AET03

Adverse Events by Greatest Intensity

Output

Standard Table
Data Setup

Preview
Try this using WebR

Code

grade_groups <- list("- Any Intensity -" = c("MILD", "MODERATE", "SEVERE", "LIFE THREATENING"))

split_fun <- trim_levels_in_group

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ACTARM") %>%
  count_occurrences_by_grade(
    var = "ASEV",
    grade_groups = grade_groups
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = TRUE,
    split_fun = split_fun("ASEV"),
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_occurrences_by_grade(
    var = "ASEV",
    grade_groups = grade_groups
  ) %>%
  split_rows_by(
    "AEDECOD",
    child_labels = "visible",
    nested = TRUE,
    indent_mod = -1L,
    split_fun = split_fun("ASEV"),
    label_pos = "topleft",
    split_label = obj_label(adae$AEDECOD)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = "unique",
    .labels = c("- Any Intensity -")
  ) %>%
  count_occurrences_by_grade(
    var = "ASEV",
    .indent_mods = -1L
  ) %>%
  append_varlabels(adae, "AESEV", indent = 2L)

result <- lyt %>%
  build_table(
    adae,
    alt_counts_df = adsl
  ) %>%
  sort_at_path(
    path = "AEBODSYS",
    scorefun = cont_n_allcols,
    decreasing = TRUE
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = cont_n_allcols,
    decreasing = TRUE
  )

result

MedDRA System Organ Class                                            
  MedDRA Preferred Term      A: Drug X    B: Placebo   C: Combination
    Severity/Intensity        (N=134)      (N=134)        (N=132)    
—————————————————————————————————————————————————————————————————————
- Any Intensity -           100 (74.6%)   98 (73.1%)    103 (78.0%)  
MILD                         5 (3.7%)      7 (5.2%)       4 (3.0%)   
MODERATE                    17 (12.7%)    21 (15.7%)     20 (15.2%)  
SEVERE                      77 (57.5%)    69 (51.5%)     77 (58.3%)  
LIFE THREATENING             1 (0.7%)      1 (0.7%)       2 (1.5%)   
cl A.1                                                               
  - Any Intensity -         68 (50.7%)    58 (43.3%)     76 (57.6%)  
  MILD                      27 (20.1%)    19 (14.2%)     34 (25.8%)  
  MODERATE                  40 (29.9%)    39 (29.1%)     41 (31.1%)  
  LIFE THREATENING           1 (0.7%)         0           1 (0.8%)   
  dcd A.1.1.1.1                                                      
    - Any Intensity -       45 (33.6%)    31 (23.1%)     52 (39.4%)  
    MILD                    45 (33.6%)    31 (23.1%)     51 (38.6%)  
    LIFE THREATENING             0            0           1 (0.8%)   
  dcd A.1.1.1.2                                                      
    - Any Intensity -       41 (30.6%)    39 (29.1%)     42 (31.8%)  
    MODERATE                40 (29.9%)    39 (29.1%)     41 (31.1%)  
    LIFE THREATENING         1 (0.7%)         0           1 (0.8%)   
cl B.2                                                               
  - Any Intensity -         62 (46.3%)    56 (41.8%)     74 (56.1%)  
  MILD                      23 (17.2%)    22 (16.4%)     28 (21.2%)  
  MODERATE                  38 (28.4%)    34 (25.4%)     45 (34.1%)  
  LIFE THREATENING           1 (0.7%)         0           1 (0.8%)   
  dcd B.2.2.3.1                                                      
    - Any Intensity -       38 (28.4%)    40 (29.9%)     45 (34.1%)  
    MILD                    38 (28.4%)    40 (29.9%)     45 (34.1%)  
  dcd B.2.1.2.1                                                      
    - Any Intensity -       39 (29.1%)    34 (25.4%)     46 (34.8%)  
    MODERATE                38 (28.4%)    34 (25.4%)     45 (34.1%)  
    LIFE THREATENING         1 (0.7%)         0           1 (0.8%)   
cl D.1                                                               
  - Any Intensity -         64 (47.8%)    54 (40.3%)     68 (51.5%)  
  MODERATE                  21 (15.7%)    22 (16.4%)     22 (16.7%)  
  SEVERE                    42 (31.3%)    32 (23.9%)     44 (33.3%)  
  LIFE THREATENING           1 (0.7%)         0           2 (1.5%)   
  dcd D.1.1.1.1                                                      
    - Any Intensity -       42 (31.3%)    32 (23.9%)     46 (34.8%)  
    SEVERE                  42 (31.3%)    32 (23.9%)     45 (34.1%)  
    LIFE THREATENING             0            0           1 (0.8%)   
  dcd D.1.1.4.2                                                      
    - Any Intensity -       38 (28.4%)    34 (25.4%)     40 (30.3%)  
    MODERATE                37 (27.6%)    34 (25.4%)     39 (29.5%)  
    LIFE THREATENING         1 (0.7%)         0           1 (0.8%)   
cl D.2                                                               
  - Any Intensity -         37 (27.6%)    46 (34.3%)     50 (37.9%)  
  MILD                      37 (27.6%)    46 (34.3%)     49 (37.1%)  
  LIFE THREATENING               0            0           1 (0.8%)   
  dcd D.2.1.5.3                                                      
    - Any Intensity -       37 (27.6%)    46 (34.3%)     50 (37.9%)  
    MILD                    37 (27.6%)    46 (34.3%)     49 (37.1%)  
    LIFE THREATENING             0            0           1 (0.8%)   
cl C.2                                                               
  - Any Intensity -         28 (20.9%)    36 (26.9%)     48 (36.4%)  
  MODERATE                  28 (20.9%)    36 (26.9%)     47 (35.6%)  
  LIFE THREATENING               0            0           1 (0.8%)   
  dcd C.2.1.2.1                                                      
    - Any Intensity -       28 (20.9%)    36 (26.9%)     48 (36.4%)  
    MODERATE                28 (20.9%)    36 (26.9%)     47 (35.6%)  
    LIFE THREATENING             0            0           1 (0.8%)   
cl B.1                                                               
  - Any Intensity -         38 (28.4%)    37 (27.6%)     36 (27.3%)  
  SEVERE                    38 (28.4%)    36 (26.9%)     36 (27.3%)  
  LIFE THREATENING               0         1 (0.7%)          0       
  dcd B.1.1.1.1                                                      
    - Any Intensity -       38 (28.4%)    37 (27.6%)     36 (27.3%)  
    SEVERE                  38 (28.4%)    36 (26.9%)     36 (27.3%)  
    LIFE THREATENING             0         1 (0.7%)          0       
cl C.1                                                               
  - Any Intensity -         36 (26.9%)    34 (25.4%)     36 (27.3%)  
  SEVERE                    36 (26.9%)    34 (25.4%)     36 (27.3%)  
  dcd C.1.1.1.3                                                      
    - Any Intensity -       36 (26.9%)    34 (25.4%)     36 (27.3%)  
    SEVERE                  36 (26.9%)    34 (25.4%)     36 (27.3%)

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Code

library(tern)
library(dplyr)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adae <- df_explicit_na(adae) %>%
  var_relabel(
    AEBODSYS = "MedDRA System Organ Class",
    AEDECOD = "MedDRA Preferred Term"
  ) %>%
  filter(ANL01FL == "Y")
adae <- adae %>% mutate(ASEV = as.character(AESEV))
adae$ASEV[1:15] <- "LIFE THREATENING"
adae <- adae %>% mutate(ASEV = factor(ASEV, levels = c("MILD", "MODERATE", "SEVERE", "LIFE THREATENING")))

Code

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADAE <- random.cdisc.data::cadae
})
datanames <- c("ADSL", "ADAE")
datanames(data) <- datanames

Warning: `datanames<-()` was deprecated in teal.data 0.6.1.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data

Code

join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADAE <- data[["ADAE"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      grade = choices_selected(
        choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
        selected = "AESEV"
      )
    )
  )
)

shinyApp(app$ui, app$server)

Experimental use!

shinylive allow you to modify to run shiny application entirely in the web browser. Modify the code below and click re-run the app to see the results. The performance is slighly worse and some of the features (e.g. downloading) might not work at all.

#| '!! shinylive warning !!': |
#|   shinylive does not work in self-contained HTML documents.
#|   Please set `embed-resources: false` in your metadata.
#| standalone: true
#| viewerHeight: 800
#| editorHeight: 200
#| components: [viewer, editor]
#| layout: vertical

# -- WEBR HELPERS --
options(webr_pkg_repos = c("r-universe" = "https://pharmaverse.r-universe.dev", getOption("webr_pkg_repos")))

# -- APP CODE --
library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADAE <- random.cdisc.data::cadae
})
datanames <- c("ADSL", "ADAE")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADAE <- data[["ADAE"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      grade = choices_selected(
        choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
        selected = "AESEV"
      )
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-20 18:09:27 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-20
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
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 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

──────────────────────────────────────────────────────────────────────────────

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Output

teal App

Reproducibility

Timestamp

Session Info

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`teal` App

`.lock` file