update fda table 2,3,4,6,7, and LBT01 to pharmaverse data (#320)

* update fda table 2,3,4,6,7, and LBT01 to pharmaverse data

* [skip style] [skip vbump] Restyle files

* update datasets for table 17, 18

* update datasets and result screenshot for tables 29-51

* [skip style] [skip vbump] Restyle files

* filter data to reduce table size

* [skip style] [skip vbump] Restyle files

* Fix stalled checks

* update template sorting

* revert table 50 for docs check

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com>

Author: 3 people

quarto/catalog/fda-table_02/index.qmd

@@ -18,18 +18,19 @@ knitr::include_graphics("result.png")
 library(dplyr)
 library(gtsummary)
 
-adsl <- random.cdisc.data::cadsl |>
-  mutate(
-    AGEGR1 = factor(
-      case_when(
-        AGE >= 17 & AGE < 65 ~ ">=17 to <65",
-        AGE >= 65 & AGE < 75 ~ "65-74",
-        AGE >= 75 ~ ">=75"
-      ),
-      levels = c(">=17 to <65", "65-74", ">=75")
-    )
+adsl <- pharmaverseadam::adsl |>
+  # removing screen failure observations
+  filter(TRT01A != "Screen Failure") |>
+  # Adding a numeric biomarker (weight)
+  left_join(
+    pharmaverseadam::advs |>
+      filter(VSTESTCD == "WEIGHT", VISIT == "BASELINE") |>
+      select(USUBJID, WEIGHTBL = AVAL),
+    by = "USUBJID",
+    relationship = "one-to-one"
   )
 
+
 # Pre-processing --------------------------------------------
 # Filter for the safety population, x
 data <- adsl |>
@@ -42,7 +43,7 @@ data <- adsl |>
 tbl <- data |>
   tbl_summary(
     by = "TRT01A",
-    include = c("SEX", "AGE", "AGEGR1", "ETHNIC", "RACE", "BMRKR1", "BMRKR2"),
+    include = c("SEX", "AGE", "AGEGR1", "ETHNIC", "RACE"),
     type = all_continuous() ~ "continuous2", # arranges statistics into multiple lines
     statistic = list(
       all_continuous() ~ c(

quarto/catalog/fda-table_02/result.png

@@ -19,64 +19,37 @@ library(dplyr)
 library(cards)
 library(gtsummary)
 
-adsl <- random.cdisc.data::cadsl
+adsl <- pharmaverseadam::adsl
 
 set.seed(1)
-adsl$RANDDT[sample(seq_len(nrow(adsl)), 100)] <- NA
 scrnfail_reas_lvls <- c(
   "Inclusion/exclusion criteria not met", "Subject noncompliance", "Consent withdrawn", "Other"
 )
 data <- adsl |>
   mutate(
     ENRLDT = RANDDT,
+    ENRLFL = !is.na(ENRLDT),
+    RANDFL = !is.na(RANDDT),
     SCRNFL = TRUE,
-    SCRNFRS = factor(sample(scrnfail_reas_lvls, size = nrow(adsl), replace = TRUE),
+    SCRNFRS = NA_character_
+  ) |>
+  mutate( # set screen failure reasons for relevant observations.
+    SCRNFRS = factor(
+      replace(
+        SCRNFRS,
+        TRT01A == "Screen Failure",
+        sample(scrnfail_reas_lvls, size = sum(TRT01A == "Screen Failure"), replace = TRUE)
+      ),
       levels = scrnfail_reas_lvls
-    ),
-    ENRLFL = !is.na(ENRLDT),
-    RANDFL = !is.na(RANDDT)
-  )
-data$SCRNFRS[data$SCRNFL == "N" | !is.na(data$ENRLDT)] <- NA
-```
-
-## Build ARD
-
-```{r ard, message=FALSE, warning=FALSE, results='hide'}
-ard <- data |>
-  ard_stack(
-    ard_tabulate_value(
-      variables = SCRNFL,
-      value = list(SCRNFL = TRUE),
-      statistic = everything() ~ c("n")
-    ),
-    ard_tabulate(
-      variables = SCRNFRS,
-      statistic = everything() ~ c("n", "p"),
-      denominator = data
-    ),
-    ard_tabulate_value(
-      variables = c(ENRLFL, RANDFL),
-      value = list(ENRLFL = TRUE, RANDFL = TRUE),
-      statistic = everything() ~ c("n", "p"),
-      denominator = data
     )
   )
-
-ard
-```
-
-```{r, echo=FALSE}
-# Print ARD
-withr::local_options(width = 9999)
-print(ard, columns = "all", n = 40)
 ```
 
 ## Build Table
 
 ```{r tbl, message=FALSE, warning=FALSE, results='hide'}
 tbl_scrn <- tbl_summary(
   data = data,
-  by = TRT01A,
   include = "SCRNFL",
   missing = "no",
   label = ~"Subjects screened"
@@ -86,7 +59,6 @@ tbl_scrnfrs <- tbl_hierarchical(
   data = data,
   denominator = adsl,
   id = USUBJID,
-  by = TRT01A,
   variables = "SCRNFRS",
   label = list(..ard_hierarchical_overall.. = "Screening failures"),
   overall_row = TRUE
@@ -96,7 +68,6 @@ tbl_scrnfrs <- tbl_hierarchical(
 
 tbl_enrl_rand <- tbl_summary(
   data = data,
-  by = TRT01A,
   include = c("ENRLFL", "RANDFL"),
   missing = "no",
   label = list(ENRLFL = "Subjects enrolled", RANDFL = "Subjects randomized")
@@ -116,4 +87,36 @@ gt::gtsave(as_gt(tbl), filename = "result.png")
 
 ```{r img, echo=FALSE, fig.align='center', out.width='60%'}
 ```
+
+## Build ARD
+
+```{r ard, message=FALSE, warning=FALSE, results='hide'}
+ard <- data |>
+  ard_stack(
+    ard_tabulate_value(
+      variables = SCRNFL,
+      value = list(SCRNFL = TRUE),
+      statistic = everything() ~ c("n")
+    ),
+    ard_tabulate(
+      variables = SCRNFRS,
+      statistic = everything() ~ c("n", "p"),
+      denominator = data
+    ),
+    ard_tabulate_value(
+      variables = c(ENRLFL, RANDFL),
+      value = list(ENRLFL = TRUE, RANDFL = TRUE),
+      statistic = everything() ~ c("n", "p"),
+      denominator = data
+    )
+  )
+
+ard
+```
+
+```{r, echo=FALSE}
+# Print ARD
+withr::local_options(width = 9999)
+print(ard, columns = "all", n = 40)
+```
 :::

quarto/catalog/fda-table_03/index.qmd

@@ -18,17 +18,19 @@ knitr::include_graphics("result.png")
 library(dplyr)
 library(gtsummary)
 
-adsl <- random.cdisc.data::cadsl
+adsl <- pharmaverseadam::adsl |>
+  filter(TRT01A != "Screen Failure") # Remove screen failure observations
 
 # Pre-processing --------------------------------------------
 pop_vars <- c("rand_fl", "ITTFL", "SAFFL", "prot_fl")
 lbl_pop_vars <- c("Subjects randomized", "ITT population", "Safety population", "Per-protocol population")
 
 data <- adsl |>
   mutate(
-    across(all_of(c("ITTFL", "SAFFL")), ~ . == "Y"),
+    across(all_of("SAFFL"), ~ . == "Y"),
+    ITTFL = !is.na(RANDDT),
     rand_fl = !is.na(RANDDT),
-    prot_fl = is.na(DCSREAS)
+    prot_fl = EOSSTT == "COMPLETED"
   )
 ```
 

quarto/catalog/fda-table_03/result.png

@@ -19,7 +19,8 @@ library(dplyr)
 library(cards)
 library(gtsummary)
 
-adsl <- pharmaverseadam::adsl
+adsl <- pharmaverseadam::adsl |>
+  filter(TRT01A != "Screen Failure") # Remove screening failure observations
 
 # Pre-processing --------------------------------------------
 data <- adsl |>
@@ -52,7 +53,7 @@ ard <- data |>
     .by = TRT01A,
 
     # Analysis of treatment duration ----------------------
-    ard_continuous(
+    ard_summary(
       variables = TRTDUR,
       statistic = everything() ~ continuous_summary_fns(
         # Specify which default statistics to include

quarto/catalog/fda-table_04/index.qmd

@@ -18,18 +18,26 @@ knitr::include_graphics("result.png")
 library(gtsummary)
 library(dplyr)
 
-adsl <- random.cdisc.data::cadsl
-adae <- random.cdisc.data::cadae
+adsl <- pharmaverseadam::adsl |>
+  filter(TRT01A != "Screen Failure")
+
+adae <- pharmaverseadam::adae
 
 # Use safety population only
 adsl <- adsl |>
   filter(SAFFL == "Y")
 
 data <- adae |>
   filter(SAFFL == "Y")
-```
-
 
+set.seed(1)
+# this data set doesn't have treatment action recorded. We can generate a variable for demonstration.
+aeacn_levels <- c("DRUG INTERRUPTED", "DOSE REDUCED", "DOSE RATE REDUCED", "DOSE INCREASED")
+data <- data |>
+  mutate(AEACN = factor(sample(aeacn_levels, size = nrow(data), replace = TRUE),
+    levels = aeacn_levels
+  ))
+```
 
 ## Build Table
 
@@ -41,9 +49,7 @@ sae_vars <- list(
   "Death" = "AESDTH",
   "Life-threatening" = "AESLIFE",
   "Initial or prolonged hospitalization" = "AESHOSP",
-  "Disability or permanent damage" = "AESDISAB",
-  "Congenital anomaly or birth defect" = "AESCONG",
-  "Other" = "AESMIE"
+  "Disability or permanent damage" = "AESDISAB"
 )
 
 # Summarize SAEs per category
@@ -69,24 +75,24 @@ tbl_sae <-
 
 # --- PART 2: Permanent discontinuation
 disc_ae <- adae |>
-  filter(AEACNOTH == "SUBJECT DISCONTINUED FROM STUDY") |>
+  # filtering for adverse events with a "discontinued" End of Study Status
+  filter(AESER == "Y" & EOSSTT == "DISCONTINUED") |>
   mutate(
     # convert label to a more meaningful value
-    AEACNOTH = "AE leading to permanent discontinuation of treatment"
+    AEDISC = "AE leading to permanent discontinuation of treatment"
   )
 
 tbl_disc_ae <- tbl_hierarchical( # calculate rates
   data = disc_ae,
-  variables = AEACNOTH,
+  variables = AEDISC,
   by = TRT01A,
   id = USUBJID,
   denominator = adsl,
-  label = AEACNOTH ~ "Event"
+  label = AEDISC ~ "Event"
 )
 
 # -- PART 3: Dose modification
-dose_mod_ae <- adae |>
-  filter(AEACN %in% c("DRUG INTERRUPTED", "DOSE REDUCED", "DOSE RATE REDUCED", "DOSE INCREASED")) |>
+dose_mod_ae <- data |>
   mutate(
     AEACN = case_when( # convert to meaningful labels
       AEACN == "DRUG INTERRUPTED" ~ "AE leading to interruption of study drug",