Calculate study timing given sdtm data.

.gitignore

@@ -1 +1,3 @@
 .Rproj.user
+.Rhistory
+.Rdata

R/getDefaultData.R

@@ -0,0 +1,17 @@
+getDefaultData <- function(standard) {
+    data <- list()
+
+    if (standard == 'sdtm') {
+        data$aes <- safetyData::sdtm_ae
+        data$dm <- safetyData::sdtm_dm
+        data$labs <- safetyData::sdtm_lb
+    }
+
+    if (standard == 'adam') {
+        data$aes <- safetyData::adam_adae
+        data$dm <- safetyData::adam_adsl
+        data$labs <- safetyData::adam_adlbc
+    }
+
+    data
+}

R/getDefaultSettings.R

@@ -0,0 +1,63 @@
+getDefaultSettings <- function(standard) {
+    settings <- list()
+
+    if (standard == 'sdtm') {
+        settings$aes <- list(
+            id_col = "USUBJID",
+            stdt_col = "AESTDTC",
+            endt_col = "AEENDTC",
+            stdy_col = NULL,
+            endy_col = NULL,
+            aeterm_col = "AETERM",
+            decod_col = 'AEDECOD',
+            bodsys_col = "AEBODSYS",
+            severity_col = "AESEV"
+        )
+
+        settings$dm <- list(
+            id_col = "USUBJID",
+            reference_date_col = 'RFSTDTC',
+            treatment_col = "ARM"
+        )
+
+        settings$labs <- list(
+            id_col = "USUBJID",
+            visit_col = 'VISIT',
+            visit_order_col = 'VISITNUM',
+            dt_col = 'LBDTC',
+            dy_col = NULL,
+            result_col = 'LBSTRESN'
+        )
+    }
+
+    if (standard == 'adam') {
+        settings$aes <- list(
+            id_col = "USUBJID",
+            stdt_col = 'ASTDT',
+            endt_col = 'AENDT',
+            stdy_col = "ASTDY",
+            endy_col = "AENDY",
+            aeterm_col = "AETERM",
+            decod_col = 'AEDECOD',
+            bodsys_col = "AEBODSYS",
+            severity_col = "AESEV"
+        )
+
+        settings$dm <- list(
+            id_col = "USUBJID",
+            reference_date_col = 'TRTSDT',
+            treatment_col = "TRT01P"
+        )
+
+        settings$labs <- list(
+            id_col = "USUBJID",
+            visit_col = 'AVISIT',
+            visit_order_col = 'AVISITN',
+            dt_col = 'ADT',
+            dy_col = 'ADY',
+            result_col = 'AVAL'
+        )
+    }
+
+    settings
+}

R/getTiming.R

@@ -0,0 +1,59 @@
+#' Calculate reference timepoint.
+#'
+#' @param params `list` Reactive list of input data and mappings
+#' @param domain `character` Name of data domain with which to calculate reference timepoint
+#' @param domainDate `character` Name of date column with which to calculate reference timepoint
+#' @param reference `character` Name of data reference with which to calculate reference timepoint
+#' @param referenceDate `character` Name of date column with which to calculate reference timepoint
+
+getTiming <- function(
+    params,
+    domain,
+    domainDate = NULL,
+    refDomain = 'dm',
+    refDate = 'RFSTDTC',
+    domainStartDate = NULL,
+    domainEndDate = NULL
+) {
+    # TODO: add stopifnot() logic
+
+    id_col <- params$settings[[ refDomain ]]$id_col
+
+    ref_data <- params$data[[ refDomain ]] %>%
+        select(
+            id_col, refDate
+        ) %>%
+        mutate(
+            # TODO: add logic around date format... lubridate::ymd?
+            refDate = as.Date(.data[[ refDate ]])
+        )
+
+    domain_data <- params$data[[ domain ]] %>%
+        left_join(
+            ref_data,
+            id_col
+        )
+
+    getStudyDay <- function(data, date_col) {
+        data[[ date_col ]] <- as.Date(data[[ date_col ]])
+
+        data[[ paste0(date_col, '_dy') ]] <- as.numeric(
+            data[[ date_col ]] - data$refDate
+        ) + (
+            data[[ date_col ]] >= data$refDate
+        )
+
+        data
+    }
+
+    if (!is.null(domainDate))
+        domain_data <- getStudyDay(domain_data, domainDate)
+
+    if (!is.null(domainStartDate))
+        domain_data <- getStudyDay(domain_data, domainStartDate)
+
+    if (!is.null(domainEndDate))
+        domain_data <- getStudyDay(domain_data, domainEndDate)
+
+    domain_data
+}

R/profileApp.R

@@ -1,53 +1,85 @@
 #' Safety Profile App
 #'
-#' @param dfAE AE Data
-#' @param dfDemog demog data
-#' @param settings safetyGraphics settings
+#' @param data `list` Named list of data domains
+#' @param settings `list` Named list of data mappings
+#' @param standard `character` Name of data standard
+#' @param runNow `logical` Run app?
 #'
-#' @import shiny
+#' @return `shiny.appobj` Shiny app
+#'
+#' @importFrom shiny shinyApp callModule
 #'
 #' @export
 
 profileApp <- function(
-    data = list(
-        aes=safetyData::adam_adae,
-        dm = safetyData::adam_adsl,
-        labs=safetyData::adam_adlbc
-    ),
-    settings=NULL,
-    runNow=TRUE
-){
-
-    ## create default settings when settings is not defined by default
-    if(is.null(settings)){
-        settings<-list(
-            labs=list(id_col="USUBJID"),
-            aes=list(id_col="USUBJID", siteid_col="SITEID", trarm_col="TRTA",
-                     bodsys_col="AEBODSYS", term_col = 'AEDECOD',
-                     aeterm_col="AETERM", severity_col="AESEV",
-                     stdy_col="ASTDY", endy_col="AENDY"),
-            dm=list(id_col="USUBJID", treatment_col="ARM")
+    data = NULL,
+    settings = NULL,
+    standard = 'adam',
+    runNow = TRUE
+) {
+    stopifnot(
+        '[ standard ] must be a character-classed variable.' =
+            class(standard) == 'character',
+        '[ standard ] must be one of "sdtm", "adam", "custom".' =
+            tolower(standard) %in% c('sdtm', 'adam', 'custom')
+    )
+
+    standard <- tolower(standard)
+
+    ## Create list of default data when undefined.
+    if (is.null(data))
+        data <- getDefaultData(standard)
+
+    ## Create list of default settings when undefined.
+    if (is.null(settings))
+        settings <- getDefaultSettings(standard)
+
+    ## Calculate study timing.
+    if (standard == 'sdtm') {
+        data$aes <- getTiming(
+            params = list(
+                data = data,
+                settings = settings,
+                standard = standard
+            ),
+            'aes',
+            domainStartDate = settings$aes$stdt_col,
+            domainEndDate = settings$aes$endt_col
+        )
+        settings$aes$stdy_col <- paste0(settings$aes$stdt_col, '_dy')
+        settings$aes$endy_col <- paste0(settings$aes$endt_col, '_dy')
+
+        data$labs <- getTiming(
+            params = list(
+                data = data,
+                settings = settings,
+                standard = standard
+            ),
+            'labs',
+            domainDate = settings$labs$dt_col
         )
+        settings$labs$dy_col <- paste0(settings$labs$dt_col, '_dy')
     }
 
-    ## create object containing data and setting to pass to server
+    ## Create reactive list of data and settings to pass to server
     params <- reactive({
         list(
-            data=data,
-            settings=settings
+            data = data,
+            settings = settings,
+            standard = standard
         )
     })
 
-    ## Create app with ui and server
+    ## Create app with UI and server
     app <- shinyApp(
         ui =  profile_ui("profile"),
-        server = function(input,output,session){
+        server = function(input,output,session) {
             callModule(profile_server, "profile", params)
         }
     )
 
-    #if(runNow)
+    if (runNow)
         runApp(app)
-    #else
-    #app
+    else
+        app
 }

R/profile_server.R

@@ -23,7 +23,6 @@ profile_server <- function(input, output, session, params) {
 
     ## set up some basic reactives for convenience
     id_col<-reactive({
-
         params()$settings$dm$id_col
     })
 
@@ -78,9 +77,7 @@ profile_server <- function(input, output, session, params) {
         print(params()$data$aes %>% filter(!!sym(id_col()) == input$idSelect))# %in% input$idSelect])
     })
 
-
-
-    # TODO Make this dynamic for any domain provided (use a sub-module?)
+    # TODO: Make this dynamic for any domain provided (use a sub-module?)
     output$overview <- renderDT({domain_choice() %>% filter(!!sym(id_col()) == input$idSelect)})
 
     output$AEplot <- renderPlot({