Merge pull request #133 from pharmaverse/tfrmt_example

closes #122 add Tfrmt demographic and ae table examples

Author: bms63

DESCRIPTION

@@ -16,6 +16,7 @@ Authors@R:
     person("Aksel", "Thomsen", , "oath@novonordisk.com", role = "aut"),
     person("Shiyu", "Chen", , "shiyu.chen@atorusresearch.com", role = "aut"),
     person("Rammprasad", "Ganapathy", , "rammprasad.ganapathy@gene.com", role = "aut")
+    person("Alanah", "Jonas", , "alanah.x.jonas@gsk.com", role = "aut"),
 Description: This is not a package, but we just use this file to declare
     the dependencies of the site.
 URL: https://github.com/pharmaverse/examples
@@ -26,6 +27,7 @@ Imports:
     cards,
     dplyr,
     filters,
+    forcats,
     gtsummary,
     lubridate,
     labelled,
@@ -50,6 +52,7 @@ Imports:
     teal.modules.clinical,
     teal.modules.general,
     tern,
+    tfrmt,
     tidyr,
     xportr,
     logr,

inst/WORDLIST

@@ -41,6 +41,7 @@ ae
 AE
 AEACN
 AEBDSYCD
+aebodsys
 AEBODSYS
 AEDECOD
 AEDIS
@@ -84,6 +85,7 @@ AESTDAT
 AESTDTC
 AESTDY
 AETERM
+aeterm
 AETHNIC
 AETHNICN
 AFRLT
@@ -164,6 +166,7 @@ bds
 BDS
 BILI
 BILIBL
+bigN
 BLAS
 blq
 BLQ
@@ -351,14 +354,19 @@ fansi
 FAS
 FASFL
 fastmap
+fct
 FDA's
 fileext
 flextable
 flx
 fmt
+fns
+forcats
 formatters
 FORMN
+freqs
 FRLTU
+frmt
 FRVDT
 fs
 Garolini
@@ -388,6 +396,7 @@ iconv
 ifelse
 iframe
 init
+inorder
 inputId
 installedpackages
 ITT
@@ -494,6 +503,7 @@ onco
 ONCO
 ontrtfl
 ONTRTFL
+ord
 os
 othgrpvars
 outfile
@@ -532,6 +542,7 @@ PCTEST
 PCTESTCD
 PCTPT
 PCTPTNUM
+pcts
 pfs
 PFS
 pharma
@@ -604,6 +615,7 @@ refdates
 refdt
 REGIONCAT
 REGIONx
+relevel
 renderPlot
 renderUI
 renv
@@ -713,6 +725,7 @@ tempfile
 TEMPLOC
 TESTCD
 tf
+tfrmt
 tformat
 tgdt
 tgt

tlg/adverse_events.R

@@ -57,3 +57,112 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
 result <- build_table(lyt, df = adae, alt_counts_df = adsl)
 
 result
+
+## ----r message=FALSE, warning=FALSE-------------------------------------------
+library(pharmaverseadam) # for clinical trial data
+library(dplyr) # for data manipulation
+library(cards) # for creating analysis result displays
+library(tfrmt) # for formatting tables in R
+
+## ----r------------------------------------------------------------------------
+# Filter to include only subjects marked as part of the safety population
+adsl <- pharmaverseadam::adsl |>
+  filter(SAFFL == "Y")
+# Load adverse event data
+adae <- pharmaverseadam::adae |>
+  filter(SAFFL == "Y" & TRTEMFL == "Y")
+
+## ----r------------------------------------------------------------------------
+# Create an ARD that stacks hierarchical data of adverse events
+# Grouping by treatment, system organ class, and preferred term
+ae_ard <- ard_stack_hierarchical(
+  data = adae,
+  by = TRT01A, # Note: by variables must be present in the denominator dataset
+  variables = c(AEBODSYS, AETERM),
+  statistic = ~ c("n", "p"), # Calculate count and percentage
+  denominator = adsl,
+  id = USUBJID,
+  over_variables = TRUE,
+  overall = TRUE
+)
+
+# Filter adae and adsl with trt01a set to "Total" and create a new ARD for the total column
+adae2 <- adae |>
+  mutate(TRT01A = "Total")
+adsl2 <- adsl |>
+  mutate(TRT01A = "Total")
+
+ae2_ard <- ard_stack_hierarchical(
+  data = adae2,
+  by = TRT01A, # Note: by variables must be present in the denominator dataset
+  variables = c(AEBODSYS, AETERM),
+  denominator = adsl2,
+  statistic = ~ c("n", "p"),
+  id = USUBJID,
+  over_variables = TRUE,
+  overall = TRUE
+) |>
+  filter(group2 == "TRT01A" | variable == "TRT01A") # filter to stats we need
+
+## ----r------------------------------------------------------------------------
+ae3_ard <- bind_ard(ae_ard, ae2_ard) |>
+  # reshape the data
+  shuffle_card(fill_hierarchical_overall = "ANY EVENT") |>
+  # transform group-level freqs/pcts into a singular "bigN" row
+  prep_big_n(vars = "TRT01A") |>
+  # for nested variables, fill any missing values with "ANY EVENT"
+  prep_hierarchical_fill(vars = c("AEBODSYS", "AETERM"), fill = "ANY EVENT") |>
+  mutate(TRT01A = ifelse(TRT01A == "Overall TRT01A", "Total", TRT01A))
+
+# create ordering columns, sort by AEBODSYS
+ordering_aebodsys <- ae3_ard |>
+  filter(TRT01A == "Total", stat_name == "n", AETERM == "ANY EVENT") |>
+  arrange(desc(stat)) |>
+  mutate(ord1 = row_number()) |>
+  select(AEBODSYS, ord1)
+
+# sort by AETERM after AEBODSYS order
+ordering_aeterm <- ae3_ard |>
+  filter(TRT01A == "Total", stat_name == "n") |>
+  group_by(AEBODSYS) |>
+  arrange(desc(stat)) |>
+  mutate(ord2 = row_number()) |>
+  select(AEBODSYS, AETERM, ord2)
+
+# join on our ordering columns and keep required columns
+ae4_ard <- ae3_ard |>
+  full_join(ordering_aebodsys, by = "AEBODSYS") |>
+  full_join(ordering_aeterm, by = c("AEBODSYS", "AETERM")) |>
+  select(AEBODSYS, AETERM, ord1, ord2, stat, stat_name, TRT01A)
+
+## ----r------------------------------------------------------------------------
+AE_T01 <- tfrmt_n_pct(
+  n = "n", pct = "p",
+  pct_frmt_when = frmt_when(
+    "==1" ~ frmt("(100%)"),
+    ">=0.995" ~ frmt("(>99%)"),
+    "==0" ~ frmt(""),
+    "<=0.01" ~ frmt("(<1%)"),
+    "TRUE" ~ frmt("(xx.x%)", transform = ~ . * 100)
+  )
+) |>
+  tfrmt(
+    group = AEBODSYS,
+    label = AETERM,
+    param = stat_name,
+    value = stat,
+    column = TRT01A,
+    sorting_cols = c(ord1, ord2),
+    col_plan = col_plan(
+      "System Organ Class
+            Preferred Term" = AEBODSYS, Placebo, `Xanomeline High Dose`, `Xanomeline Low Dose`,
+      -ord1, -ord2
+    ),
+    row_grp_plan = row_grp_plan(row_grp_structure(
+      group_val = ".default", element_block(post_space = " ")
+    )),
+    big_n = big_n_structure(param_val = "bigN", n_frmt = frmt(" (N=xx)"))
+  ) |>
+  print_to_gt(ae4_ard)
+
+AE_T01