ONCL01

Listing of Individual Efficacy Data

Standard Listing
Data Setup

Preview
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Code

lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "ID"),
  disp_cols = names(out),
  main_title = "Listing of Individual Efficacy Data",
  main_footer = "PFS = Progression Free Survival"
)

head(lsting, 20)

Listing of Individual Efficacy Data

————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                   Best Confirmed      Investigator                                                          Duration of    
                                Number of Doses   Overall Response   End Of Induction   Overall Survival    PFS      Triggering Event     Confirmed Response
Treatment   Center/Patient ID      Received       by Investigator        Response            (days)        (days)         for PFS               (days)      
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X     BRA-1/id-105             7                 CR                 CR               402.6         235.7    Disease Progression         119.6       
                                       7                 CR                 CR               402.6         235.7            NA                  119.6       
                                       7                 CR                 CR               402.6         235.7            NA                  119.6       
              BRA-1/id-134             7                 CR                 CR                90.1          90.1           Death                 90.1       
                                       7                 CR                 CR                90.1          90.1           Death                 90.1       
                                       7                 CR                 CR                90.1          90.1           Death                 90.1       
               BRA-1/id-42             7                 PR                 PR               407.0         204.6    Disease Progression         193.9       
                                       7                 PR                 PR               407.0         204.6            NA                  193.9       
                                       7                 PR                 PR               407.0         204.6            NA                  193.9       
               BRA-1/id-93             7                 CR                 PD               316.0         255.7            NA                  140.3       
                                       7                 CR                 PD               316.0         255.7            NA                  140.3       
                                       7                 CR                 PD               316.0         255.7            NA                  140.3       
              BRA-11/id-217            7                 CR                 CR               293.0         293.0    Disease Progression         153.2       
                                       7                 CR                 CR               293.0         293.0           Death                153.2       
                                       7                 CR                 CR               293.0         293.0           Death                153.2       
              BRA-11/id-345            7                 CR                 CR               305.5         272.6            NA                  150.6       
                                       7                 CR                 CR               305.5         272.6            NA                  150.6       
                                       7                 CR                 CR               305.5         272.6            NA                  150.6       
              BRA-11/id-397            7                 PR                 PR               138.7         138.7           Death                138.7       
                                       7                 PR                 PR               138.7         138.7           Death                138.7       
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

PFS = Progression Free Survival

Experimental use!

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Code

library(dplyr)
library(rlistings)

adrs <- random.cdisc.data::cadrs
adtte <- random.cdisc.data::cadtte
adex <- random.cdisc.data::cadex

out_ex <- adex %>%
  filter(PARAMCD == "TNDOSE") %>%
  mutate(ID = paste(SITEID, SUBJID, sep = "/")) %>%
  select(ID, AVAL)

out_rs <- adrs %>%
  filter(PARAM %in% c("Investigator End Of Induction Response", "Best Confirmed Overall Response by Investigator")) %>%
  mutate(ID = paste(SITEID, SUBJID, sep = "/")) %>%
  select(ID, AVALC, PARAM) %>%
  tidyr::pivot_wider(
    id_cols = ID,
    names_from = PARAM,
    values_from = AVALC
  ) %>%
  right_join(out_ex, ., by = "ID", multiple = "all")

adtte_flt <- adtte %>%
  filter(PARAMCD %in% c("OS", "PFS", "CRSD")) %>%
  mutate(
    PARAM = paste(PARAM, paste0("(", AVALU, ")"), sep = " "), ID = paste(SITEID, SUBJID, sep = "/"),
    trigeventpfs = ifelse(CNSR == 0, EVNTDESC, NA)
  )

# Select triggering event variable
out_trg <- adtte_flt %>%
  select(ID, trigeventpfs)

out_tte <- adtte_flt %>%
  select(ID, TRT01A, PARAM, AVAL, trigeventpfs) %>%
  tidyr::pivot_wider(
    id_cols = c(ID, TRT01A),
    names_from = PARAM,
    values_from = AVAL
  ) %>%
  mutate_at(
    c("Overall Survival (DAYS)", "Progression Free Survival (DAYS)", "Duration of Confirmed Response (DAYS)"),
    function(x) format(round(x, 1), nsmall = 1)
  ) %>%
  select(
    ID,
    TRT01A,
    `Overall Survival (DAYS)`,
    `Progression Free Survival (DAYS)`,
    `Duration of Confirmed Response (DAYS)`
  ) %>%
  right_join(out_trg, ., by = "ID", multiple = "all")

out <- out_tte %>%
  right_join(out_rs, ., by = "ID", multiple = "all") %>%
  select(
    "ID", "TRT01A", "AVAL", "Best Confirmed Overall Response by Investigator",
    "Investigator End Of Induction Response", "Overall Survival (DAYS)", "Progression Free Survival (DAYS)",
    "trigeventpfs", "Duration of Confirmed Response (DAYS)"
  )

var_labels(out) <- names(out)
out <- out %>%
  var_relabel(
    ID = "Center/Patient ID",
    TRT01A = "Treatment",
    AVAL = "Number of Doses\nReceived",
    `Best Confirmed Overall Response by Investigator` = "Best Confirmed\nOverall Response\nby Investigator",
    `Investigator End Of Induction Response` = "Investigator\nEnd Of Induction\nResponse",
    trigeventpfs = "Triggering Event\n for PFS",
    `Overall Survival (DAYS)` = "Overall Survival\n(days)",
    `Progression Free Survival (DAYS)` = "PFS\n(days)",
    `Duration of Confirmed Response (DAYS)` = "Duration of\nConfirmed Response\n(days)"
  )

Reproducibility

Timestamp

[1] "2024-11-02 18:40:06 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     2024-11-02
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
 backports           1.5.0   2024-05-23 [1] CRAN (R 4.4.1)
 brio                1.1.5   2024-04-24 [1] CRAN (R 4.4.1)
 checkmate           2.3.2   2024-07-29 [1] CRAN (R 4.4.1)
 cli                 3.6.3   2024-06-21 [1] CRAN (R 4.4.1)
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.4.1)
 digest              0.6.37  2024-08-19 [1] CRAN (R 4.4.1)
 dplyr             * 1.1.4   2023-11-17 [1] CRAN (R 4.4.1)
 evaluate            1.0.1   2024-10-10 [1] CRAN (R 4.4.1)
 fansi               1.0.6   2023-12-08 [1] CRAN (R 4.4.1)
 fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.4.1)
 formatters        * 0.5.9   2024-09-12 [1] CRAN (R 4.4.1)
 generics            0.1.3   2022-07-05 [1] CRAN (R 4.4.1)
 glue                1.8.0   2024-09-30 [1] CRAN (R 4.4.1)
 htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets         1.6.4   2023-12-06 [1] CRAN (R 4.4.1)
 jsonlite            1.8.9   2024-09-20 [1] CRAN (R 4.4.1)
 knitr               1.48    2024-07-07 [1] CRAN (R 4.4.1)
 lifecycle           1.0.4   2023-11-07 [1] CRAN (R 4.4.1)
 magrittr            2.0.3   2022-03-30 [1] CRAN (R 4.4.1)
 pillar              1.9.0   2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig           2.0.3   2019-09-22 [1] CRAN (R 4.4.1)
 purrr               1.0.2   2023-08-10 [1] CRAN (R 4.4.1)
 R6                  2.5.1   2021-08-19 [1] CRAN (R 4.4.1)
 random.cdisc.data   0.3.16  2024-11-02 [1] https://insightsengineering.r-universe.dev (R 4.4.1)
 rlang               1.1.4   2024-06-04 [1] CRAN (R 4.4.1)
 rlistings         * 0.2.9   2024-06-20 [1] CRAN (R 4.4.1)
 rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.4.1)
 sessioninfo         1.2.2   2021-12-06 [1] CRAN (R 4.4.1)
 stringi             1.8.4   2024-05-06 [1] CRAN (R 4.4.1)
 stringr             1.5.1   2023-11-14 [1] CRAN (R 4.4.1)
 testthat            3.2.1.1 2024-04-14 [1] CRAN (R 4.4.1)
 tibble            * 3.2.1   2023-03-20 [1] CRAN (R 4.4.1)
 tidyr               1.3.1   2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect          1.2.1   2024-03-11 [1] CRAN (R 4.4.1)
 utf8                1.2.4   2023-10-22 [1] CRAN (R 4.4.1)
 vctrs               0.6.5   2023-12-01 [1] CRAN (R 4.4.1)
 withr               3.0.2   2024-10-28 [1] CRAN (R 4.4.1)
 xfun                0.49    2024-10-31 [1] CRAN (R 4.4.1)
 yaml                2.3.10  2024-07-26 [1] CRAN (R 4.4.1)

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

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

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Reproducibility

Timestamp

Session Info

.lock file

`.lock` file