LBT10_BL

Liver Laboratory Tests – Patients with Elevated Post-Baseline AST or ALT Levels at Two Consecutive Visits (with Respect to Baseline)

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Code

tbl <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ACTARMCD") %>%
  split_rows_by("PARAMCAT") %>%
  split_rows_by("PARAM", split_fun = drop_split_levels, child_labels = "hidden") %>%
  count_occurrences(
    vars = "AVALC_FORMAT",
    .stats = c("fraction"),
    denom = "n",
    drop = TRUE
  ) %>%
  build_table(anl, alt_counts_df = adsl)

criteria_fun <- function(tr) {
  row_label <- obj_label(tr)
  ifelse(row_label == "Criteria not met", TRUE, FALSE)
}

result <- tbl %>% trim_rows(criteria = criteria_fun)
result

                               ARM A            ARM B            ARM C     
                              (N=134)          (N=134)          (N=132)    
———————————————————————————————————————————————————————————————————————————
Total Bilirubin <= 2xULN                                                   
  ALT >3xULN at 2 Visits   25/134 (18.7%)   20/134 (14.9%)   27/132 (20.5%)
  AST >3xULN at 2 Visits   22/134 (16.4%)   14/134 (10.4%)   37/132 (28.0%)
Total Bilirubin > 2xULN                                                    
  ALT >3xULN at 2 Visits   26/134 (19.4%)   31/134 (23.1%)   23/132 (17.4%)
  AST >3xULN at 2 Visits   30/134 (22.4%)   27/134 (20.1%)   26/132 (19.7%)

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Code

tbl2 <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ACTARMCD") %>%
  split_rows_by("PARAMCAT", split_fun = remove_split_levels("Total Bilirubin > 2xULN")) %>%
  split_rows_by("PARAM", split_fun = drop_split_levels, child_labels = "hidden") %>%
  count_occurrences(
    vars = "AVALC_FORMAT",
    .stats = c("fraction"),
    denom = "n",
    drop = TRUE
  ) %>%
  build_table(anl, alt_counts_df = adsl)

criteria_fun <- function(tr) {
  row_label <- obj_label(tr)
  ifelse(row_label == "Criteria not met", TRUE, FALSE)
}

result <- tbl2 %>% trim_rows(criteria = criteria_fun)
result

                               ARM A            ARM B            ARM C     
                              (N=134)          (N=134)          (N=132)    
———————————————————————————————————————————————————————————————————————————
Total Bilirubin <= 2xULN                                                   
  ALT >3xULN at 2 Visits   25/134 (18.7%)   20/134 (14.9%)   27/132 (20.5%)
  AST >3xULN at 2 Visits   22/134 (16.4%)   14/134 (10.4%)   37/132 (28.0%)

Experimental use!

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Code

library(dplyr)
library(tern)

adsl <- random.cdisc.data::cadsl
adhy <- random.cdisc.data::cadhy

adhy_liver <- adhy %>%
  filter(PARAMCD %in% c(
    "BL2AL2CB", "BL2AS2CB", "BG2AL2CB", "BG2AS2CB", "B2A2L2CB", "B2A2S2CB", "B2A5L2CB", "B2A5S2CB"
  )) %>%
  mutate(PARAMCAT = case_when(
    PARAMCD %in% c("BL2AL2CB", "BL2AS2CB") ~ "Total Bilirubin <= 2xULN",
    PARAMCD %in% c("BG2AL2CB", "BG2AS2CB") ~ "Total Bilirubin > 2xULN",
    PARAMCD %in% c("B2A2L2CB", "B2A2S2CB") ~ "Total Bilirubin > 2xULN and Alkaline Phosphatase <= 2xULN",
    PARAMCD %in% c("B2A5L2CB", "B2A5S2CB") ~ "Total Bilirubin > 2xULN and Alkaline Phosphatase <= 5xULN"
  )) %>%
  mutate(AVALC_FORMAT = case_when(
    PARAMCD %in% c("BL2AL2CB", "BG2AL2CB", "B2A2L2CB", "B2A5L2CB") & AVALC == "Y" ~ "ALT >3xULN at 2 Visits",
    PARAMCD %in% c("BL2AS2CB", "BG2AS2CB", "B2A2S2CB", "B2A5S2CB") & AVALC == "Y" ~ "AST >3xULN at 2 Visits",
    TRUE ~ "Criteria not met"
  ))

# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
anl <- df_explicit_na(adhy_liver)

Reproducibility

Timestamp

[1] "2024-11-02 18:18:02 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     2024-11-02
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
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 evaluate            1.0.1   2024-10-10 [1] CRAN (R 4.4.1)
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 pillar              1.9.0   2023-03-22 [1] CRAN (R 4.4.1)
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 purrr               1.0.2   2023-08-10 [1] CRAN (R 4.4.1)
 R6                  2.5.1   2021-08-19 [1] CRAN (R 4.4.1)
 random.cdisc.data   0.3.16  2024-11-02 [1] https://insightsengineering.r-universe.dev (R 4.4.1)
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 rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.4.1)
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 scales              1.3.0   2023-11-28 [1] CRAN (R 4.4.1)
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 stringi             1.8.4   2024-05-06 [1] CRAN (R 4.4.1)
 stringr             1.5.1   2023-11-14 [1] CRAN (R 4.4.1)
 survival            3.7-0   2024-06-05 [2] CRAN (R 4.4.1)
 tern              * 0.9.6   2024-09-24 [1] CRAN (R 4.4.1)
 testthat            3.2.1.1 2024-04-14 [1] CRAN (R 4.4.1)
 tibble              3.2.1   2023-03-20 [1] CRAN (R 4.4.1)
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 xfun                0.49    2024-10-31 [1] CRAN (R 4.4.1)
 yaml                2.3.10  2024-07-26 [1] CRAN (R 4.4.1)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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Reproducibility

Timestamp

Session Info

.lock file

`.lock` file