiny)
+importFrom(DT,DTOutput)
+importFrom(DT,renderDT)
+importFrom(RColorBrewer,brewer.pal)
+importFrom(Tendril,Tendril)
+importFrom(dplyr,left_join)
+importFrom(dplyr,select)
+importFrom(forcats,fct_drop)
+importFrom(forcats,fct_reorder)
+importFrom(htmltools,br)
+importFrom(htmltools,div)
+importFrom(htmlwidgets,createWidget)
+importFrom(htmlwidgets,sizingPolicy)
 importFrom(huxtable,as_hux)
 importFrom(huxtable,set_align)
 importFrom(huxtable,set_bold)
@@ -37,19 +54,28 @@ importFrom(huxtable,set_escape_contents)
 importFrom(huxtable,set_valign)
 importFrom(huxtable,set_width)
 importFrom(jsonlite,toJSON)
+importFrom(magrittr,"%>%")
 importFrom(pharmaRTF,add_footnotes)
 importFrom(pharmaRTF,add_titles)
 importFrom(pharmaRTF,hf_line)
 importFrom(pharmaRTF,rtf_doc)
 importFrom(pharmaRTF,set_column_header_buffer)
 importFrom(pharmaRTF,set_font_size)
 importFrom(pharmaRTF,set_ignore_cell_padding)
+importFrom(pharmaRTF,write_rtf)
 importFrom(plotly,animation_slider)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(plotly,plotlyOutput)
 importFrom(plotly,renderPlotly)
+importFrom(purrr,imap)
 importFrom(purrr,list_modify)
+importFrom(purrr,map)
 importFrom(rlang,.data)
+importFrom(rlang,set_names)
+importFrom(rlang,sym)
+importFrom(stats,setNames)
 importFrom(stringr,str_detect)
+importFrom(tibble,as_tibble)
+importFrom(tidyr,unite)
 importFrom(utils,hasName)

R/QT_Outlier_Explorer.R

@@ -19,18 +19,17 @@
 #'
 #' @return returns a chart object
 #'
+#' @import dplyr
 #' @importFrom plotly plot_ly animation_slider layout
 #' @import rlang
 #' @importFrom rlang .data
-#' @import dplyr
 #'
 #' @export
 
-
-
-
-QT_Outlier_Explorer <- function(data, settings)
-{
+QT_Outlier_Explorer <- function(
+    data,
+    settings
+) {
 
     # horizontal reference line
     hline <- function(y = 0, color = "blue") {

R/aeExplorer.R

@@ -0,0 +1,97 @@
+#' Make standalone aeExplorer html widget
+#' 
+#' Convience mapping of render_widget for aeExplorer.
+#' 
+#' The [data](https://github.com/RhoInc/aeexplorer/wiki/Data-Guidelines) and
+#' [mapping](https://github.com/RhoInc/aeexplorer/wiki/Configuration) should match the specs
+#' described in the [aeExplorer](https://github.com/RhoInc/aeexplorer/wiki/Configuration)
+#' JavaScript library. Items passed in ... are added to mapping, and then the list is converted to
+#' JSON via `jsonlite::toJSON(mapping, auto_unbox=TRUE, NULL="NULL")`.
+#' 
+#' The default mapping shown below is designed to work with data in the CDISC ADaM format (like
+#' `safetydata::adam_adlbc`).    
+#' 
+#' ```
+#' mapping <- list(
+#'     dm = list(
+#'         id_col = 'USUBJID',
+#'         treatment_col = 'ARM'
+#'     ),
+#'     aes = list(
+#'         id_col = 'USUBJID',
+#'         bodsys_col = 'AEBODSYS',
+#'         term_col = 'AEDECOD'
+#'     )
+#' )
+#' ```
+#'
+#' Parameters that are not included in the default mapping can be accessed via ....
+#'
+#' For more options see the [full specs](https://github.com/RhoInc/aeexplorer/wiki/Configuration) in
+#' the JavaScript library.
+#' 
+#' @examples 
+#' \dontrun{
+#' # Render widget with defaults.
+#' aeExplorer() 
+#' 
+#' # Render widget without stratification.
+#' aeExplorer(
+#'     mapping = list(
+#'         dm = list(
+#'             id_col = 'USUBJID'
+#'         ),
+#'         aes = list(
+#'             id_col = 'USUBJID',
+#'             bodsys_col = 'AEBODSYS',
+#'             term_col = 'AEDECOD'
+#'         )
+#'     )
+#' )
+#' }
+#' 
+#' @param data `list` Named list of data frames that includes participant-level subject data (`dm`)
+#' and event-level adverse event data (`aes`).
+#' @param mapping `list` Named list with current data mappings. See details for default mapping. 
+#' @param ... additional options to be added to mapping. Will overwrite mapping. 
+#' 
+#' @importFrom purrr list_modify
+#' 
+#' @export
+
+aeExplorer <- function(
+    data = list(
+        dm = safetyData::sdtm_dm,
+        aes = safetyData::sdtm_ae
+    ),
+    mapping = NULL,
+    ...
+) {
+    # Default mapping - TODO: retrieve mapping from a dedicated file or object (in safetyGraphics?).
+    if (is.null(mapping)) {
+        mapping <- list(
+            dm = list(
+                id_col = 'USUBJID',
+                treatment_col = 'ARM'
+            ),
+            aes = list(
+                id_col = 'USUBJID',
+                bodsys_col = 'AEBODSYS',
+                term_col = 'AEDECOD'
+            )
+        )
+    }
+
+    # Add ... to mapping.
+    if (length(list(...)) > 0) {
+        mapping <-  purrr::list_modify(mapping, !!!list(...))
+    }
+
+    initialized <- init_aeExplorer(
+        data = data,
+        settings = mapping
+    )
+
+    # Render widget as standalone HTML page.
+    render_widget("aeExplorer", initialized$data, initialized$settings)
+}

R/hepExplorer.R

@@ -2,7 +2,7 @@
 #' 
 #' Convience mapping of render_widget for hepExplorer. 
 #' 
-#' @details The [data](https://github.com/SafetyGraphics/hep-explorer/wiki/Data-Guidelines) and [mapping](https://github.com/SafetyGraphics/hep-explorer/wiki/Configuration) should match the specs described in the [hepExplorer](https://github.com/SafetyGraphics/hep-explorer/wiki/Configuration) javascript library. Items passed in ... are added to mapping, and then the list is converted to json via `jsonlite::toJSON(mapping, auto_unbox=TRUE, null="null")`.
+#' The [data](https://github.com/SafetyGraphics/hep-explorer/wiki/Data-Guidelines) and [mapping](https://github.com/SafetyGraphics/hep-explorer/wiki/Configuration) should match the specs described in the [hepExplorer](https://github.com/SafetyGraphics/hep-explorer/wiki/Configuration) javascript library. Items passed in ... are added to mapping, and then the list is converted to json via `jsonlite::toJSON(mapping, auto_unbox=TRUE, null="null")`.
 #' 
 #' The default mapping shown below is designed to work with data in the CDISC ADaM format (like `safetydata::adam_adlbc`).    
 #' 
@@ -48,7 +48,7 @@
 #' 
 #' # Use custom mapping for SDTM data
 #' hepExplorer(
-#'     df=safetyData::sdtm_lb,
+#'     data=safetyData::sdtm_lb,
 #'     measure_col = "LBTEST", 
 #'     measure_values = list(
 #'         ALT = "Alanine Aminotransferase", 
@@ -66,17 +66,20 @@
 #' )
 #' }
 #' 
-#' @param df data frame containing lab data used to render for hepExplorer. Default is safetyData::adam_adlbc. 
-#' @param mapping named list with the current data mappings. See details for default mapping. 
+#' @param data `data.frame` Data frame containing lab data used to render `hepExplorer`. Default: `safetyData::adam_adlbc`
+#' @param mapping `list` named list with the current data mappings. See details for default mapping. 
 #' @param ... additional options to be added to mapping. Will overwrite mapping. 
 #' 
 #' @importFrom purrr list_modify
 #' 
 #' @export
 
-hepExplorer <- function(df=safetyData::adam_adlbc, mapping=NULL, ...){
-
-    #default mapping
+hepExplorer <- function(
+    data = safetyData::adam_adlbc,
+    mapping = NULL,
+    ...
+) {
+    # default mapping
     if(is.null(mapping)){
         mapping <- list(
             measure_col = "PARAM", 
@@ -102,5 +105,5 @@ hepExplorer <- function(df=safetyData::adam_adlbc, mapping=NULL, ...){
     }
 
     # render widget as standalone html page
-    render_widget("hepExplorer" ,df, mapping)
-}
+    render_widget("hepExplorer" ,data, mapping)
+}

R/init_aeExplorer.R

@@ -1,17 +1,42 @@
 #' Initialize Settings for Adverse Event Explorer widget
 #'
-#' @param data labs data structured as one record per person per visit per measurement. See details for column requirements.
-#' @param settings named list of settings
+#' @param data `list` Named list of data frames that includes participant-level subject data (`dm`)
+#' and event-level adverse event data (`aes`).
+#' @param settings `list` Named list of settings.
 #' 
 #' @return returns list with data and settings
 #'
+#' @import dplyr
+#'
 #' @export
 
-
 init_aeExplorer <- function(data, settings) {
+
+    # creates flag if treatment_col is missing to trigger actions to avoid downstream JS errors and enable visualization of blinded(no treatment_col) data
+    missing_trt_flag <- (
+        is.null(settings[["dm"]][["treatment_col"]]) || # Check NULL first and evaluate logic left to right
+        trimws(settings[["dm"]][["treatment_col"]])==""
+    )
+
+    #if no treatment_col provided, create dummy treatment_col for group setting so that ae explorer JS doesn't bomb
+    if (missing_trt_flag) {
+        data$dm <- data$dm %>% dplyr::mutate(group_placeholder="All")
+        settings[["dm"]][["treatment_col"]] <- "group_placeholder"
+    }
+
     # Merge treatment with adverse events.
-    dm_sub <- data$dm %>% select(settings[["dm"]][["id_col"]], settings[["dm"]][["treatment_col"]])
-    anly <- dm_sub %>% left_join(data$aes) # left join to keep all rows in dm (even if there were no AEs)
+    dm_sub <- data$dm %>%
+        dplyr::select(
+            settings[["dm"]][["id_col"]],
+            settings[["dm"]][["treatment_col"]]
+        )
+
+    # left join to keep all rows in dm (even if there were no AEs)
+    anly <- dm_sub %>%
+        dplyr::left_join(
+            data$aes,
+            settings[['dm']][['id_col']]
+        )
 
     ae_settings <- list()
 
@@ -37,5 +62,12 @@ init_aeExplorer <- function(data, settings) {
             values = c("", NA, NULL)
         )
     )
+
+    #if no treatment_col provided, remove total column and group selection dropdown
+    if (missing_trt_flag){
+        ae_settings$defaults[["groupCols"]] = FALSE
+        ae_settings$defaults[["useVariableControls"]] = FALSE
+    }
+
     return(list(data = anly, settings = ae_settings))
 }

R/init_aeTimelines.R

@@ -1,6 +1,6 @@
 #' Initialize Settings for AE Timeline widget
 #' 
-#' @param data labs data structured as one record per person per visit per measurement. See details for column requirements.
+#' @param data adverse events data structured as one record per event. See details for column requirements.
 #' @param settings named list of settings
 #'
 #' @return returns list with data and settings