AEL02_ED

Listing of Adverse Events (for Early Development Studies)

Output

Standard Listing
Data Setup

Preview
Try this using WebR

Code

lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "cent_subj", "ASR"),
  disp_cols = names(out),
  main_title = "Listing of Adverse Events (for early development studies)",
  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    3 = dose reduced; 4 = drug interrupted; 5 = drug withdrawn; 6 = not applicable;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.
*  Study day derived from imputed onset date.
** Duration derived from imputed onset date and/or end date."
)

head(lsting, 20)

Listing of Adverse Events (for early development studies)

————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                           Time from   Time from   Time from                                                                            
                                                                    Adverse       Study    Last Dose   Last Dose   Last Dose      AE                  Most      Caused by                         Action
                                                                  Event MedDRA    Day of   to Onset    to Onset    to Onset    Duration              Extreme      Study     Outcome   Treatment   Taken 
Treatment   Center/Patient ID            Age/Sex/Race            Preferred Term   Onset      days         hrs        mins      in Days    Serious   Intensity     Drug        (1)      for AE      (2)  
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X     BRA-1/id-134                47/M/WHITE             dcd B.2.1.2.1     162         7          19           4         173        No      MODERATE       No          5         Yes        2   
                                                                 dcd D.1.1.4.2     196         1          20          48         166        No      MODERATE       No          5         No         2   
                                                                 dcd A.1.1.1.2     321        28          12          54         149        Yes     MODERATE       No          5         Yes        2   
                                                                 dcd A.1.1.1.2     393        12          19          17          43        Yes     MODERATE       No          5         No         5   
               BRA-1/id-42      36/M/BLACK OR AFRICAN AMERICAN   dcd C.2.1.2.1      39        30           9           4         506        No      MODERATE       Yes         2         No         6   
                                                                 dcd D.1.1.1.1      64        26          17          10         630        Yes      SEVERE        Yes         1         No         6   
                                                                 dcd C.2.1.2.1      95         4          12          58         306        No      MODERATE       Yes         5         No         2   
                                                                 dcd A.1.1.1.2     160        24           5          57         259        Yes     MODERATE       No          2         Yes        2   
                                                                 dcd B.2.2.3.1     292         9          23           4          50        Yes       MILD         No          3         No         2   
                                                                 dcd A.1.1.1.2     459         9           5           4         195        Yes     MODERATE       No          5         Yes        2   
                                                                 dcd B.1.1.1.1     470         6           5           0         131        Yes      SEVERE        Yes         1         No         6   
                                                                 dcd A.1.1.1.2     475        20          16          16         113        Yes     MODERATE       No          4         Yes        2   
                                                                 dcd C.1.1.1.3     496         5           5          28         162        No       SEVERE        Yes         5         Yes        2   
                                                                 dcd B.1.1.1.1     641         8          17           4          15        Yes      SEVERE        Yes         1         Yes        6   
               BRA-1/id-93                34/F/ASIAN             dcd D.1.1.4.2      44        18          15          39          47        No      MODERATE       No          5         Yes        2   
                                                                 dcd D.2.1.5.3      79         2           3          58         300        No        MILD         Yes         5         No         3   
                                                                 dcd A.1.1.1.1     136        22           1          19          78        No        MILD         No          3         Yes        2   
                                                                 dcd D.2.1.5.3     260        12          12          26         305        No        MILD         Yes         5         No         2   
                                                                 dcd C.1.1.1.3     281         4          14          52         106        No       SEVERE        Yes         5         Yes        2   
                                                                 dcd D.1.1.1.1     316         6          12          43         250        Yes      SEVERE        Yes         1         No         6   
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————


(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.
*  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)
library(lubridate)

adae <- random.cdisc.data::cadae

adae_anl <- adae %>%
  filter(SAFFL == "Y") %>%
  mutate(
    DHM = as.period(LDOSEDTM %--% ASTDTM),
    TMOM = minute(DHM) + ifelse(second(DHM) >= 30, 1, 0),
    TMOH = hour(DHM) + ifelse(TMOM == 60, 1, 0),
    TMOD = day(DHM) + ifelse(TMOH == 24, 1, 0)
  ) %>%
  mutate(
    TMOM = TMOM %% 60,
    TMOH = TMOH %% 24
  )

out <- adae_anl %>%
  mutate(
    ADURN = AENDY - ASTDY + 1,
    cent_subj = paste(SITEID, SUBJID, sep = "/"),
    ASR = paste(AGE, SEX, RACE, sep = "/"),
    AESER_F = if_else(AESER == "Y", "Yes", "No", ""),
    AEREL_F = if_else(AEREL == "Y", "Yes", "No", ""),
    AECONTRT_F = if_else(AECONTRT == "Y", "Yes", "No", ""),
    AEOUT_F = 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
    ),
    AEACN_F = 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
    )
  ) %>%
  select(
    cent_subj, ASR, TRT01A, AEDECOD, ASTDY, TMOD, TMOH, TMOM,
    ADURN, AESER_F, AESEV, AEREL_F, AEOUT_F, AECONTRT_F, AEACN_F
  )

out <- out %>% var_relabel(
  cent_subj  = "Center/Patient ID",
  ASR        = "Age/Sex/Race",
  TRT01A     = "Treatment",
  AEDECOD    = "Adverse\nEvent MedDRA\nPreferred Term",
  ASTDY      = "Study\nDay of\nOnset",
  TMOD       = "Time from\nLast Dose\nto Onset\ndays",
  TMOH       = "Time from\nLast Dose\nto Onset\nhrs",
  TMOM       = "Time from\nLast Dose\nto Onset\nmins",
  ADURN      = "AE\nDuration\nin Days",
  AESER_F    = "Serious",
  AESEV      = "Most\nExtreme\nIntensity",
  AEREL_F    = "Caused by\nStudy\nDrug",
  AEOUT_F    = "Outcome\n(1)",
  AECONTRT_F = "Treatment\nfor AE",
  AEACN_F    = "Action\nTaken\n(2)"
)

Reproducibility

Timestamp

[1] "2024-12-21 18:08:17 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
 checkmate           2.3.2       2024-07-29 [1] RSPM
 cli                 3.6.3       2024-06-21 [1] RSPM
 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
 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
 evaluate            1.0.1       2024-10-10 [1] RSPM
 fastmap             1.2.0       2024-05-15 [1] RSPM
 formatters        * 0.5.9.9008  2024-12-21 [1] https://p~
 generics            0.1.3       2022-07-05 [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            1.8.9       2024-09-20 [1] RSPM
 knitr               1.49        2024-11-08 [1] RSPM
 lifecycle           1.0.4       2023-11-07 [1] RSPM
 lubridate         * 1.9.4       2024-12-08 [1] RSPM
 magrittr            2.0.3       2022-03-30 [1] RSPM
 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
 ps                  1.8.1       2024-10-28 [1] RSPM
 R6                  2.5.1       2021-08-19 [1] RSPM
 random.cdisc.data   0.3.16.9001 2024-12-21 [1] https://p~
 rlang               1.1.4       2024-06-04 [1] RSPM
 rlistings         * 0.2.9.9012  2024-12-21 [1] https://p~
 rmarkdown           2.29        2024-11-04 [1] RSPM
 sessioninfo         1.2.2       2021-12-06 [1] any (@1.2.2)
 stringi             1.8.4       2024-05-06 [1] RSPM
 stringr             1.5.1       2023-11-14 [1] RSPM
 testthat            3.2.2       2024-12-10 [1] RSPM
 tibble            * 3.2.1       2023-03-20 [1] RSPM
 tidyselect          1.2.1       2024-03-11 [1] RSPM
 timechange          0.3.0       2024-01-18 [1] RSPM
 vctrs               0.6.5       2023-12-01 [1] RSPM
 withr               3.0.2       2024-10-28 [1] RSPM
 xfun                0.49        2024-10-31 [1] RSPM
 yaml                2.3.10      2024-07-26 [1] RSPM

 [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

Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file