LBT12

Liver Laboratory Tests by Time on Treatment – Patients with Elevated Post-Baseline AST or ALT Levels (with Respect to ULN)

Code
result <- basic_table() %>%
  split_cols_by("TITLE") %>%
  split_cols_by("APERIODC") %>%
  split_rows_by("PARAM") %>%
  split_rows_by("ACTARM", split_fun = drop_split_levels, child_labels = "hidden") %>%
  count_occurrences("ARM_AVALC", .stats = "fraction", denom = "n", drop = TRUE) %>%
  build_table(anl)

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

result <- result %>% trim_rows(criteria = criteria_fun)
result
                              First Elevated Result Occurring During  
                                  PERIOD 1              PERIOD 2      
——————————————————————————————————————————————————————————————————————
AST >3x ULN                                                           
  A: Drug X                     11/134 (8.2%)        21/134 (15.7%)   
  B: Placebo                   17/134 (12.7%)        16/134 (11.9%)   
  C: Combination                10/132 (7.6%)         8/132 (6.1%)    
ALT >3x ULN                                                           
  A: Drug X                    14/134 (10.4%)         8/134 (6.0%)    
  B: Placebo                   24/134 (17.9%)        18/134 (13.4%)   
  C: Combination               16/132 (12.1%)         10/132 (7.6%)   
AST >3x ULN or ALT >x3 ULN                                            
  A: Drug X                    14/134 (10.4%)        15/134 (11.2%)   
  B: Placebo                    8/134 (6.0%)          13/134 (9.7%)   
  C: Combination                11/132 (8.3%)         12/132 (9.1%)

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Code
library(dplyr)
library(tern)

adhy <- random.cdisc.data::cadhy

anl <- adhy
anl$APERIODC <- as.factor(anl$APERIODC) # to ensure the table is built even if there is no patients after filtering
anl$ACTARM <- as.factor(anl$ACTARM) # to ensure the table is built even if there is no patients after filtering

anl <- anl %>%
  filter(
    SAFFL == "Y",
    PARAMCD %in% c("ASTPULN", "ALTPULN", "ALTASTPU") & AVISIT == "POST-BASELINE"
  ) %>%
  mutate(
    ARM_AVALC = factor(
      case_when(
        AVALC == "Y" ~ as.character(ACTARM),
        TRUE ~ "Criteria not met"
      ),
      levels = c(levels(anl$ACTARM), "Criteria not met")
    ),
    PARAM = factor(
      case_when(
        PARAMCD == "ASTPULN" ~ "AST >3x ULN",
        PARAMCD == "ALTPULN" ~ "ALT >3x ULN",
        PARAMCD == "ALTASTPU" ~ "AST >3x ULN or ALT >x3 ULN"
      ),
      levels = c("AST >3x ULN", "ALT >3x ULN", "AST >3x ULN or ALT >x3 ULN")
    ),
    TITLE = factor("First Elevated Result Occurring During")
  )

anl <- df_explicit_na(anl)

Reproducibility

Timestamp

[1] "2024-11-02 18:00:01 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
 backports           1.5.0       2024-05-23 [1] CRAN (R 4.4.1)
 brio                1.1.5       2024-04-24 [1] CRAN (R 4.4.1)
 broom               1.0.7       2024-09-26 [1] CRAN (R 4.4.1)
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 cli                 3.6.3       2024-06-21 [1] CRAN (R 4.4.1)
 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
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 digest              0.6.37      2024-08-19 [1] CRAN (R 4.4.1)
 dplyr             * 1.1.4       2023-11-17 [1] CRAN (R 4.4.1)
 evaluate            1.0.1       2024-10-10 [1] CRAN (R 4.4.1)
 fansi               1.0.6       2023-12-08 [1] CRAN (R 4.4.1)
 fastmap             1.2.0       2024-05-15 [1] CRAN (R 4.4.1)
 forcats             1.0.0       2023-01-29 [1] CRAN (R 4.4.1)
 formatters        * 0.5.9.9003  2024-11-02 [1] git2r (https://github.com/insightsengineering/formatters.git@84e8c3e)
 generics            0.1.3       2022-07-05 [1] CRAN (R 4.4.1)
 ggplot2             3.5.1       2024-04-23 [1] CRAN (R 4.4.1)
 glue                1.8.0       2024-09-30 [1] CRAN (R 4.4.1)
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 Matrix              1.7-0       2024-04-26 [1] CRAN (R 4.4.1)
 munsell             0.5.1       2024-04-01 [1] CRAN (R 4.4.1)
 nestcolor           0.1.2.9017  2024-11-02 [1] git2r (https://github.com/insightsengineering/nestcolor.git@3d2ce62)
 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   0.3.16.9001 2024-11-02 [1] git2r (https://github.com/insightsengineering/random.cdisc.data.git@a65bfbe)
 rbibutils           2.3         2024-10-04 [1] CRAN (R 4.4.1)
 Rdpack              2.6.1       2024-08-06 [1] CRAN (R 4.4.1)
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 rmarkdown           2.28        2024-08-17 [1] CRAN (R 4.4.1)
 rtables           * 0.6.10.9002 2024-11-02 [1] git2r (https://github.com/insightsengineering/rtables.git@d2cc7a0)
 scales              1.3.0       2023-11-28 [1] CRAN (R 4.4.1)
 sessioninfo         1.2.2       2021-12-06 [1] CRAN (R 4.4.1)
 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              * 0.9.6.9013  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.git@435fd51)
 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)
 tidyr               1.3.1       2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect          1.2.1       2024-03-11 [1] CRAN (R 4.4.1)
 utf8                1.2.4       2023-10-22 [1] CRAN (R 4.4.1)
 vctrs               0.6.5       2023-12-01 [1] CRAN (R 4.4.1)
 xfun                0.48        2024-10-03 [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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