LBL01

Listing of Laboratory Test Results

Output

Standard Listing
Data Setup

Preview
Try this using WebR

Code

lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CPID"),
  disp_cols = names(out),
  main_title = "Listing of Laboratory Test Results",
  main_footer = "NCI CTCAE grade is displayed as abnormal high (H) or low (L) followed by the grade."
)

head(lsting, 20)

Listing of Laboratory Test Results

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                         Days Since                                                                                
                                Study   Last Dose of             ALT                       CRP                        IGA          
Treatment   Center/Patient ID    Day     Study Drug    (U/L / NCI CTCAE grade)   (mg/L / NCI CTCAE grade)   (g/L / NCI CTCAE grade)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X     BRA-1/id-105       80          NA               4.30 / L4                    9.09                       2.84         
                                 149         69                 24.70                      9.15                       2.93         
                                 314        165                 24.87                   10.89 / H2                    2.66         
                                 398         84               3.67 / L3                    8.14                       2.86         
                                 470         72                 18.55                   10.59 / H3                    2.88         
                                 528         58                  7.73                   10.09 / H3                    2.93         
                                 535         7                  23.51                      9.20                       2.88         
              BRA-1/id-134       225         NA                  7.37                   10.46 / H1                    2.86         
                                 227         2                  16.42                    7.43 / L1                    2.76         
                                 255         28                 11.16                      9.41                       2.75         
                                 269         14                 15.89                   10.02 / H4                    2.84         
                                 357         88                 24.35                      8.01                       2.86         
                                 436         79                 16.03                      8.51                       2.98         
                                 440         4                  17.21                    7.63 / L3                    2.78         
               BRA-1/id-42       176         NA                 16.56                      8.88                       2.75         
                                 477        301                 16.49                      8.11                       2.95         
                                 534         57                 18.71                      8.78                       2.95         
                                 550         16                 11.44                      9.53                       2.99         
                                 569         19                 21.66                   10.32 / H2                 3.00 / H1       
                                 608         39                 24.61                    7.95 / L2                    2.78         
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

NCI CTCAE grade is displayed as abnormal high (H) or low (L) followed by the grade.

Experimental use!

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Code

library(dplyr)
library(rlistings)

adlb <- random.cdisc.data::cadlb

adlb_x <- adlb %>%
  filter(!is.na(AVAL) & !is.na(LBSEQ) & !is.na(ADY) & ANRIND != "") %>%
  mutate(
    CPID = paste(SITEID, SUBJID, sep = "/"),
    PARAM_U = paste0(PARAMCD, "\n(", AVALU, " / NCI CTCAE grade)"),
    ANRIND = factor(
      case_when(
        ANRIND == "LOW" ~ "L",
        ANRIND == "HIGH" ~ "H",
        TRUE ~ as.character(ANRIND)
      ),
      levels = c("", "H", "L", "NORMAL")
    ),
    AVALC = as.character(format(round(AVAL, 2), nsmall = 2))
  ) %>%
  mutate(AVAL_GR = ifelse(
    !ANRIND %in% c("H", "L"),
    AVALC,
    paste(AVALC, paste0(ANRIND, sub("-", "", ATOXGR)), sep = " / ")
  )) %>%
  select(CPID, TRT01A, ADY, LBSEQ, PARAM_U, AVAL_GR) %>%
  unique()

out <- adlb_x %>%
  arrange(CPID, ADY, PARAM_U, LBSEQ) %>%
  tidyr::pivot_wider(
    id_cols = c(TRT01A, CPID, ADY),
    names_from = PARAM_U,
    values_from = AVAL_GR
  ) %>%
  group_by(CPID) %>%
  mutate(DLD = ADY - lag(ADY)) %>%
  ungroup() %>%
  select(CPID, TRT01A, ADY, DLD, unique(adlb_x$PARAM_U))

var_labels(out) <- names(out)
out <- out %>%
  var_relabel(
    TRT01A = "Treatment",
    CPID = "Center/Patient ID",
    ADY = "Study\nDay",
    DLD = "Days Since\nLast Dose of\nStudy Drug"
  )

Reproducibility

Timestamp

[1] "2024-11-20 09:51:48 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   2024-09-12 [1] RSPM
 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  2024-10-10 [1] RSPM
 rlang               1.1.4   2024-06-04 [1] RSPM
 rlistings         * 0.2.9   2024-06-20 [1] RSPM
 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