EGT04

Shift Table of Qualitative ECG Assessments

Output

Standard Table
Data Setup

The EGT04 template consists of a stacked list of contingency tables, one per group. For each group, the n’s across all cells must add up to the group N in the analysis, and percentages are calculated using N as the denominator.

Preview
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Code

# Define the split function
split_fun <- drop_split_levels

lyt <- basic_table() %>%
  split_cols_by("postbaseline_label") %>%
  split_cols_by("AVALC") %>%
  split_rows_by("ARM", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adeg_f$ARM)) %>%
  add_rowcounts() %>%
  analyze_vars(
    "BASEC",
    denom = "N_row",
    .stats = "count_fraction",
    na.rm = FALSE
  ) %>%
  append_varlabels(adeg_f, c("BASEC"), indent = 1L)

result <- build_table(lyt, adeg_f)
result

Description of Planned Arm             Post-Baseline           
  Baseline                     Normal      Abnormal    Missing 
———————————————————————————————————————————————————————————————
A: Drug X (N=134)                                              
  Normal                     20 (14.9%)   81 (60.4%)   1 (0.7%)
  Abnormal                   11 (8.2%)    19 (14.2%)      0    
  Missing                        0         1 (0.7%)    1 (0.7%)
B: Placebo (N=134)                                             
  Normal                     18 (13.4%)   81 (60.4%)   2 (1.5%)
  Abnormal                    3 (2.2%)    28 (20.9%)      0    
  Missing                        0         2 (1.5%)       0    
C: Combination (N=132)                                         
  Normal                     26 (19.7%)   69 (52.3%)   1 (0.8%)
  Abnormal                    6 (4.5%)     29 (22%)       0    
  Missing                     1 (0.8%)        0           0

Experimental use!

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R Code

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# Define the split function

split_fun <- drop_split_levels

lyt <- basic_table() %>%

split_cols_by("postbaseline_label") %>%

split_cols_by("AVALC") %>%

split_rows_by("ARM", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adeg_f$ARM)) %>%

add_rowcounts() %>%

analyze_vars(

"BASEC",

denom = "N_row",

.stats = "count_fraction",

na.rm = FALSE

) %>%

append_varlabels(adeg_f, c("BASEC"), indent = 1L)

result <- build_table(lyt, adeg_f)

result

_webr_editor_2 = Object {code: "# Define the split function\nsplit_fun <- drop_spli… = 1L)\n\nresult <- build_table(lyt, adeg_f)\nresult", options: Object, indicator: Ke}

For the EGT04 template, data imputation should be avoided, and missing data explicit and accounted for, so the contingency table sum adds up to the group N. For illustration purposes, missing data are added to the example dataset.

Code

library(tern)
library(dplyr)
set.seed(123)

adsl <- random.cdisc.data::cadsl
adeg <- random.cdisc.data::cadeg

# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adeg <- df_explicit_na(adeg, omit_columns = c("AVALC", "BASEC"))

adeg_labels <- var_labels(adeg)

adeg_f <- subset(
  adeg,
  PARAMCD == "ECGINTP" & # Analysis in terms of "NORMAL"/"ABNORMAL" (AVALC)
    SAFFL == "Y" & # "Safety Population Flag"
    ONTRTFL == "Y" & # "On Treatment Record Flag"
    WORS02FL == "Y" # "Worst Post-Baseline Observation"
)

adeg_f$AVALC[sample(seq_len(nrow(adeg_f)), size = 5)] <- "Missing"
adeg_f$BASEC[sample(seq_len(nrow(adeg_f)), size = 5)] <- "Missing"
adeg_f$AVALC <- factor(
  adeg_f$AVALC,
  levels = c("NORMAL", "ABNORMAL", "Missing"),
  labels = c("Normal", "Abnormal", "Missing")
)
adeg_f$BASEC <- factor(
  adeg_f$BASEC,
  levels = c("NORMAL", "ABNORMAL", "Missing"),
  labels = c("Normal", "Abnormal", "Missing")
)

var_labels(adeg_f) <- adeg_labels
adeg_f <- adeg_f %>%
  var_relabel(BASEC = "Baseline")

# Temprary solution for over arching column
adeg_f <- adeg_f %>% mutate(postbaseline_label = "Post-Baseline")

Reproducibility

Timestamp

[1] "2025-04-09 17:47:22 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 (2024-10-31)
 os       Ubuntu 24.04.1 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-04-09
 pandoc   3.6.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.6.43 @ /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
 broom               1.0.8       2025-03-28 [1] RSPM
 checkmate           2.3.2       2024-07-29 [1] RSPM
 cli                 3.6.4       2025-02-13 [1] RSPM
 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.2)
 colorspace          2.1-1       2024-07-26 [1] RSPM
 curl                6.2.2       2025-03-24 [1] RSPM
 digest              0.6.37      2024-08-19 [1] RSPM
 dplyr             * 1.1.4       2023-11-17 [1] RSPM
 evaluate            1.0.3       2025-01-10 [1] RSPM
 fastmap             1.2.0       2024-05-15 [1] RSPM
 forcats             1.0.0       2023-01-29 [1] RSPM
 formatters        * 0.5.11.9000 2025-04-09 [1] https://p~
 generics            0.1.3       2022-07-05 [1] RSPM
 ggplot2             3.5.2       2025-04-09 [1] CRAN (R 4.4.2)
 glue                1.8.0       2024-09-30 [1] RSPM
 gtable              0.3.6       2024-10-25 [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
 lattice             0.22-7      2025-04-02 [2] CRAN (R 4.4.2)
 lifecycle           1.0.4       2023-11-07 [1] RSPM
 magrittr          * 2.0.3       2022-03-30 [1] RSPM
 Matrix              1.7-3       2025-03-11 [1] CRAN (R 4.4.2)
 munsell             0.5.1       2024-04-01 [1] RSPM
 nestcolor           0.1.3.9000  2025-04-09 [1] https://p~
 pillar              1.10.2      2025-04-05 [1] RSPM
 pkgcache            2.2.3       2024-09-12 [1] RSPM
 pkgconfig           2.0.3       2019-09-22 [1] RSPM
 processx            3.8.6       2025-02-21 [1] RSPM
 ps                  1.9.0       2025-02-18 [1] RSPM
 purrr               1.0.4       2025-02-05 [1] RSPM
 R6                  2.6.1       2025-02-15 [1] RSPM
 random.cdisc.data   0.3.16.9002 2025-04-09 [1] https://p~
 rbibutils           2.3         2024-10-04 [1] RSPM
 Rdpack              2.6.4       2025-04-09 [1] RSPM
 rlang               1.1.5       2025-01-17 [1] RSPM
 rmarkdown           2.29        2024-11-04 [1] RSPM
 rtables           * 0.6.11.9019 2025-04-09 [1] https://p~
 scales              1.3.0       2023-11-28 [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
 survival            3.8-3       2024-12-17 [2] CRAN (R 4.4.2)
 tern              * 0.9.7.9018  2025-04-09 [1] https://p~
 testthat            3.2.3       2025-01-13 [1] RSPM
 tibble              3.2.1       2023-03-20 [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
 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/4.4
 * ── Packages attached to the search path.

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

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Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file