EGT02

ECG Abnormalities (EGT02_1 & EGT02_2)

Preview
Try this using WebR

Code

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by(var = "ACTARM") %>%
  split_rows_by(
    "PARAM",
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adeg_f$PARAM)
  ) %>%
  count_abnormal("ANRIND", abnormal = list(Low = "LOW", High = "HIGH"), exclude_base_abn = FALSE) %>%
  append_varlabels(adeg_f, "ANRIND", indent = 1L)

result <- build_table(lyt = lyt, df = adeg_f, alt_counts_df = adsl)
result

Assessment        A: Drug X        B: Placebo     C: Combination
  Abnormality      (N=134)          (N=134)          (N=132)    
————————————————————————————————————————————————————————————————
Heart Rate                                                      
  Low           40/134 (29.9%)   43/134 (32.1%)    37/132 (28%) 
  High          39/134 (29.1%)   45/134 (33.6%)   36/132 (27.3%)
QT Duration                                                     
  Low           33/134 (24.6%)   44/134 (32.8%)   47/132 (35.6%)
  High          30/134 (22.4%)   42/134 (31.3%)   34/132 (25.8%)
RR Duration                                                     
  Low           45/134 (33.6%)   26/134 (19.4%)   38/132 (28.8%)
  High          29/134 (21.6%)   49/134 (36.6%)   27/132 (20.5%)

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.

Preview
Try this using WebR

Code

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by(var = "ACTARM") %>%
  split_rows_by(
    "PARAM",
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adeg_f$PARAM)
  ) %>%
  count_abnormal("ANRIND", abnormal = list(Low = "LOW", High = "HIGH"), exclude_base_abn = TRUE) %>%
  append_varlabels(adeg_f, "ANRIND", indent = 1L)

result <- build_table(lyt = lyt, df = adeg_f, alt_counts_df = adsl)
result

Assessment        A: Drug X        B: Placebo     C: Combination
  Abnormality      (N=134)          (N=134)          (N=132)    
————————————————————————————————————————————————————————————————
Heart Rate                                                      
  Low           39/128 (30.5%)   42/124 (33.9%)   33/117 (28.2%)
  High          37/127 (29.1%)   43/129 (33.3%)   31/122 (25.4%)
QT Duration                                                     
  Low           29/113 (25.7%)   42/126 (33.3%)   43/124 (34.7%)
  High           30/125 (24%)    40/130 (30.8%)   30/119 (25.2%)
RR Duration                                                     
  Low           45/129 (34.9%)   26/123 (21.1%)   37/126 (29.4%)
  High          27/127 (21.3%)   43/122 (35.2%)    25/125 (20%)

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(tern)

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)

# Note:  We keep only post-baseline for analysis.
adeg_f <- adeg %>%
  filter(ONTRTFL == "Y") %>%
  filter(PARAM %in% c("Heart Rate", "QT Duration", "RR Duration")) %>%
  filter(ANRIND != "<Missing>") %>%
  var_relabel(
    PARAM = "Assessment",
    ANRIND = "Abnormality"
  )

Code

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADEG <- random.cdisc.data::cadeg
})
datanames <- c("ADSL", "ADEG")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_abnormality(
      label = "Abnormality Table",
      dataname = "ADEG",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      by_vars = choices_selected(
        choices = variable_choices(ADEG, subset = c("EGCAT", "PARAM", "AVISIT")),
        selected = c("PARAM"),
        keep_order = TRUE
      ),
      grade = choices_selected(
        choices = variable_choices(ADEG, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      abnormal = list(Low = "LOW", High = "HIGH"),
      exclude_base_abn = FALSE
    )
  )
)

shinyApp(app$ui, app$server)

Experimental use!

shinylive allow you to modify to run shiny application entirely in the web browser. Modify the code below and click re-run the app to see the results. The performance is slighly worse and some of the features (e.g. downloading) might not work at all.

#| standalone: true
#| viewerHeight: 800
#| editorHeight: 200
#| components: [viewer, editor]
#| layout: vertical

# -- WEBR HELPERS --
options(webr_pkg_repos = c("r-universe" = "https://pharmaverse.r-universe.dev", getOption("webr_pkg_repos")))

# -- APP CODE --
library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADEG <- random.cdisc.data::cadeg
})
datanames <- c("ADSL", "ADEG")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_abnormality(
      label = "Abnormality Table",
      dataname = "ADEG",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      by_vars = choices_selected(
        choices = variable_choices(ADEG, subset = c("EGCAT", "PARAM", "AVISIT")),
        selected = c("PARAM"),
        keep_order = TRUE
      ),
      grade = choices_selected(
        choices = variable_choices(ADEG, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      abnormal = list(Low = "LOW", High = "HIGH"),
      exclude_base_abn = FALSE
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-02 18:20:35 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)
 bslib                   0.8.0       2024-07-29 [1] CRAN (R 4.4.1)
 cachem                  1.1.0       2024-05-16 [1] CRAN (R 4.4.1)
 callr                   3.7.6       2024-03-25 [1] CRAN (R 4.4.1)
 checkmate               2.3.2       2024-07-29 [1] CRAN (R 4.4.1)
 chromote                0.3.1       2024-08-30 [1] CRAN (R 4.4.1)
 cli                     3.6.3       2024-06-21 [1] CRAN (R 4.4.1)
 coda                    0.19-4.1    2024-01-31 [1] CRAN (R 4.4.1)
 codetools               0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
 colorspace              2.1-1       2024-07-26 [1] CRAN (R 4.4.1)
 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)
 emmeans                 1.10.5      2024-10-14 [1] CRAN (R 4.4.1)
 estimability            1.5.1       2024-05-12 [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)
 fontawesome             0.5.2       2023-08-19 [1] CRAN (R 4.4.1)
 forcats                 1.0.0       2023-01-29 [1] CRAN (R 4.4.1)
 formatR                 1.14        2023-01-17 [1] CRAN (R 4.4.1)
 formatters            * 0.5.9.9003  2024-11-02 [1] git2r (https://github.com/insightsengineering/formatters.git@84e8c3e)
 geepack                 1.3.12      2024-09-23 [1] CRAN (R 4.4.1)
 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)
 gtable                  0.3.5       2024-04-22 [1] CRAN (R 4.4.1)
 htmltools               0.5.8.1     2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets             1.6.4       2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                  1.6.15      2024-03-26 [1] CRAN (R 4.4.1)
 jquerylib               0.1.4       2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite                1.8.9       2024-09-20 [1] CRAN (R 4.4.1)
 knitr                   1.48        2024-07-07 [1] CRAN (R 4.4.1)
 later                   1.3.2       2023-12-06 [1] CRAN (R 4.4.1)
 lattice                 0.22-6      2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle               1.0.4       2023-11-07 [1] CRAN (R 4.4.1)
 logger                  0.3.0       2024-03-05 [1] CRAN (R 4.4.1)
 magrittr              * 2.0.3       2022-03-30 [1] CRAN (R 4.4.1)
 MASS                    7.3-61      2024-06-13 [2] CRAN (R 4.4.1)
 Matrix                  1.7-0       2024-04-26 [1] CRAN (R 4.4.1)
 memoise                 2.0.1       2021-11-26 [1] CRAN (R 4.4.1)
 mime                    0.12        2021-09-28 [1] CRAN (R 4.4.1)
 multcomp                1.4-26      2024-07-18 [1] CRAN (R 4.4.1)
 munsell                 0.5.1       2024-04-01 [1] CRAN (R 4.4.1)
 mvtnorm                 1.3-1       2024-09-03 [1] CRAN (R 4.4.1)
 nestcolor               0.1.2.9017  2024-11-02 [1] git2r (https://github.com/insightsengineering/nestcolor.git@3d2ce62)
 nlme                    3.1-166     2024-08-14 [2] CRAN (R 4.4.1)
 pillar                  1.9.0       2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig               2.0.3       2019-09-22 [1] CRAN (R 4.4.1)
 processx                3.8.4       2024-03-16 [1] CRAN (R 4.4.1)
 promises                1.3.0       2024-04-05 [1] CRAN (R 4.4.1)
 ps                      1.8.0       2024-09-12 [1] CRAN (R 4.4.1)
 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)
 Rcpp                    1.0.13      2024-07-17 [1] CRAN (R 4.4.1)
 Rdpack                  2.6.1       2024-08-06 [1] CRAN (R 4.4.1)
 rlang                   1.1.4       2024-06-04 [1] CRAN (R 4.4.1)
 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)
 sandwich                3.1-1       2024-09-15 [1] CRAN (R 4.4.1)
 sass                    0.4.9       2024-03-15 [1] CRAN (R 4.4.1)
 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)
 shiny                 * 1.9.1       2024-08-01 [1] CRAN (R 4.4.1)
 shinycssloaders         1.1.0       2024-07-30 [1] CRAN (R 4.4.1)
 shinyjs                 2.1.0       2021-12-23 [1] CRAN (R 4.4.1)
 shinyvalidate           0.1.3       2023-10-04 [1] CRAN (R 4.4.1)
 shinyWidgets            0.8.7       2024-09-23 [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)
 teal                  * 0.15.2.9079 2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.git@53c423d)
 teal.code             * 0.5.0.9012  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.code.git@86aa265)
 teal.data             * 0.6.0.9015  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.data.git@eca9695)
 teal.logger             0.3.0.9000  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.logger.git@cd9cc7e)
 teal.modules.clinical * 0.9.1.9030  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.modules.clinical.git@5cf76ac)
 teal.reporter           0.3.1.9016  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.reporter.git@4fefa7e)
 teal.slice            * 0.5.1.9015  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.slice.git@25f4101)
 teal.transform        * 0.5.0.9015  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.transform.git@0b855e3)
 teal.widgets            0.4.2.9022  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.widgets.git@8a39dd4)
 tern                  * 0.9.6.9013  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.git@435fd51)
 tern.gee                0.1.5.9004  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.gee.git@458172d)
 testthat                3.2.1.1     2024-04-14 [1] CRAN (R 4.4.1)
 TH.data                 1.1-2       2023-04-17 [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)
 webshot                 0.5.5       2023-06-26 [1] CRAN (R 4.4.1)
 webshot2                0.1.1       2023-08-11 [1] CRAN (R 4.4.1)
 websocket               1.4.2       2024-07-22 [1] CRAN (R 4.4.1)
 withr                   3.0.1       2024-07-31 [1] CRAN (R 4.4.1)
 xfun                    0.48        2024-10-03 [1] CRAN (R 4.4.1)
 xtable                  1.8-4       2019-04-21 [1] CRAN (R 4.4.1)
 yaml                    2.3.10      2024-07-26 [1] CRAN (R 4.4.1)
 zoo                     1.8-12      2023-04-13 [1] CRAN (R 4.4.1)

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

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

`.lock` file

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

Download

teal App

Reproducibility

Timestamp

Session Info

.lock file

`teal` App

`.lock` file