EGL01

Listing of ECG Data: Safety-Evaluable Patients

Output

Standard Listing
Data Setup

Preview
Try this using WebR

Code

lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CRTNPT", "AGSXRC", "AVISIT", "ADY"),
  disp_cols = names(out),
  main_title = "Listing of ECG Data: Safety-Evaluable Patients",
  main_footer = "Baseline is the patient's last observation prior to initiation of study drug. Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range." 
)

head(lsting, 20)

Listing of ECG Data: Safety-Evaluable Patients

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                         Heart Rate Result                    QT Duration Result                    RR Duration Result                 
                                                                                 Study     (beats/min);        Heart Rate          (msec);          QT Duration          (msec);          RR Duration  
Treatment   Center/Subject ID            Age/Sex/Race                Visit        Day     Range:(40-100)     Change from BL    Range:(200-500)     Change from BL    Range:(600-1500)    Change from BL
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X       BRA-1/105       38/M/BLACK OR AFRICAN AMERICAN     BASELINE       149           66.94                 NA            441.78                  NA            896.59                  NA   
                                                                 WEEK 1 DAY 8     314           63.18              -3.76            365.68              -76.10           1376.26              479.67   
                                                                 WEEK 2 DAY 15    398           57.57              -9.37            355.48              -86.29            799.57              -97.02   
                                                                 WEEK 3 DAY 22    470           73.36               6.42            352.45              -89.33           1015.00              118.41   
                                                                 WEEK 4 DAY 29    528           53.72             -13.22            388.42              -53.36           1189.29              292.70   
                                                                 WEEK 5 DAY 36    535           58.25              -8.69            291.77             -150.01            936.09               39.50   
                BRA-1/134                 47/M/WHITE               BASELINE       227           46.99                 NA            385.29                  NA            835.17                  NA   
                                                                 WEEK 1 DAY 8     255           48.38               1.39            453.74               68.46            901.86               66.68   
                                                                 WEEK 2 DAY 15    269          35.40/L            -11.59            413.54               28.26            892.01               56.84   
                                                                 WEEK 3 DAY 22    357           60.50              13.51            394.23                8.95           490.18/L            -344.99   
                                                                 WEEK 4 DAY 29    436           82.28              35.29            398.29               13.00            757.96              -77.21   
                                                                 WEEK 5 DAY 36    440          38.89/L             -8.10            339.38              -45.91            880.26               45.08   
                BRA-1/42        36/M/BLACK OR AFRICAN AMERICAN     BASELINE       477           56.19                 NA           190.94/L                 NA           1276.65                  NA   
                                                                 WEEK 1 DAY 8     534           85.24              29.05            483.71              292.77            735.11             -541.54   
                                                                 WEEK 2 DAY 15    550           55.53              -0.66            386.60              195.66           1092.71             -183.94   
                                                                 WEEK 3 DAY 22    569           65.37               9.18            311.08              120.14           1227.15              -49.50   
                                                                 WEEK 4 DAY 29    608           65.13               8.93            329.78              138.83           250.18/L           -1026.47   
                                                                 WEEK 5 DAY 36    675           49.03              -7.16            470.67              279.73           1321.21               44.56   
                BRA-1/93                  34/F/ASIAN               BASELINE       73            72.12                 NA            306.64                  NA           1324.80                  NA   
                                                                 WEEK 1 DAY 8     207           66.88              -5.24           190.50/L            -116.14           1495.37              170.58   
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

Baseline is the patient's last observation prior to initiation of study drug. Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range.

Experimental use!

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Code

library(dplyr)
library(rlistings)

adeg <- random.cdisc.data::cadeg

get_param_unit_range <- function(dataset) {
  u_rng <- lapply(unique(dataset$PARAMCD), function(p) {
    dat <- dataset %>% filter(PARAMCD == p)
    list(
      unit = unique(dat$AVALU),
      range = paste0(unique(dat$ANRLO), "-", unique(dat$ANRHI))
    )
  })
  names(u_rng) <- unique(dataset$PARAMCD)
  u_rng
}

eg_u_rng <- get_param_unit_range(adeg)

adeg_sub <- adeg %>%
  filter(!is.na(AVAL) & SAFFL == "Y" & ANL01FL == "Y" & !is.na(EGSEQ) & PARAMCD != "ECGINTP") %>%
  mutate(
    CRTNPT = paste(SITEID, sub("^.*-([[:alnum:]]+)$", "\\1", SUBJID), sep = "/"),
    AGSXRC = paste(AGE, SEX, RACE, sep = "/"),
    AVAL = format(round(AVAL, 2), nsmall = 2),
    AVAL_ANRIND = ifelse(ANRIND %in% c("NORMAL", ""), AVAL, paste(AVAL, substr(ANRIND, 1, 1), sep = "/")),
    CHG = format(round(CHG, 2), nsmall = 2)
  )

anl_eg <- adeg_sub %>%
  select(SUBJID, CRTNPT, AGSXRC, TRT01A, PARAMCD, AVAL_ANRIND, CHG, ADY, AVISIT, ADTM) %>%
  tidyr::pivot_wider(
    id_cols = c(SUBJID, CRTNPT, AGSXRC, TRT01A, ADY, AVISIT, ADTM),
    names_from = PARAMCD,
    values_from = c(AVAL_ANRIND, CHG)
  )

out <- anl_eg %>%
  select(
    CRTNPT,
    AGSXRC,
    TRT01A,
    AVISIT,
    ADY,
    AVAL_ANRIND_HR,
    CHG_HR,
    AVAL_ANRIND_QT,
    CHG_QT,
    AVAL_ANRIND_RR,
    CHG_RR
  ) %>%
  var_relabel(
    CRTNPT = "Center/Subject ID",
    AGSXRC = "Age/Sex/Race",
    TRT01A = "Treatment",
    AVISIT = "Visit",
    ADY = "Study\nDay",
    AVAL_ANRIND_HR = paste0("Heart Rate Result\n(", eg_u_rng$HR$unit, ");\nRange:(", eg_u_rng$HR$range, ")"),
    CHG_HR = "Heart Rate\nChange from BL",
    AVAL_ANRIND_QT = paste0("QT Duration Result\n(", eg_u_rng$QT$unit, ");\nRange:(", eg_u_rng$QT$range, ")"),
    CHG_QT = "QT Duration\nChange from BL",
    AVAL_ANRIND_RR = paste0("RR Duration Result\n(", eg_u_rng$RR$unit, ");\nRange:(", eg_u_rng$RR$range, ")"),
    CHG_RR = "RR Duration\nChange from BL"
  )

Reproducibility

Timestamp

[1] "2024-11-20 18:17:41 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     2024-11-20
 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
 fansi               1.0.6       2023-12-08 [1] RSPM
 fastmap             1.2.0       2024-05-15 [1] RSPM
 formatters        * 0.5.9.9003  2024-11-20 [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
 magrittr            2.0.3       2022-03-30 [1] RSPM
 pillar              1.9.0       2023-03-22 [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
 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 2024-11-20 [1] https://p~
 rlang               1.1.4       2024-06-04 [1] RSPM
 rlistings         * 0.2.9.9009  2024-11-20 [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            3.2.1.1     2024-04-14 [1] RSPM
 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
 utf8                1.2.4       2023-10-22 [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

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

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Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file