RMPT01

Duration of Exposure for Risk Management Plan

Output

Standard Table
Data Setup

Preview
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Code

lyt <- basic_table(
  title = "Duration of Exposure: Safety-Evaluable Patients",
  main_footer = "* Patient Time is the sum of exposure across all patients in days.",
  show_colcounts = TRUE
) %>%
  summarize_patients_exposure_in_cols(
    var = "AVAL", col_split = TRUE,
    .labels = c(n_patients = "Number of Patients", sum_exposure = "Patient Time*"),
    custom_label = "Total Number of Patients and Patient Time"
  ) %>%
  analyze_patients_exposure_in_cols(
    var = "aval_months_cat",
    col_split = FALSE
  ) %>%
  append_topleft(c("", "Duration of exposure"))

result <- build_table(lyt, df = anl, alt_counts_df = adsl_f)
result

Duration of Exposure: Safety-Evaluable Patients

——————————————————————————————————————————————————————————————————————————————
                                            Number of Patients   Patient Time*
Duration of exposure                             (N=400)            (N=400)   
——————————————————————————————————————————————————————————————————————————————
Total Number of Patients and Patient Time      217 (54.2%)           20641    
  < 1 month                                     28 (7.0%)             504     
  1 to <3 months                                79 (19.8%)           4727     
  3 to <6 months                               101 (25.2%)           13690    
  >=6 months                                     9 (2.2%)            1720     
——————————————————————————————————————————————————————————————————————————————

* Patient Time is the sum of exposure across all patients in days.

Experimental use!

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R Code

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lyt <- basic_table(

title = "Duration of Exposure: Safety-Evaluable Patients",

main_footer = "* Patient Time is the sum of exposure across all patients in days.",

show_colcounts = TRUE

) %>%

summarize_patients_exposure_in_cols(

var = "AVAL", col_split = TRUE,

.labels = c(n_patients = "Number of Patients", sum_exposure = "Patient Time*"),

custom_label = "Total Number of Patients and Patient Time"

) %>%

analyze_patients_exposure_in_cols(

var = "aval_months_cat",

col_split = FALSE

) %>%

append_topleft(c("", "Duration of exposure"))

result <- build_table(lyt, df = anl, alt_counts_df = adsl_f)

result

_webr_editor_2 = Object {code: "lyt <- basic_table(\n title = \"Duration of Exposur…ble(lyt, df = anl, alt_counts_df = adsl_f)\nresult", options: Object, indicator: Ke}

Code

library(tern)
library(dplyr)

adsl <- random.cdisc.data::cadsl
adex <- random.cdisc.data::cadex

# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adex <- df_explicit_na(adex)

# Simulate ADEX records with PARAMCD == "TDURD" as they are not in sample random.cdisc.data dataset.
set.seed(1, kind = "Mersenne-Twister")
adex2 <- adex %>%
  distinct(USUBJID, .keep_all = TRUE) %>%
  mutate(
    PARAMCD = "TDURD",
    PARAM = "Overall duration (days)",
    AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE)
  ) %>%
  bind_rows(adex)

# Now pre-processing steps are carried out.
anl <- adex2 %>%
  filter(
    PARAMCD == "TDURD",
    PARCAT2 == "Drug A",
    SAFFL == "Y"
  ) %>%
  mutate(
    aval_months = day2month(AVAL),
    aval_months_cat = factor(case_when(
      aval_months < 1 ~ "< 1 month",
      aval_months >= 1 & aval_months < 3 ~ "1 to <3 months",
      aval_months >= 3 & aval_months < 6 ~ "3 to <6 months",
      TRUE ~ ">=6 months"
    ), levels = c("< 1 month", "1 to <3 months", "3 to <6 months", ">=6 months"))
  )

adsl_f <- adsl %>% filter(adsl$SAFFL == "Y")

Code

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  library(dplyr)

  ADSL <- random.cdisc.data::cadsl
  ADEX <- random.cdisc.data::cadex

  labels <- col_labels(ADEX)
  set.seed(1, kind = "Mersenne-Twister")
  ADEX <- ADEX %>%
    distinct(USUBJID, .keep_all = TRUE) %>%
    mutate(
      PARAMCD = "TDURD",
      PARAM = "Overall duration (days)",
      AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
      AVALU = "Days"
    ) %>%
    bind_rows(ADEX)

  ADEX <- ADEX %>%
    mutate(
      aval_months = day2month(AVAL),
      aval_months_cat = factor(case_when(
        aval_months < 1 ~ "< 1 month",
        aval_months >= 1 & aval_months < 3 ~ "1 to <3 months",
        aval_months >= 3 & aval_months < 6 ~ "3 to <6 months",
        TRUE ~ ">=6 months"
      ), levels = c("< 1 month", "1 to <3 months", "3 to <6 months", ">=6 months")) %>% with_label("Overall duration")
    ) %>%
    select(-aval_months)
})
datanames <- c("ADSL", "ADEX")
datanames(data) <- datanames

Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
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
ADEX <- data[["ADEX"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_exposure(
      label = "Duration of Exposure Table",
      dataname = "ADEX",
      paramcd = choices_selected(
        choices = value_choices(ADEX, "PARAMCD", "PARAM"),
        selected = "TDURD"
      ),
      col_by_var = choices_selected(
        choices = variable_choices(ADEX, subset = c("ARM")),
        selected = "ARM"
      ),
      row_by_var = choices_selected(
        choices = variable_choices(ADEX, subset = c("aval_months_cat", "RACE", "STRATA1", "SEX")),
        selected = "aval_months_cat"
      ),
      parcat = choices_selected(
        choices = value_choices(ADEX, "PARCAT2"),
        selected = "Drug A"
      ),
      add_total = FALSE
    )
  ),
  filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)

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.

Reproducibility

Timestamp

[1] "2025-04-09 17:40:25 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 (2024-10-31)
 os       Ubuntu 24.04.1 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-04-09
 pandoc   3.6.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.6.43 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version     date (UTC) lib source
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 stringr                 1.5.1       2023-11-14 [1] RSPM
 survival                3.8-3       2024-12-17 [2] CRAN (R 4.4.2)
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 teal.data             * 0.7.0.9002  2025-04-09 [1] https://p~
 teal.logger             0.3.2.9000  2025-04-09 [1] https://p~
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 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library
 [3] /github/home/R/x86_64-pc-linux-gnu-library/4.4
 * ── Packages attached to the search path.

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

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Reproducibility

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Session Info

.lock file

`teal` App

`.lock` file