fix #5

SafetyGraphics · Jan 27, 2023 · 4d17e57 · 4d17e57
1 parent 679005c
commit 4d17e57
Show file tree

Hide file tree

Showing 4 changed files with 59 additions and 31 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
 .Rproj.user
+.Rhistory
+.Rdata
diff --git a/R/getDefaultSettings.R b/R/getDefaultSettings.R
@@ -4,8 +4,8 @@ getDefaultSettings <- function(standard) {
     if (standard == 'sdtm') {
         settings$aes <- list(
             id_col = "USUBJID",
-            stdt_col = "AESTDT",
-            endt_col = "AEENDT",
+            stdt_col = "AESTDTC",
+            endt_col = "AEENDTC",
             stdy_col = NULL,
             endy_col = NULL,
             aeterm_col = "AETERM",
@@ -24,7 +24,7 @@ getDefaultSettings <- function(standard) {
             id_col = "USUBJID",
             visit_col = 'VISIT',
             visit_order_col = 'VISITNUM',
-            dt_col = 'LBDT',
+            dt_col = 'LBDTC',
             dy_col = NULL,
             result_col = 'LBSTRESN'
         )
@@ -33,12 +33,12 @@ getDefaultSettings <- function(standard) {
     if (standard == 'adam') {
         settings$aes <- list(
             id_col = "USUBJID",
-            stdt_col = NULL,
-            endt_col = NULL,
+            stdt_col = 'ASTDT',
+            endt_col = 'AENDT',
             stdy_col = "ASTDY",
             endy_col = "AENDY",
             aeterm_col = "AETERM",
-            term_col = 'AEDECOD',
+            decod_col = 'AEDECOD',
             bodsys_col = "AEBODSYS",
             severity_col = "AESEV"
         )

diff --git a/R/getTiming.R b/R/getTiming.R
@@ -17,44 +17,43 @@ getTiming <- function(
 ) {
     # TODO: add stopifnot() logic
 
-    id_col <- reactive({
-        params()$settings[[ refDomain ]]$id_col
-    })
+    id_col <- params$settings[[ refDomain ]]$id_col
 
-    ref_data <- params()$data[[ refDomain ]] %>%
+    ref_data <- params$data[[ refDomain ]] %>%
         select(
             id_col, refDate
         ) %>%
         mutate(
-            refDate = as.Date(.data$refDate)
+            # TODO: add logic around date format... lubridate::ymd?
+            refDate = as.Date(.data[[ refDate ]])
         )
 
-    domain_data <- params()$data[[ domain ]] %>%
+    domain_data <- params$data[[ domain ]] %>%
         left_join(
             ref_data,
             id_col
         )
 
-    if (!is.null(domainDate)) {
-        domain_date[[ domainDate ]] <- as.Date(domain_data[[ domainDate ]])
+    getStudyDay <- function(data, date_col) {
+        data[[ date_col ]] <- as.Date(data[[ date_col ]])
 
-        domain_data[[ paste0(domainDate, '_dy') ]] <- as.numeric(domain_data[[ domainDate ]] -
-            ref_data[[ refDate ]]) + (domain_data[[ domainDate ]] >= ref_data[[ refDate ]])
-    }
-
-    if (!is.null(domainStartDate)) {
-        domain_date[[ domainStartDate ]] <- as.Date(domain_data[[ domainStartDate ]])
+        data[[ paste0(date_col, '_dy') ]] <- as.numeric(
+            data[[ date_col ]] - data$refDate
+        ) + (
+            data[[ date_col ]] >= data$refDate
+        )
 
-        domain_data[[ paste0(domainDate, '_stdy') ]] <- as.numeric(domain_data[[ domainStartDate ]] -
-            ref_data[[ refDate ]]) + (domain_data[[ domainStartDate ]] >= ref_data[[ refDate ]])
+        data
     }
 
-    if (!is.null(domainEndDate)) {
-        domain_date[[ domainEndDate ]] <- as.Date(domain_data[[ domainEndDate ]])
+    if (!is.null(domainDate))
+        domain_data <- getStudyDay(domain_data, domainDate)
 
-        domain_data[[ paste0(domainDate, '_endy') ]] <- as.numeric(domain_data[[ domainEndDate ]] -
-            ref_data[[ refDate ]]) + (domain_data[[ domainEndDate ]] >= ref_data[[ refDate ]])
-    }
+    if (!is.null(domainStartDate))
+        domain_data <- getStudyDay(domain_data, domainStartDate)
+
+    if (!is.null(domainEndDate))
+        domain_data <- getStudyDay(domain_data, domainEndDate)
 
     domain_data
 }
diff --git a/R/profileApp.R b/R/profileApp.R
@@ -26,15 +26,42 @@ profileApp <- function(
 
     standard <- tolower(standard)
 
-    ## create list of default data when undefined
+    ## Create list of default data when undefined.
     if (is.null(data))
         data <- getDefaultData(standard)
 
-    ## create list of default settings when undefined
+    ## Create list of default settings when undefined.
     if (is.null(settings))
         settings <- getDefaultSettings(standard)
-browser()
-    ## create reactive list of data and settings to pass to server
+
+    ## 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 reactive list of data and settings to pass to server
     params <- reactive({
         list(
             data = data,