LBT10

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

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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   20/134 (14.9%)   21/134 (15.7%)   20/132 (15.2%)
  AST >3xULN at 2 Visits   30/134 (22.4%)   25/134 (18.7%)   27/132 (20.5%)
Total Bilirubin > 2xULN                                                    
  ALT >3xULN at 2 Visits   24/134 (17.9%)   32/134 (23.9%)   24/132 (18.2%)
  AST >3xULN at 2 Visits   33/134 (24.6%)   29/134 (21.6%)   25/132 (18.9%)

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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   20/134 (14.9%)   21/134 (15.7%)   20/132 (15.2%)
  AST >3xULN at 2 Visits   30/134 (22.4%)   25/134 (18.7%)   27/132 (20.5%)

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(
    "BL2AL2CU", "BL2AS2CU", "BG2AL2CU", "BG2AS2CU", "B2A2L2CU", "B2A2S2CU", "B2A5L2CU", "B2A5S2CU"
  )) %>%
  mutate(PARAMCAT = case_when(
    PARAMCD %in% c("BL2AL2CU", "BL2AS2CU") ~ "Total Bilirubin <= 2xULN",
    PARAMCD %in% c("BG2AL2CU", "BG2AS2CU") ~ "Total Bilirubin > 2xULN",
    PARAMCD %in% c("B2A2L2CU", "B2A2S2CU") ~ "Total Bilirubin > 2xULN and Alkaline Phosphatase <= 2xULN",
    PARAMCD %in% c("B2A5L2CU", "B2A5S2CU") ~ "Total Bilirubin > 2xULN and Alkaline Phosphatase <= 5xULN"
  )) %>%
  mutate(AVALC_FORMAT = case_when(
    PARAMCD %in% c("BL2AL2CU", "BG2AL2CU", "B2A2L2CU", "B2A5L2CU") & AVALC == "Y" ~ "ALT >3xULN at 2 Visits",
    PARAMCD %in% c("BL2AS2CU", "BG2AS2CU", "B2A2S2CU", "B2A5S2CU") & 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 18:17:56 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 ───────────────────────────────────────────────────────────────────
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 R6                  2.5.1   2021-08-19 [1] CRAN (R 4.4.1)
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 [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