LBT04

Laboratory Abnormalities Not Present at Baseline

Output

Standard Table
Data Setup

Preview
Try this using WebR

Code

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

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

result

Laboratory Test                          A: Drug X        B: Placebo     C: Combination
  Direction of Abnormality                (N=134)          (N=134)          (N=132)    
———————————————————————————————————————————————————————————————————————————————————————
Alanine Aminotransferase Measurement                                                   
  Low                                  57/113 (50.4%)    62/117 (53%)    61/123 (49.6%)
  High                                     0/134            0/134            0/132     
C-Reactive Protein Measurement                                                         
  Low                                  78/119 (65.5%)   71/113 (62.8%)   62/112 (55.4%)
  High                                 69/114 (60.5%)   57/112 (50.9%)   58/115 (50.4%)
Immunoglobulin A Measurement                                                           
  Low                                      0/134            0/134            0/132     
  High                                 64/119 (53.8%)   62/116 (53.4%)   62/113 (54.9%)

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.

R Code

Start Over

Run Code

lyt <- basic_table(show_colcounts = TRUE) %>%

split_cols_by("ACTARM") %>%

split_rows_by("PARAM",

split_fun = drop_split_levels,

label_pos = "topleft",

split_label = obj_label(adlb_f$PARAM)

) %>%

count_abnormal(

var = "ANRIND",

abnormal = list(Low = c("LOW", "LOW LOW"), High = c("HIGH", "HIGH HIGH")),

exclude_base_abn = TRUE

) %>%

append_varlabels(adlb_f, "ANRIND", indent = 1L)

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

result

_webr_editor_2 = Object {code: "lyt <- basic_table(show_colcounts = TRUE) %>%\n sp…= lyt, df = adlb_f, alt_counts_df = adsl)\n\nresult", options: Object, indicator: Ke}

Code

library(dplyr)
library(tern)

adsl <- random.cdisc.data::cadsl
adlb <- random.cdisc.data::cadlb

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

adlb_f <- adlb %>%
  filter(ONTRTFL == "Y", ANRIND != "<Missing>") %>%
  var_relabel(
    PARAM = "Laboratory Test",
    ANRIND = "Direction of Abnormality"
  )

Code

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADLB <- random.cdisc.data::cadlb %>%
    col_relabel(PARAM = "Laboratory Test", ANRIND = "Direction of Abnormality")
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames

Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data

Code

join_keys(data) <- default_cdisc_join_keys[datanames]

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

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

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.

Reproducibility

Timestamp

[1] "2025-03-26 17:46:31 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     2025-03-26
 pandoc   3.6.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.6.42 @ /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                   1.0.7    2024-09-26 [1] RSPM
 bslib                   0.9.0    2025-01-30 [1] RSPM
 cachem                  1.1.0    2024-05-16 [1] RSPM
 callr                   3.7.6    2024-03-25 [1] RSPM
 checkmate               2.3.2    2024-07-29 [1] RSPM
 chromote                0.5.0    2025-03-21 [1] RSPM
 cli                     3.6.4    2025-02-13 [1] RSPM
 coda                    0.19-4.1 2024-01-31 [1] CRAN (R 4.4.2)
 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
 emmeans                 1.11.0   2025-03-20 [1] RSPM
 estimability            1.5.1    2024-05-12 [1] RSPM
 evaluate                1.0.3    2025-01-10 [1] RSPM
 fastmap                 1.2.0    2024-05-15 [1] RSPM
 fontawesome             0.5.3    2024-11-16 [1] RSPM
 forcats                 1.0.0    2023-01-29 [1] RSPM
 formatR                 1.14     2023-01-17 [1] CRAN (R 4.4.2)
 formatters            * 0.5.10   2025-01-09 [1] RSPM
 geepack                 1.3.12   2024-09-23 [1] RSPM
 generics                0.1.3    2022-07-05 [1] RSPM
 ggplot2                 3.5.1    2024-04-23 [1] RSPM
 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
 httpuv                  1.6.15   2024-03-26 [1] RSPM
 jquerylib               0.1.4    2021-04-26 [1] RSPM
 jsonlite                1.9.1    2025-03-03 [1] RSPM
 knitr                   1.50     2025-03-16 [1] RSPM
 later                   1.4.1    2024-11-27 [1] RSPM
 lattice                 0.22-6   2024-03-20 [2] CRAN (R 4.4.2)
 lifecycle               1.0.4    2023-11-07 [1] RSPM
 logger                  0.4.0    2024-10-22 [1] RSPM
 magrittr              * 2.0.3    2022-03-30 [1] RSPM
 MASS                    7.3-65   2025-02-28 [2] CRAN (R 4.4.2)
 Matrix                  1.7-3    2025-03-11 [1] CRAN (R 4.4.2)
 memoise                 2.0.1    2021-11-26 [1] RSPM
 mime                    0.13     2025-03-17 [1] RSPM
 multcomp                1.4-28   2025-01-29 [1] RSPM
 munsell                 0.5.1    2024-04-01 [1] RSPM
 mvtnorm                 1.3-3    2025-01-10 [1] RSPM
 nestcolor               0.1.3    2025-01-21 [1] RSPM
 nlme                    3.1-167  2025-01-27 [2] CRAN (R 4.4.2)
 pillar                  1.10.1   2025-01-07 [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
 promises                1.3.2    2024-11-28 [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   2024-10-10 [1] RSPM
 rbibutils               2.3      2024-10-04 [1] RSPM
 Rcpp                    1.0.14   2025-01-12 [1] RSPM
 Rdpack                  2.6.3    2025-03-16 [1] RSPM
 rlang                   1.1.5    2025-01-17 [1] RSPM
 rmarkdown               2.29     2024-11-04 [1] RSPM
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 scales                  1.3.0    2023-11-28 [1] RSPM
 sessioninfo             1.2.3    2025-02-05 [1] any (@1.2.3)
 shiny                 * 1.10.0   2024-12-14 [1] RSPM
 shinycssloaders         1.1.0    2024-07-30 [1] RSPM
 shinyjs                 2.1.0    2021-12-23 [1] RSPM
 shinyvalidate           0.1.3    2023-10-04 [1] RSPM
 shinyWidgets            0.9.0    2025-02-21 [1] RSPM
 stringi                 1.8.4    2024-05-06 [1] RSPM
 stringr                 1.5.1    2023-11-14 [1] RSPM
 survival                3.8-3    2024-12-17 [2] CRAN (R 4.4.2)
 teal                  * 0.16.0   2025-02-23 [1] RSPM
 teal.code             * 0.6.1    2025-02-14 [1] RSPM
 teal.data             * 0.7.0    2025-01-28 [1] RSPM
 teal.logger             0.3.2    2025-02-14 [1] RSPM
 teal.modules.clinical * 0.10.0   2025-02-28 [1] RSPM
 teal.reporter           0.4.0    2025-01-24 [1] RSPM
 teal.slice            * 0.6.0    2025-02-03 [1] RSPM
 teal.transform        * 0.6.0    2025-02-12 [1] RSPM
 teal.widgets            0.4.3    2025-01-31 [1] RSPM
 tern                  * 0.9.7    2025-01-17 [1] RSPM
 tern.gee                0.1.5    2024-08-23 [1] RSPM
 testthat                3.2.3    2025-01-13 [1] RSPM
 TH.data                 1.1-3    2025-01-17 [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
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 webshot2                0.1.1    2023-08-11 [1] RSPM
 websocket               1.4.2    2024-07-22 [1] RSPM
 withr                   3.0.2    2024-10-28 [1] RSPM
 xfun                    0.51     2025-02-19 [1] RSPM
 xtable                  1.8-4    2019-04-21 [1] RSPM
 yaml                    2.3.10   2024-07-26 [1] RSPM
 zoo                     1.8-13   2025-02-22 [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

teal App

Reproducibility

Timestamp

Session Info

.lock file

`teal` App

`.lock` file