TLG Catalog - Stable
  • Stable
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  3. LBL01_RLS
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      • LBL01_RLS
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  • Appendix
    • Reproducibility

  • Index

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  • Output
  • Reproducibility
    • Timestamp
    • Session Info
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  • Edit this page
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  1. Listings
  2. Lab Results
  3. LBL01_RLS

LBL01_RLS

Listing of Laboratory Test Results Using Roche Safety Lab Standardization


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

head(lsting, 20)
Listing of Laboratory Test Results Using Roche Safety Lab Standardization

————————————————————————————————————————————————————————————————————————————————————————
                                         Days Since                                     
                                Study   Last Dose of      ALT         CRP         IGA   
Treatment   Center/Patient ID    Day     Study Drug      (U/L)      (mg/L)       (g/L)  
————————————————————————————————————————————————————————————————————————————————————————
A: Drug X     BRA-1/id-105       80          NA         4.30 / L      9.09        2.84  
                                 149         69          24.70        9.15        2.93  
                                 314        165          24.87     10.89 / H      2.66  
                                 398         84         3.67 / L      8.14        2.86  
                                 470         72          18.55     10.59 / H      2.88  
                                 528         58           7.73     10.09 / H      2.93  
                                 535         7           23.51        9.20        2.88  
              BRA-1/id-134       225         NA           7.37     10.46 / H      2.86  
                                 227         2           16.42      7.43 / L      2.76  
                                 255         28          11.16        9.41        2.75  
                                 269         14          15.89     10.02 / H      2.84  
                                 357         88          24.35        8.01        2.86  
                                 436         79          16.03        8.51        2.98  
                                 440         4           17.21      7.63 / L      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 / H    3.00 / H
                                 608         39          24.61      7.95 / L      2.78  
————————————————————————————————————————————————————————————————————————————————————————

Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range; high high (HH) or low low (LL) if outside the Roche marked reference range with a clinically relevant change from baseline. 
Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Code
library(dplyr)
library(rlistings)

adlb <- random.cdisc.data::cadlb %>%
  filter(!is.na(AVAL))

adlb_x <- adlb %>%
  mutate(ANRIND = factor(
    case_when(
      ANRIND == "LOW" & AVAL > stats::quantile(adlb$AVAL, probs = c(0.1)) ~ "L",
      ANRIND == "HIGH" & AVAL < stats::quantile(adlb$AVAL, probs = c(0.9)) ~ "H",
      ANRIND == "LOW" & AVAL <= stats::quantile(adlb$AVAL, probs = c(0.1)) ~ "LL",
      ANRIND == "HIGH" & AVAL >= stats::quantile(adlb$AVAL, probs = c(0.9)) ~ "HH",
      TRUE ~ as.character(ANRIND)
    ),
    levels = c("", "H", "HH", "L", "LL", "NORMAL")
  ))

adlb_x <- adlb_x %>%
  filter(!is.na(LBSEQ) & !is.na(ADY) & ANRIND != "") %>%
  mutate(
    CPID = paste(SITEID, SUBJID, sep = "/"),
    PARAM_U = paste0(PARAMCD, "\n(", AVALU, ")"),
    AVALC = as.character(format(round(AVAL, 2), nsmall = 2))
  ) %>%
  mutate(AVAL_GR = ifelse(
    !ANRIND %in% c("H", "HH", "L", "LL"),
    AVALC,
    paste(AVALC, ANRIND, 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] "2025-07-09 17:35:31 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-07-09
 pandoc   3.7.0.2 @ /usr/bin/ (via rmarkdown)
 quarto   1.7.32 @ /usr/local/bin/quarto

─ 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                 3.6.5   2025-04-23 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.5.0)
 curl                6.4.0   2025-06-22 [1] RSPM
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.4   2025-06-18 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.11  2025-04-09 [1] RSPM
 generics            0.1.4   2025-05-09 [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            2.0.0   2025-03-27 [1] RSPM
 knitr               1.50    2025-03-16 [1] RSPM
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr            2.0.3   2022-03-30 [1] RSPM
 pillar              1.11.0  2025-07-04 [1] RSPM
 pkgcache            2.2.4   2025-05-26 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.6   2025-02-21 [1] RSPM
 ps                  1.9.1   2025-04-12 [1] RSPM
 purrr               1.0.4   2025-02-05 [1] RSPM
 R6                  2.6.1   2025-02-15 [1] RSPM
 random.cdisc.data   0.3.16  2024-10-10 [1] RSPM
 rlang               1.1.6   2025-04-11 [1] RSPM
 rlistings         * 0.2.12  2025-06-15 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 sessioninfo         1.2.3   2025-02-05 [1] any (@1.2.3)
 stringi             1.8.7   2025-03-27 [1] RSPM
 stringr             1.5.1   2023-11-14 [1] RSPM
 testthat            3.2.3   2025-01-13 [1] RSPM
 tibble            * 3.3.0   2025-06-08 [1] RSPM
 tidyr               1.3.1   2024-01-24 [1] RSPM
 tidyselect          1.2.1   2024-03-11 [1] RSPM
 vctrs               0.6.5   2023-12-01 [1] RSPM
 withr               3.0.2   2024-10-28 [1] RSPM
 xfun                0.52    2025-04-02 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library
 [3] /github/home/R/x86_64-pc-linux-gnu-library/4.5
 * ── Packages attached to the search path.

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

.lock file

Download the .lock file and use renv::restore() on it to recreate environment used to generate this website.

Download

LBL01
LBL02A
Source Code
---
title: LBL01_RLS
subtitle: Listing of Laboratory Test Results Using Roche Safety Lab Standardization
---

------------------------------------------------------------------------

{{< include ../../_utils/envir_hook.qmd >}}

```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(dplyr)
library(rlistings)

adlb <- random.cdisc.data::cadlb %>%
  filter(!is.na(AVAL))

adlb_x <- adlb %>%
  mutate(ANRIND = factor(
    case_when(
      ANRIND == "LOW" & AVAL > stats::quantile(adlb$AVAL, probs = c(0.1)) ~ "L",
      ANRIND == "HIGH" & AVAL < stats::quantile(adlb$AVAL, probs = c(0.9)) ~ "H",
      ANRIND == "LOW" & AVAL <= stats::quantile(adlb$AVAL, probs = c(0.1)) ~ "LL",
      ANRIND == "HIGH" & AVAL >= stats::quantile(adlb$AVAL, probs = c(0.9)) ~ "HH",
      TRUE ~ as.character(ANRIND)
    ),
    levels = c("", "H", "HH", "L", "LL", "NORMAL")
  ))

adlb_x <- adlb_x %>%
  filter(!is.na(LBSEQ) & !is.na(ADY) & ANRIND != "") %>%
  mutate(
    CPID = paste(SITEID, SUBJID, sep = "/"),
    PARAM_U = paste0(PARAMCD, "\n(", AVALU, ")"),
    AVALC = as.character(format(round(AVAL, 2), nsmall = 2))
  ) %>%
  mutate(AVAL_GR = ifelse(
    !ANRIND %in% c("H", "HH", "L", "LL"),
    AVALC,
    paste(AVALC, ANRIND, 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"
  )
```

```{r include = FALSE}
webr_code_labels <- c("setup")
```

{{< include ../../_utils/webr_no_include.qmd >}}

## Output

:::: panel-tabset
## Standard Listing

::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview

```{r lsting, test = list(lsting = "lsting")}
lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CPID"),
  disp_cols = names(out),
  main_title = "Listing of Laboratory Test Results Using Roche Safety Lab Standardization",
  main_footer = "Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range; high high (HH) or low low (LL) if outside the Roche marked reference range with a clinically relevant change from baseline. " # nolint: line_length.
)

head(lsting, 20)
```

```{r include = FALSE}
webr_code_labels <- c("lsting")
```

{{< include ../../_utils/webr.qmd >}}
:::

## Data Setup

```{r setup}
#| code-fold: show
```
::::

{{< include ../../_utils/save_results.qmd >}}

{{< include ../../repro.qmd >}}

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