03-AET02.qmd

---
title: "Adverse Events (AET02)"
editor: source
format: 
  html:
    page-layout: full
    code-fold: true
    code-summary: "Show the code"
---

## Calculaing AET02 statistics using the {cards} package

In this example below we perform different data pre-processing for the different ARDs we want to create. 
We then generate separate ARDs for the different sections of the AET02 table and then merge them all together. 

```{r}
#| code-summary: "Show the code"

library(cards)
library(chevron)

adsl <- syn_data$adsl
adae <- syn_data$adae |>
  dplyr::filter(AEBODSYS == 'cl A.1' | AEBODSYS == "cl D.1")


# Keep only 1 record per patient
adae_one_sub <- adae %>% 
  dplyr::filter(!duplicated(adae[c("USUBJID")]))

# Keep only 1 record per patient for each AEBODSYS
adae_one_sub_aebod <- adae %>% 
  dplyr::filter(!duplicated(adae[c("USUBJID", "AEBODSYS")]))


# ----- ARDS -----
# Total number of patients with at least one adverse event
tot_pat_ae <- ard_hierarchical(
  data = adae_one_sub,
  variables = c(SAFFL),
  by = c(ARM),
  denominator = adsl,
  fmt_fn = ~ list(p = label_cards(digits = 1, scale = 100))) |>
  apply_fmt_fn() |> 
  shuffle_ard(trim = FALSE) |>
  dplyr::mutate(tbl_name = 'tot_pat_ae')

# Total number of AEs 
tot_ae <- ard_hierarchical(
  data = adae,
  variables = c(SAFFL),
  by = c(ARM),
  denominator = adsl) |> 
  shuffle_ard(trim = FALSE) |>
  dplyr::mutate(tbl_name = 'tot_ae')

# Total number of patients with at least one adverse event within each AEBODSYS
tot_pat_ae_aebod <- ard_hierarchical(
  data = adae_one_sub_aebod,
  variables = c(AEBODSYS),
  by = c(ARM),
  denominator = adsl,
  fmt_fn = ~ list(p = label_cards(digits = 1, scale = 100))) |>
  apply_fmt_fn()|> 
  shuffle_ard(trim = FALSE) |>
  dplyr::mutate(tbl_name = 'tot_pat_ae_aebod')

# Total number of AEs for each AEBODSYS
tot_ae_aebod <- ard_hierarchical(
  data = adae,
  variables = c(AEBODSYS),
  by = c(ARM),
  denominator = adsl) |> 
  shuffle_ard(trim = FALSE) |>
  dplyr::mutate(tbl_name = 'tot_ae_aebod')

# Count and Percent for each AEDECOD within each AEBODSYS
ae_n_p_aedecod <- ard_hierarchical(
  data = adae,
  variables = c(AEBODSYS, AEDECOD),
  by = c(ARM),
  denominator = adsl,
  fmt_fn = ~ list(p = label_cards(digits = 2, scale = 100))) |> 
  apply_fmt_fn()|> 
  shuffle_ard(trim = FALSE) |> 
  dplyr::mutate(tbl_name = 'ae_n_p_aedecod ')

# bind the ARDs
final_aet02_ard <- dplyr::bind_rows(tot_pat_ae, tot_ae, tot_pat_ae_aebod, tot_ae_aebod, ae_n_p_aedecod) |> 
  as.data.frame() |> 
  dplyr::select(-c(variable, context, warning, error))


final_aet02_ard
rmarkdown::paged_table(final_aet02_ard)
```