LBL02A

Listing of Laboratory Abnormalities (constant units)

Output

Standard Listing
Data Setup

Preview
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Code

lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "LBTEST_U", "CPID"),
  disp_cols = names(out),
  main_title = "Listing of Laboratory Abnormalities Defined by NCI CTCAE Grade >= 1",
  main_footer = "NCI CTCAE grade is displayed as abnormal high (H) or low (L) followed by the grade."
)

head(lsting, 20)

Listing of Laboratory Abnormalities Defined by NCI CTCAE Grade >= 1

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                                  Days Since                           NCI 
                                                                             Study               Last Dose of            Lab Normal   CTCAE
Treatment                Lab Test (Unit)                 Center/Patient ID    Day      Date       Study Drug    Result     Range      Grade
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X   Alanine Aminotransferase Measurement (U/L)     BRA-1/id-105       80     27MAY2020        0           4.3    7.0 - 55.0    L4  
                                                                              398    10APR2021       318          3.7    7.0 - 55.0    L3  
                                                            BRA-1/id-93       207    13JAN2021        0           6.1    7.0 - 55.0    L1  
                                                           BRA-11/id-397      326    19MAY2021        0           1.5    7.0 - 55.0    L1  
                                                           BRA-14/id-23       594    22JUN2021        0           0.6    7.0 - 55.0    L1  
                                                           BRA-2/id-296       281    30OCT2021        0           2.6    7.0 - 55.0    L1  
                                                                              734    26JAN2023       453          3.9    7.0 - 55.0    L1  
                                                            CAN-1/id-18       465    12APR2022        0           1.8    7.0 - 55.0    L2  
                                                           CHN-1/id-133       127    13DEC2020        0           5.6    7.0 - 55.0    L2  
                                                                              197    21FEB2021        70          1.2    7.0 - 55.0    L4  
                                                           CHN-1/id-199       277    11OCT2020        0           5.3    7.0 - 55.0    L4  
                                                                              672    10NOV2021       395          6.8    7.0 - 55.0    L2  
                                                           CHN-1/id-235       348    25JUN2020        0           3.0    7.0 - 55.0    L3  
                                                                              381    28JUL2020        33          4.7    7.0 - 55.0    L1  
                                                            CHN-1/id-26       905    07JAN2023        0           1.1    7.0 - 55.0    L1  
                                                           CHN-1/id-275       364    01JUN2021        0           5.1    7.0 - 55.0    L2  
                                                           CHN-1/id-277       483    12MAY2022        0           1.1    7.0 - 55.0    L4  
                                                           CHN-1/id-287       182    23MAY2020        0           5.9    7.0 - 55.0    L2  
                                                                              191    01JUN2020        9           5.3    7.0 - 55.0    L3  
                                                                              515    21APR2021       324          2.9    7.0 - 55.0    L4  
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

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(
    ANRIND %in% c("LOW", "HIGH"),
    !ATOXGR %in% c("0", ""),
    LBTEST != ""
  ) %>%
  mutate(
    LBTEST_U = paste0(LBTEST, " (", AVALU, ")"),
    CPID = paste(SITEID, SUBJID, sep = "/"),
    ADTM = toupper(format(as.Date(ADTM), "%d%b%Y")),
    AVAL = format(round(AVAL, 1), nsmall = 1),
    LBNRNG = paste(format(round(ANRLO, 1), nsmall = 1), format(round(ANRHI, 1), nsmall = 1), sep = " - "),
    ANRIND_GR = factor(
      case_when(
        ANRIND == "LOW" ~ paste0("L", sub("-", "", ATOXGR)),
        ANRIND == "HIGH" ~ paste0("H", ATOXGR)
      )
    )
  ) %>%
  select(LBTEST_U, TRT01A, CPID, ADY, ADTM, AVAL, ADY, LBNRNG, ANRIND_GR) %>%
  unique() %>%
  arrange(CPID, ADY) %>%
  group_by(LBTEST_U, CPID) %>%
  mutate(DLD = ADY - lag(ADY)) %>%
  ungroup() %>%
  mutate(DLD = ifelse(is.na(DLD), 0, DLD))

out <- adlb_x %>%
  select(LBTEST_U, TRT01A, CPID, ADY, ADTM, DLD, AVAL, LBNRNG, ANRIND_GR)

var_labels(out) <- names(out)
out <- out %>%
  var_relabel(
    LBTEST_U = "Lab Test (Unit)",
    TRT01A = "Treatment",
    CPID = "Center/Patient ID",
    ADY = "Study\nDay",
    ADTM = "Date",
    DLD = "Days Since\nLast Dose of\nStudy Drug",
    AVAL = "Result",
    LBNRNG = "Lab Normal\nRange",
    ANRIND_GR = "NCI\nCTCAE\nGrade"
  )

Reproducibility

Timestamp

[1] "2024-11-20 09:52:02 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
 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
 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