AET10

Most Common (\(\geq\) 5%) Adverse Events

Output

The “All Patients” column is not required in this table but for illustrative purposes we include it to show correct sorting.

Code
lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by(
    var = "ARM",
    split_fun = add_overall_level("All Patients", first = FALSE)
  ) %>%
  count_occurrences(vars = "AEDECOD")

tbl1 <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
)

tbl2 <- prune_table(
  tt = tbl1,
  prune_func = keep_rows(
    has_fraction_in_any_col(
      atleast = 0.05, # specify threshold
      col_names = levels(adsl$ARM)
    )
  )
)

result <- sort_at_path(
  tbl2,
  path = c("AEDECOD"),
  scorefun = score_occurrences
)

result
                A: Drug X    B: Placebo   C: Combination   All Patients
                 (N=134)      (N=134)        (N=132)         (N=400)   
———————————————————————————————————————————————————————————————————————
dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) 
dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%) 
dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%) 
dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%) 
dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%) 
dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%) 
dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%) 
dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%) 
dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%) 
dcd C.1.1.1.3   43 (32.1%)   46 (34.3%)     43 (32.6%)     132 (33.0%)

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
lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by(
    var = "ARM",
    split_fun = add_overall_level("All Patients", first = FALSE)
  ) %>%
  count_occurrences(vars = "AEDECOD")

tbl1 <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
)

tbl2 <- prune_table(
  tt = tbl1,
  prune_func = keep_rows(
    has_fraction_in_any_col(
      atleast = 0.35, # specify threshold
      col_names = levels(adsl$ARM)
    )
  )
)

result <- sort_at_path(
  tbl2,
  path = c("AEDECOD"),
  scorefun = score_occurrences
)

result
                A: Drug X    B: Placebo   C: Combination   All Patients
                 (N=134)      (N=134)        (N=132)         (N=400)   
———————————————————————————————————————————————————————————————————————
dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) 
dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%) 
dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%) 
dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%) 
dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%) 
dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%) 
dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%) 
dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%) 
dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%)

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)

teal App

The desired frequency is specified in prune_freq. For illustration, frequency is set to \(\geq\) 35%.

Code
library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  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)
})
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(
      label = "Adverse Event 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 = NULL
      ),
      add_total = TRUE,
      event_type = "adverse event",
      prune_freq = 35,
    )
  )
)

shinyApp(app$ui, app$server)

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

  # 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)
})
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(
      label = "Adverse Event 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 = NULL
      ),
      add_total = TRUE,
      event_type = "adverse event",
      prune_freq = 35,
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-12-21 18:02:31 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     2024-12-21
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version     date (UTC) lib source
 backports               1.5.0       2024-05-23 [1] RSPM
 brio                    1.1.5       2024-04-24 [1] RSPM
 broom                   1.0.7       2024-09-26 [1] RSPM
 bslib                   0.8.0       2024-07-29 [1] RSPM
 cachem                  1.1.0       2024-05-16 [1] RSPM
 callr                   3.7.6       2024-03-25 [1] RSPM
 checkmate               2.3.2       2024-07-29 [1] RSPM
 chromote                0.3.1       2024-08-30 [1] RSPM
 cli                     3.6.3       2024-06-21 [1] RSPM
 coda                    0.19-4.1    2024-01-31 [1] CRAN (R 4.4.1)
 codetools               0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
 colorspace              2.1-1       2024-07-26 [1] RSPM
 curl                    6.0.1       2024-11-14 [1] RSPM
 digest                  0.6.37      2024-08-19 [1] RSPM
 dplyr                 * 1.1.4       2023-11-17 [1] RSPM
 emmeans                 1.10.6      2024-12-12 [1] RSPM
 estimability            1.5.1       2024-05-12 [1] RSPM
 evaluate                1.0.1       2024-10-10 [1] RSPM
 fastmap                 1.2.0       2024-05-15 [1] RSPM
 fontawesome             0.5.3       2024-11-16 [1] RSPM
 forcats                 1.0.0       2023-01-29 [1] RSPM
 formatR                 1.14        2023-01-17 [1] CRAN (R 4.4.1)
 formatters            * 0.5.9.9008  2024-12-21 [1] https://p~
 geepack                 1.3.12      2024-09-23 [1] RSPM
 generics                0.1.3       2022-07-05 [1] RSPM
 ggplot2                 3.5.1       2024-04-23 [1] RSPM
 glue                    1.8.0       2024-09-30 [1] RSPM
 gtable                  0.3.6       2024-10-25 [1] RSPM
 htmltools               0.5.8.1     2024-04-04 [1] RSPM
 htmlwidgets             1.6.4       2023-12-06 [1] RSPM
 httpuv                  1.6.15      2024-03-26 [1] RSPM
 jquerylib               0.1.4       2021-04-26 [1] RSPM
 jsonlite                1.8.9       2024-09-20 [1] RSPM
 knitr                   1.49        2024-11-08 [1] RSPM
 later                   1.4.1       2024-11-27 [1] RSPM
 lattice                 0.22-6      2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle               1.0.4       2023-11-07 [1] RSPM
 logger                  0.4.0       2024-10-22 [1] RSPM
 magrittr              * 2.0.3       2022-03-30 [1] RSPM
 MASS                    7.3-61      2024-06-13 [2] CRAN (R 4.4.1)
 Matrix                  1.7-1       2024-10-18 [1] RSPM
 memoise                 2.0.1       2021-11-26 [1] RSPM
 mime                    0.12        2021-09-28 [1] RSPM
 multcomp                1.4-26      2024-07-18 [1] CRAN (R 4.4.1)
 munsell                 0.5.1       2024-04-01 [1] RSPM
 mvtnorm                 1.3-2       2024-11-04 [1] RSPM
 nestcolor               0.1.2.9017  2024-12-21 [1] https://p~
 nlme                    3.1-166     2024-08-14 [2] CRAN (R 4.4.1)
 pillar                  1.10.0      2024-12-17 [1] RSPM
 pkgcache                2.2.3       2024-09-12 [1] RSPM
 pkgconfig               2.0.3       2019-09-22 [1] RSPM
 processx                3.8.4       2024-03-16 [1] RSPM
 promises                1.3.2       2024-11-28 [1] RSPM
 ps                      1.8.1       2024-10-28 [1] RSPM
 purrr                   1.0.2       2023-08-10 [1] RSPM
 R6                      2.5.1       2021-08-19 [1] RSPM
 random.cdisc.data       0.3.16.9001 2024-12-21 [1] https://p~
 rbibutils               2.3         2024-10-04 [1] RSPM
 Rcpp                    1.0.13-1    2024-11-02 [1] RSPM
 Rdpack                  2.6.2       2024-11-15 [1] RSPM
 rlang                   1.1.4       2024-06-04 [1] RSPM
 rmarkdown               2.29        2024-11-04 [1] RSPM
 rtables               * 0.6.10.9014 2024-12-21 [1] https://p~
 sandwich                3.1-1       2024-09-15 [1] CRAN (R 4.4.1)
 sass                    0.4.9       2024-03-15 [1] RSPM
 scales                  1.3.0       2023-11-28 [1] RSPM
 sessioninfo             1.2.2       2021-12-06 [1] any (@1.2.2)
 shiny                 * 1.10.0      2024-12-14 [1] RSPM
 shinycssloaders         1.1.0       2024-07-30 [1] RSPM
 shinyjs                 2.1.0       2021-12-23 [1] RSPM
 shinyvalidate           0.1.3       2023-10-04 [1] RSPM
 shinyWidgets            0.8.7       2024-09-23 [1] RSPM
 stringi                 1.8.4       2024-05-06 [1] RSPM
 stringr                 1.5.1       2023-11-14 [1] RSPM
 survival                3.8-3       2024-12-17 [1] RSPM
 teal                  * 0.15.2.9097 2024-12-21 [1] https://p~
 teal.code             * 0.5.0.9021  2024-12-21 [1] https://p~
 teal.data             * 0.6.0.9023  2024-12-21 [1] https://p~
 teal.logger             0.3.0.9003  2024-12-21 [1] https://p~
 teal.modules.clinical * 0.9.1.9043  2024-12-21 [1] https://p~
 teal.reporter           0.3.1.9021  2024-12-21 [1] https://p~
 teal.slice            * 0.5.1.9019  2024-12-21 [1] https://p~
 teal.transform        * 0.5.0.9018  2024-12-21 [1] https://p~
 teal.widgets            0.4.2.9025  2024-12-21 [1] https://p~
 tern                  * 0.9.6.9017  2024-12-21 [1] https://p~
 tern.gee                0.1.5.9004  2024-12-21 [1] https://p~
 testthat                3.2.2       2024-12-10 [1] RSPM
 TH.data                 1.1-2       2023-04-17 [1] CRAN (R 4.4.1)
 tibble                  3.2.1       2023-03-20 [1] RSPM
 tidyr                   1.3.1       2024-01-24 [1] RSPM
 tidyselect              1.2.1       2024-03-11 [1] RSPM
 vctrs                   0.6.5       2023-12-01 [1] RSPM
 webshot                 0.5.5       2023-06-26 [1] CRAN (R 4.4.1)
 webshot2                0.1.1       2023-08-11 [1] RSPM
 websocket               1.4.2       2024-07-22 [1] RSPM
 withr                   3.0.2       2024-10-28 [1] RSPM
 xfun                    0.49        2024-10-31 [1] RSPM
 xtable                  1.8-4       2019-04-21 [1] RSPM
 yaml                    2.3.10      2024-07-26 [1] RSPM
 zoo                     1.8-12      2023-04-13 [1] CRAN (R 4.4.1)

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

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

.lock file

Download the .lock file and use renv::restore() on it to recreate environment used to generate this website.

Download