roxygen stuff and vignettes

R/derive_param_exposure.R

@@ -8,6 +8,13 @@
 #'   `PARAMCD` is expected as well,
 #'   + Either `ASTDTM` and `AENDTM` or `ASTDT` and `AENDT` are also expected.
 #'
+#' @param dataset_add Additional dataset
+#'
+#'   The variables specified for `by_vars` are expected.
+#'   Observations from the specified dataset are going to be used to calculate and added
+#'   as new records to the input dataset (`dataset`).
+#'
+#'
 #' @param filter Filter condition
 #'
 #'   The specified condition is applied to the input dataset before deriving the
@@ -95,6 +102,7 @@
 #' # Cumulative dose
 #' adex %>%
 #'   derive_param_exposure(
+#'     dataset_add = adex,
 #'     by_vars = exprs(USUBJID),
 #'     set_values_to = exprs(PARAMCD = "TDOSE", PARCAT1 = "OVERALL"),
 #'     input_code = "DOSE",
@@ -106,6 +114,7 @@
 #' # average dose in w2-24
 #' adex %>%
 #'   derive_param_exposure(
+#'     dataset_add = adex,
 #'     by_vars = exprs(USUBJID),
 #'     filter = VISIT %in% c("WEEK 2", "WEEK 24"),
 #'     set_values_to = exprs(PARAMCD = "AVDW224", PARCAT1 = "WEEK2-24"),
@@ -118,6 +127,7 @@
 #' # Any dose adjustment?
 #' adex %>%
 #'   derive_param_exposure(
+#'     dataset_add = adex,
 #'     by_vars = exprs(USUBJID),
 #'     set_values_to = exprs(PARAMCD = "TADJ", PARCAT1 = "OVERALL"),
 #'     input_code = "ADJ",

R/derive_summary_records.R

@@ -112,6 +112,7 @@
 #' # Summarize the average of the triplicate ECG interval values (AVAL)
 #' derive_summary_records(
 #'   adeg,
+#'   dataset_add = adeg,
 #'   by_vars = exprs(USUBJID, PARAM, AVISIT),
 #'   set_values_to = exprs(
 #'     AVAL = mean(AVAL, na.rm = TRUE),
@@ -123,6 +124,7 @@
 #' # Derive more than one summary variable
 #' derive_summary_records(
 #'   adeg,
+#'   dataset_add = adeg,
 #'   by_vars = exprs(USUBJID, PARAM, AVISIT),
 #'   set_values_to = exprs(
 #'     AVAL = mean(AVAL),
@@ -156,6 +158,7 @@
 #' # by group
 #' derive_summary_records(
 #'   adeg,
+#'   dataset_add = adeg,
 #'   by_vars = exprs(USUBJID, PARAM, AVISIT),
 #'   filter = n() > 2,
 #'   set_values_to = exprs(
@@ -172,17 +175,11 @@ derive_summary_records <- function(dataset,
                                    filter_add = NULL,
                                    analysis_var,
                                    summary_fun,
-                                   set_values_to = NULL,
+                                   set_values_to,
                                    missing_values = NULL) {
   assert_vars(by_vars)
-  assert_data_frame(
-    dataset,
-    required_vars = expr_c(by_vars)
-  )
-  assert_data_frame(
-    dataset_add,
-    required_vars = expr_c(by_vars),
-  )
+  assert_data_frame(dataset, required_vars = by_vars)
+  assert_data_frame(dataset_add, required_vars = by_vars)
   assert_data_frame(
     dataset_ref,
     required_vars = by_vars,

tests/testthat/test-compute_scale.R

@@ -95,6 +95,7 @@ test_that("compute_scale Test 5: compute_scale() works as expected within
   expect_equal(
     derive_summary_records(
       input,
+      dataset_add = input,
       by_vars = exprs(STUDYID, USUBJID, AVISIT, AVISITN),
       filter_add = (PARAMCD %in% c("ITEM1", "ITEM2", "ITEM3")),
       set_values_to = exprs(

tests/testthat/test-derive_param_exposure.R

@@ -128,20 +128,23 @@ test_that("derive_param_exposure Test 2: works with DT variables", {
 
   actual_output <- input_no_dtm %>%
     derive_param_exposure(
+      dataset_add = input_no_dtm,
       by_vars = exprs(USUBJID),
       input_code = "DOSE",
       analysis_var = AVAL,
       summary_fun = function(x) sum(x, na.rm = TRUE),
       set_values_to = exprs(PARAMCD = "TDOSE", PARCAT1 = "OVERALL")
     ) %>%
     derive_param_exposure(
+      dataset_add = input_no_dtm,
       by_vars = exprs(USUBJID),
       input_code = "DOSE",
       analysis_var = AVAL,
       summary_fun = function(x) mean(x, na.rm = TRUE),
       set_values_to = exprs(PARAMCD = "AVDOSE", PARCAT1 = "OVERALL")
     ) %>%
     derive_param_exposure(
+      dataset_add = input_no_dtm,
       by_vars = exprs(USUBJID),
       input_code = "ADJ",
       analysis_var = AVALC,
@@ -162,6 +165,7 @@ test_that("derive_param_exposure Test 3: Errors", {
   expect_error(
     input <- input %>%
       derive_param_exposure(
+        dataset_add = input,
         by_vars = exprs(USUBJID),
         input_code = "DOSE",
         analysis_var = AVAL,
@@ -174,6 +178,7 @@ test_that("derive_param_exposure Test 3: Errors", {
   expect_error(
     input <- input %>%
       derive_param_exposure(
+        dataset_add = input,
         by_vars = exprs(USUBJID),
         input_code = "DOSED",
         analysis_var = AVAL,
@@ -191,6 +196,8 @@ test_that("derive_param_exposure Test 3: Errors", {
     input <- input %>%
       select(-starts_with("AST"), -starts_with("AEN")) %>%
       derive_param_exposure(
+        dataset = .,
+        dataset_add = .,
         by_vars = exprs(USUBJID),
         input_code = "DOSE",
         analysis_var = AVAL,

vignettes/bds_exposure.Rmd

@@ -361,6 +361,7 @@ For example, to calculate the total dose by subject and treatment,
 ```{r eval=TRUE, echo=TRUE}
 adex <- derive_param_exposure(
   adex,
+  dataset_add = adex,
   by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars),
   input_code = "DOSE",
   analysis_var = AVAL,
@@ -428,6 +429,7 @@ adex <- adex %>%
         summary_fun = function(x) if_else(sum(!is.na(x)) > 0, "Y", NA_character_)
       )
     ),
+    dataset_add = adex,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars)
   )
 

vignettes/bds_finding.Rmd

@@ -989,9 +989,10 @@ Set `DTYPE` to `AVERAGE`.
 ```{r eval=TRUE}
 advs_ex2 <- derive_summary_records(
   advs,
+  dataset_add = advs,
   by_vars = exprs(STUDYID, USUBJID, PARAMCD, VISITNUM, ADT),
   set_values_to = exprs(
-    AVAL = mean(AVAL),
+    AVAL = mean(AVAL, na.rm = TRUE),
     DTYPE = "AVERAGE"
   )
 )

vignettes/questionnaires.Rmd

@@ -141,6 +141,8 @@ adgad7 <- adqs %>%
   # Select records to keep in the GAD-7 ADaM
   filter(PARCAT1 == "GAD-7 V2") %>%
   derive_summary_records(
+    dataset = .,
+    dataset_add = .,
     by_vars = exprs(STUDYID, USUBJID, AVISIT, ADT, ADY, TRTSDT, DTHCAUS),
     # Select records contributing to total score
     filter_add = str_detect(PARAMCD, "GAD020[1-7]"),
@@ -169,6 +171,8 @@ adgdssf <- adqs %>%
   # Select records to keep in the GDS-SF ADaM
   filter(PARCAT1 == "GDS SHORT FORM") %>%
   derive_summary_records(
+    dataset = .,
+    dataset_add = .,
     by_vars = exprs(STUDYID, USUBJID, AVISIT, ADT, ADY, TRTSDT, DTHCAUS),
     # Select records contributing to total score
     filter_add = str_detect(PARAMCD, "GDS02[01][0-9]"),
@@ -518,6 +522,7 @@ be derived by `derive_summary_records()`.
 ```{r}
 adgdssf <- adgdssf %>%
   derive_summary_records(
+    dataset_add = adgdssf,
     filter_add = str_detect(PARAMCD, "GDS02[01][0-9]"),
     by_vars = exprs(USUBJID, AVISIT),
     set_values_to = exprs(
@@ -567,6 +572,8 @@ adgdssf <- adgdssf %>%
     )
   ) %>%
   derive_summary_records(
+    dataset = .,
+    dataset_add = .,
     filter_add = str_detect(PARAMCD, "GDS02[01][0-9]"),
     by_vars = exprs(USUBJID, AVISIT),
     set_values_to = exprs(