LBL02A_RLS

Listing of Laboratory Abnormalities Defined by Roche Safety Lab Standardization

Output

Code
lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "LBTEST_U", "CPID"),
  disp_cols = names(out),
  main_title = "Listing of Laboratory Abnormalities Defined by Roche Safety Lab Standardization",
  main_footer = "Standard reference range, marked reference range and clinically relevant change from baseline are from the Roche Safety Lab Standardization guideline.  Abnormalities are flagged as high (H) or low (L) if outside the standard reference range; high high (HH) or low low (LL) if outside the marked reference range with a clinically relevant change from baseline." 
)

head(lsting, 20)
Listing of Laboratory Abnormalities Defined by Roche Safety Lab Standardization

——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                                                                                  Clinically              
                                                                                      Days Since             % Change     Standard     Marked      Relevant               
                                                                             Study   Last Dose of              from      Reference    Reference     Change     Abnormality
Treatment                Lab Test (Unit)                 Center/Patient ID    Day     Study Drug    Result   Baseline      Range        Range     Dec./Inc.       Flag    
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X   Alanine Aminotransferase Measurement (U/L)     BRA-1/id-105       80          0           4.3           NA   5.5 - 31.1    7 - 55     40% / 40%        LL     
                                                                              149         69         24.7          0.0   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              314        165         24.9          0.7   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              398         84          3.7        -85.2   5.5 - 31.1    7 - 55     40% / 40%        LL     
                                                                              470         72         18.5        -24.9   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              528         58          7.7        -68.7   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              535         7          23.5         -4.8   5.5 - 31.1    7 - 55     40% / 40%               
                                                           BRA-1/id-134       225         0           7.4           NA   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              227         2          16.4          0.0   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              255         28         11.2        -32.0   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              269         14         15.9         -3.2   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              357         88         24.4         48.3   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              436         79         16.0         -2.4   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              440         4          17.2          4.8   5.5 - 31.1    7 - 55     40% / 40%               
                                                            BRA-1/id-42       176         0          16.6           NA   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              477        301         16.5          0.0   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              534         57         18.7         13.4   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              550         16         11.4        -30.6   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              569         19         21.7         31.3   5.5 - 31.1    7 - 55     40% / 40%               
                                                                              608         39         24.6         49.2   5.5 - 31.1    7 - 55     40% / 40%               
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

Standard reference range, marked reference range and clinically relevant change from baseline are from the Roche Safety Lab Standardization guideline.  Abnormalities are flagged as high (H) or low (L) if outside the standard reference range; high high (HH) or low low (LL) if outside the marked reference range with a clinically relevant change from baseline.

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Code
library(dplyr)
library(rlistings)

adlb <- random.cdisc.data::cadlb

adlb_x <- adlb %>%
  filter(
    LBTEST != ""
  ) %>%
  mutate(
    LBTEST_U = paste0(LBTEST, " (", AVALU, ")"),
    CPID = paste(SITEID, SUBJID, sep = "/")
  ) %>%
  mutate(CRC = paste("40%", "40%", sep = " / "))

std_rng <- adlb_x %>%
  group_by(LBTEST_U) %>%
  summarise(
    STD_RNG_LO = stats::quantile(AVAL, probs = c(0.1), na.rm = TRUE),
    STD_RNG_HI = stats::quantile(AVAL, probs = c(0.9), na.rm = TRUE)
  ) %>%
  ungroup()

adlb_x <- adlb_x %>%
  left_join(std_rng, by = "LBTEST_U") %>%
  mutate(
    AVAL = format(round(AVAL, 1), nsmall = 1),
    PCHG = format(round(PCHG, 1), nsmall = 1),
    LBNRNG = paste(ANRLO, ANRHI, sep = " - "),
    STD_RNG_LO = format(round(STD_RNG_LO, 1), nsmall = 1),
    STD_RNG_HI = format(round(STD_RNG_HI, 1), nsmall = 1)
  ) %>%
  mutate(
    STD_RNG = paste(STD_RNG_LO, STD_RNG_HI, sep = " - "),
    ANRIND = factor(case_when(
      ANRIND == "LOW" & AVAL > STD_RNG_LO ~ "L",
      ANRIND == "HIGH" & AVAL < STD_RNG_HI ~ "H",
      ANRIND == "LOW" & AVAL <= STD_RNG_LO ~ "LL",
      ANRIND == "HIGH" & AVAL >= STD_RNG_HI ~ "HH",
      TRUE ~ ""
    ))
  ) %>%
  select(LBTEST_U, TRT01A, CPID, ADY, AVAL, PCHG, STD_RNG, LBNRNG, CRC, ANRIND) %>%
  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, DLD, AVAL, PCHG, STD_RNG, LBNRNG, CRC, ANRIND)

var_labels(out) <- names(out)
out <- out %>%
  var_relabel(
    LBTEST_U = "Lab Test (Unit)",
    TRT01A = "Treatment",
    CPID = "Center/Patient ID",
    ADY = "Study\nDay",
    DLD = "Days Since\nLast Dose of\nStudy Drug",
    AVAL = "Result",
    PCHG = "% Change\nfrom\nBaseline",
    STD_RNG = "Standard\nReference\nRange",
    LBNRNG = "Marked\nReference\nRange",
    CRC = "Clinically\nRelevant\nChange\nDec./Inc.",
    ANRIND = "Abnormality\nFlag"
  )

Reproducibility

Timestamp

[1] "2024-11-21 15:29:02 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     2024-11-21
 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
 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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