TLG Catalog - Stable
  • Stable
    • Dev
  1. Listings
  2. Adverse Events
  3. AEL03
  • Introduction

  • Tables
    • ADA
      • ADAT01
      • ADAT02
      • ADAT03
      • ADAT04A
      • ADAT04B
    • Adverse Events
      • AET01
      • AET01_AESI
      • AET02
      • AET02_SMQ
      • AET03
      • AET04
      • AET04_PI
      • AET05
      • AET05_ALL
      • AET06
      • AET06_SMQ
      • AET07
      • AET09
      • AET09_SMQ
      • AET10
    • Concomitant Medications
      • CMT01
      • CMT01A
      • CMT01B
      • CMT02_PT
    • Deaths
      • DTHT01
    • Demography
      • DMT01
    • Disclosures
      • DISCLOSUREST01
      • EUDRAT01
      • EUDRAT02
    • Disposition
      • DST01
      • PDT01
      • PDT02
    • ECG
      • EGT01
      • EGT02
      • EGT03
      • EGT04
      • EGT05_QTCAT
    • Efficacy
      • AOVT01
      • AOVT02
      • AOVT03
      • CFBT01
      • CMHT01
      • COXT01
      • COXT02
      • DORT01
      • LGRT02
      • MMRMT01
      • ONCT05
      • RATET01
      • RBMIT01
      • RSPT01
      • TTET01
    • Exposure
      • EXT01
    • Lab Results
      • LBT01
      • LBT02
      • LBT03
      • LBT04
      • LBT05
      • LBT06
      • LBT07
      • LBT08
      • LBT09
      • LBT10
      • LBT10_BL
      • LBT11
      • LBT11_BL
      • LBT12
      • LBT12_BL
      • LBT13
      • LBT14
      • LBT15
    • Medical History
      • MHT01
    • Pharmacokinetic
      • PKCT01
      • PKPT02
      • PKPT03
      • PKPT04
      • PKPT05
      • PKPT06
      • PKPT07
      • PKPT08
      • PKPT11
    • Risk Management Plan
      • RMPT01
      • RMPT03
      • RMPT04
      • RMPT05
      • RMPT06
    • Safety
      • ENTXX
    • Vital Signs
      • VST01
      • VST02
  • Listings
    • ADA
      • ADAL02
    • Adverse Events
      • AEL01
      • AEL01_NOLLT
      • AEL02
      • AEL02_ED
      • AEL03
      • AEL04
    • Concomitant Medications
      • CML01
      • CML02A_GL
      • CML02B_GL
    • Development Safety Update Report
      • DSUR4
    • Disposition
      • DSL01
      • DSL02
    • ECG
      • EGL01
    • Efficacy
      • ONCL01
    • Exposure
      • EXL01
    • Lab Results
      • LBL01
      • LBL01_RLS
      • LBL02A
      • LBL02A_RLS
      • LBL02B
    • Medical History
      • MHL01
    • Pharmacokinetic
      • ADAL01
      • PKCL01
      • PKCL02
      • PKPL01
      • PKPL02
      • PKPL04
    • Vital Signs
      • VSL01
  • Graphs
    • Efficacy
      • FSTG01
      • FSTG02
      • KMG01
      • MMRMG01
      • MMRMG02
    • Other
      • BRG01
      • BWG01
      • CIG01
      • IPPG01
      • LTG01
      • MNG01
    • Pharmacokinetic
      • PKCG01
      • PKCG02
      • PKCG03
      • PKPG01
      • PKPG02
      • PKPG03
      • PKPG04
      • PKPG06

  • Appendix
    • Reproducibility

  • Index

On this page

  • Output
  • Reproducibility
    • Timestamp
    • Session Info
    • .lock file
  • Edit this page
  • Report an issue
  1. Listings
  2. Adverse Events
  3. AEL03

AEL03

Listing of Serious Adverse Events


Output

  • Standard Listing
  • Data Setup
  • Preview
  • Try this using WebR
Code
lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CPID", "ASR"),
  disp_cols = names(out),
  main_title = "Listing of Serious Adverse Events",
  main_footer = "
(1) Outcome: 1 = fatal; 2 = not recovered/not resolved; 3 = recovered/resolved;
    4 = recovered/resolved with sequelae; 5 = recovering/resolving; 6 = unknown.
(2) Action taken with study drug: 1 = dose increased; 2 = dose not changed;
    3 = dose reduced; 4 = drug interrupted; 5 = drug withdrawn; 6 = not applicable;
    7 = unknown.
(3) Reason classified as serious: 1 = resulted in death; 2 = life threatening;
    3 = required prolonged in patient hospitalization; 4 = disabling;
    5 = a congenital anomaly/birth defect in offspring of study subject;
    6 = does not meet any of the above serious criteria, but may jeopardize the subject,
    and may require medical or surgical intervention to prevent one of the outcomes listed above.
*  Study day derived from imputed onset date.
** Duration derived from imputed onset date and/or end date."
)

head(lsting, 20)
Listing of Serious Adverse Events

————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                     Date of                                                                                    Reason  
                                                                    Adverse        First Study     Study       AE        Most      Caused by                         Action   Classified
                                                                  Event MedDRA         Drug        Day of   Duration    Extreme      Study     Outcome   Treatment   Taken    as Serious
Treatment   Center/Patient ID            Age/Sex/Race            Preferred Term   Administration   Onset    in Days    Intensity     Drug        (1)      for AE      (2)        (3)    
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X     BRA-1/id-134                47/M/WHITE             dcd A.1.1.1.2      04NOV2020       321       149      MODERATE       No          5         Yes        2         4, 5   
                                                                 dcd A.1.1.1.2      04NOV2020       393        43      MODERATE       No          5         No         5          5     
               BRA-1/id-42      36/M/BLACK OR AFRICAN AMERICAN   dcd D.1.1.1.1      01JAN2020        64       630       SEVERE        Yes         1         No         6          1     
                                                                 dcd A.1.1.1.2      01JAN2020       160       259      MODERATE       No          2         Yes        2          4     
                                                                 dcd B.2.2.3.1      01JAN2020       292        50        MILD         No          3         No         2          4     
                                                                 dcd A.1.1.1.2      01JAN2020       459       195      MODERATE       No          5         Yes        2          5     
                                                                 dcd B.1.1.1.1      01JAN2020       470       131       SEVERE        Yes         1         No         6          1     
                                                                 dcd A.1.1.1.2      01JAN2020       475       113      MODERATE       No          4         Yes        2          4     
                                                                 dcd B.1.1.1.1      01JAN2020       641        15       SEVERE        Yes         1         Yes        6          1     
               BRA-1/id-93                34/F/ASIAN             dcd D.1.1.1.1      20JUN2020       316       250       SEVERE        Yes         1         No         6          1     
                                                                 dcd B.1.1.1.1      20JUN2020       523        24       SEVERE        Yes         1         No         6          1     
                                                                 dcd B.2.2.3.1      20JUN2020       596        10        MILD         No          3         Yes        2          4     
              BRA-11/id-345               37/F/WHITE             dcd B.1.1.1.1      18AUG2020       1009       35       SEVERE        Yes         1         No         6          1     
              BRA-11/id-397               38/M/ASIAN             dcd D.1.1.1.1      27JUN2020       516       441       SEVERE        Yes         1         No         6          1     
                                                                 dcd B.1.1.1.1      27JUN2020       1011       30       SEVERE        Yes         1         Yes        6          1     
              BRA-11/id-50      26/M/BLACK OR AFRICAN AMERICAN   dcd A.1.1.1.2      28APR2019       1007       68      MODERATE       No          3         Yes        2          5     
              BRA-13/id-177               24/M/WHITE             dcd B.1.1.1.1      30AUG2020       249       470       SEVERE        Yes         1         No         6          1     
                                                                 dcd B.1.1.1.1      30AUG2020       1012       33       SEVERE        Yes         1         No         6          1     
              BRA-15/id-36                38/F/ASIAN             dcd B.1.1.1.1      08JAN2020       372       154       SEVERE        Yes         1         Yes        6          1     
                                                                 dcd A.1.1.1.2      08JAN2020       573       134      MODERATE       No          3         Yes        2          3     
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————


(1) Outcome: 1 = fatal; 2 = not recovered/not resolved; 3 = recovered/resolved;
    4 = recovered/resolved with sequelae; 5 = recovering/resolving; 6 = unknown.
(2) Action taken with study drug: 1 = dose increased; 2 = dose not changed;
    3 = dose reduced; 4 = drug interrupted; 5 = drug withdrawn; 6 = not applicable;
    7 = unknown.
(3) Reason classified as serious: 1 = resulted in death; 2 = life threatening;
    3 = required prolonged in patient hospitalization; 4 = disabling;
    5 = a congenital anomaly/birth defect in offspring of study subject;
    6 = does not meet any of the above serious criteria, but may jeopardize the subject,
    and may require medical or surgical intervention to prevent one of the outcomes listed above.
*  Study day derived from imputed onset date.
** Duration derived from imputed onset date and/or end date.
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(dplyr)
library(rlistings)

adae <- random.cdisc.data::cadae
adae$AESCONG[which(adae$AESER == "Y")[seq(3)]] <- "Y" # To mimic possibility of overlap

out <- adae %>%
  filter(AESER == "Y") %>%
  mutate(
    CPID = paste(SITEID, SUBJID, sep = "/"),
    ASR = paste(AGE, SEX, RACE, sep = "/"),
    Date_First = toupper(format(as.Date(TRTSDTM), "%d%b%Y")),
    Duration = AENDY - ASTDY + 1,
    Related = ifelse(AEREL == "Y", "Yes", ifelse(AEREL == "N", "No", "")),
    Outcome = case_when(
      AEOUT == "FATAL" ~ 1,
      AEOUT == "NOT RECOVERED/NOT RESOLVED" ~ 2,
      AEOUT == "RECOVERED/RESOLVED" ~ 3,
      AEOUT == "RECOVERED/RESOLVED WITH SEQUELAE" ~ 4,
      AEOUT == "RECOVERING/RESOLVING" ~ 5,
      AEOUT == "UNKNOWN" ~ 6
    ),
    Treated = ifelse(AECONTRT == "Y", "Yes", ifelse(AECONTRT == "N", "No", "")),
    Action = case_when(
      AEACN == "DOSE INCREASED" ~ 1,
      AEACN == "DOSE NOT CHANGED" ~ 2,
      AEACN == "DOSE REDUCED" | AEACN == "DOSE RATE REDUCED" ~ 3,
      AEACN == "DRUG INTERRUPTED" ~ 4,
      AEACN == "DRUG WITHDRAWN" ~ 5,
      AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
      AEACN == "UNKNOWN" ~ 7
    )
  ) %>%
  rowwise() %>%
  mutate(
    SERREAS = paste(
      which(
        c(AESDTH, AESLIFE, AESHOSP, AESDISAB, AESCONG, AESMIE) == "Y"
      ),
      collapse = ", "
    )
  ) %>%
  ungroup()

out <- out %>%
  select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, AESEV, Related, Outcome, Treated, Action, SERREAS)

var_labels(out) <- c(
  CPID = "Center/Patient ID",
  ASR = "Age/Sex/Race",
  TRT01A = "Treatment",
  AEDECOD = "Adverse\nEvent MedDRA\nPreferred Term",
  Date_First = "Date of\nFirst Study\nDrug\nAdministration",
  ASTDY = "Study\nDay of\nOnset",
  Duration = "AE\nDuration\nin Days",
  AESEV = "Most\nExtreme\nIntensity",
  Related = "Caused by\nStudy\nDrug",
  Outcome = "Outcome\n(1)",
  Treated = "Treatment\nfor AE",
  Action = "Action\nTaken\n(2)",
  SERREAS = "Reason\nClassified\nas Serious\n(3)"
)

Reproducibility

Timestamp

[1] "2025-07-09 17:36:57 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-07-09
 pandoc   3.7.0.2 @ /usr/bin/ (via rmarkdown)
 quarto   1.7.32 @ /usr/local/bin/quarto

─ 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
 checkmate           2.3.2   2024-07-29 [1] RSPM
 cli                 3.6.5   2025-04-23 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.5.0)
 curl                6.4.0   2025-06-22 [1] RSPM
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.4   2025-06-18 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.11  2025-04-09 [1] RSPM
 generics            0.1.4   2025-05-09 [1] RSPM
 glue                1.8.0   2024-09-30 [1] RSPM
 htmltools           0.5.8.1 2024-04-04 [1] RSPM
 htmlwidgets         1.6.4   2023-12-06 [1] RSPM
 jsonlite            2.0.0   2025-03-27 [1] RSPM
 knitr               1.50    2025-03-16 [1] RSPM
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr            2.0.3   2022-03-30 [1] RSPM
 pillar              1.11.0  2025-07-04 [1] RSPM
 pkgcache            2.2.4   2025-05-26 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.6   2025-02-21 [1] RSPM
 ps                  1.9.1   2025-04-12 [1] RSPM
 R6                  2.6.1   2025-02-15 [1] RSPM
 random.cdisc.data   0.3.16  2024-10-10 [1] RSPM
 rlang               1.1.6   2025-04-11 [1] RSPM
 rlistings         * 0.2.12  2025-06-15 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 sessioninfo         1.2.3   2025-02-05 [1] any (@1.2.3)
 stringi             1.8.7   2025-03-27 [1] RSPM
 stringr             1.5.1   2023-11-14 [1] RSPM
 testthat            3.2.3   2025-01-13 [1] RSPM
 tibble            * 3.3.0   2025-06-08 [1] RSPM
 tidyselect          1.2.1   2024-03-11 [1] RSPM
 vctrs               0.6.5   2023-12-01 [1] RSPM
 withr               3.0.2   2024-10-28 [1] RSPM
 xfun                0.52    2025-04-02 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library
 [3] /github/home/R/x86_64-pc-linux-gnu-library/4.5
 * ── Packages attached to the search path.

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

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

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AEL02_ED
AEL04
Source Code
---
title: AEL03
subtitle: Listing of Serious Adverse Events
---

------------------------------------------------------------------------

{{< include ../../_utils/envir_hook.qmd >}}

```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(dplyr)
library(rlistings)

adae <- random.cdisc.data::cadae
adae$AESCONG[which(adae$AESER == "Y")[seq(3)]] <- "Y" # To mimic possibility of overlap

out <- adae %>%
  filter(AESER == "Y") %>%
  mutate(
    CPID = paste(SITEID, SUBJID, sep = "/"),
    ASR = paste(AGE, SEX, RACE, sep = "/"),
    Date_First = toupper(format(as.Date(TRTSDTM), "%d%b%Y")),
    Duration = AENDY - ASTDY + 1,
    Related = ifelse(AEREL == "Y", "Yes", ifelse(AEREL == "N", "No", "")),
    Outcome = case_when(
      AEOUT == "FATAL" ~ 1,
      AEOUT == "NOT RECOVERED/NOT RESOLVED" ~ 2,
      AEOUT == "RECOVERED/RESOLVED" ~ 3,
      AEOUT == "RECOVERED/RESOLVED WITH SEQUELAE" ~ 4,
      AEOUT == "RECOVERING/RESOLVING" ~ 5,
      AEOUT == "UNKNOWN" ~ 6
    ),
    Treated = ifelse(AECONTRT == "Y", "Yes", ifelse(AECONTRT == "N", "No", "")),
    Action = case_when(
      AEACN == "DOSE INCREASED" ~ 1,
      AEACN == "DOSE NOT CHANGED" ~ 2,
      AEACN == "DOSE REDUCED" | AEACN == "DOSE RATE REDUCED" ~ 3,
      AEACN == "DRUG INTERRUPTED" ~ 4,
      AEACN == "DRUG WITHDRAWN" ~ 5,
      AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
      AEACN == "UNKNOWN" ~ 7
    )
  ) %>%
  rowwise() %>%
  mutate(
    SERREAS = paste(
      which(
        c(AESDTH, AESLIFE, AESHOSP, AESDISAB, AESCONG, AESMIE) == "Y"
      ),
      collapse = ", "
    )
  ) %>%
  ungroup()

out <- out %>%
  select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, AESEV, Related, Outcome, Treated, Action, SERREAS)

var_labels(out) <- c(
  CPID = "Center/Patient ID",
  ASR = "Age/Sex/Race",
  TRT01A = "Treatment",
  AEDECOD = "Adverse\nEvent MedDRA\nPreferred Term",
  Date_First = "Date of\nFirst Study\nDrug\nAdministration",
  ASTDY = "Study\nDay of\nOnset",
  Duration = "AE\nDuration\nin Days",
  AESEV = "Most\nExtreme\nIntensity",
  Related = "Caused by\nStudy\nDrug",
  Outcome = "Outcome\n(1)",
  Treated = "Treatment\nfor AE",
  Action = "Action\nTaken\n(2)",
  SERREAS = "Reason\nClassified\nas Serious\n(3)"
)
```

```{r include = FALSE}
webr_code_labels <- c("setup")
```

{{< include ../../_utils/webr_no_include.qmd >}}

## Output

:::: panel-tabset
## Standard Listing

::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview

```{r lsting, test = list(lsting = "lsting")}
lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CPID", "ASR"),
  disp_cols = names(out),
  main_title = "Listing of Serious Adverse Events",
  main_footer = "
(1) Outcome: 1 = fatal; 2 = not recovered/not resolved; 3 = recovered/resolved;
    4 = recovered/resolved with sequelae; 5 = recovering/resolving; 6 = unknown.
(2) Action taken with study drug: 1 = dose increased; 2 = dose not changed;
    3 = dose reduced; 4 = drug interrupted; 5 = drug withdrawn; 6 = not applicable;
    7 = unknown.
(3) Reason classified as serious: 1 = resulted in death; 2 = life threatening;
    3 = required prolonged in patient hospitalization; 4 = disabling;
    5 = a congenital anomaly/birth defect in offspring of study subject;
    6 = does not meet any of the above serious criteria, but may jeopardize the subject,
    and may require medical or surgical intervention to prevent one of the outcomes listed above.
*  Study day derived from imputed onset date.
** Duration derived from imputed onset date and/or end date."
)

head(lsting, 20)
```

```{r include = FALSE}
webr_code_labels <- c("lsting")
```

{{< include ../../_utils/webr.qmd >}}
:::

## Data Setup

```{r setup}
#| code-fold: show
```
::::

{{< include ../../_utils/save_results.qmd >}}

{{< include ../../repro.qmd >}}

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