LBT06

Laboratory Abnormalities by Visit and Baseline Status

Output

Preview
Try this using WebR

Code

# Define the split function
split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_rows_by("AVISIT", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adlb_f_crp$AVISIT)) %>%
  count_abnormal_by_baseline(
    "ANRIND",
    abnormal = c(Low = "LOW", High = "HIGH"),
    .indent_mods = 4L
  ) %>%
  append_varlabels(adlb_f_crp, "ANRIND", indent = 1L) %>%
  append_topleft("    Baseline Status")

result <- build_table(
  lyt = lyt,
  df = adlb_f_crp,
  alt_counts_df = adsl
) %>%
  trim_rows()

result

Visit                                                                                  
  Analysis Reference Range Indicator     A: Drug X        B: Placebo     C: Combination
    Baseline Status                       (N=134)          (N=134)          (N=132)    
———————————————————————————————————————————————————————————————————————————————————————
WEEK 1 DAY 8                                                                           
  Low                                                                                  
            Not low                    16/119 (13.4%)   22/113 (19.5%)   24/112 (21.4%)
            Low                         2/15 (13.3%)     2/21 (9.5%)       7/20 (35%)  
            Total                      18/134 (13.4%)   24/134 (17.9%)   31/132 (23.5%)
  High                                                                                 
            Not high                   21/114 (18.4%)   20/112 (17.9%)   17/115 (14.8%)
            High                         2/20 (10%)      4/22 (18.2%)     3/17 (17.6%) 
            Total                      23/134 (17.2%)   24/134 (17.9%)   20/132 (15.2%)
WEEK 2 DAY 15                                                                          
  Low                                                                                  
            Not low                    26/119 (21.8%)   20/113 (17.7%)   12/112 (10.7%)
            Low                         2/15 (13.3%)     3/21 (14.3%)      4/20 (20%)  
            Total                      28/134 (20.9%)   23/134 (17.2%)   16/132 (12.1%)
  High                                                                                 
            Not high                   15/114 (13.2%)   17/112 (15.2%)    15/115 (13%) 
            High                         2/20 (10%)      4/22 (18.2%)     4/17 (23.5%) 
            Total                      17/134 (12.7%)   21/134 (15.7%)   19/132 (14.4%)
WEEK 3 DAY 22                                                                          
  Low                                                                                  
            Not low                    15/119 (12.6%)   21/113 (18.6%)   18/112 (16.1%)
            Low                             0/15         3/21 (14.3%)         0/20     
            Total                      15/134 (11.2%)   24/134 (17.9%)   18/132 (13.6%)
  High                                                                                 
            Not high                   22/114 (19.3%)   18/112 (16.1%)   17/115 (14.8%)
            High                         2/20 (10%)      5/22 (22.7%)     1/17 (5.9%)  
            Total                      24/134 (17.9%)   23/134 (17.2%)   18/132 (13.6%)
WEEK 4 DAY 29                                                                          
  Low                                                                                  
            Not low                    30/119 (25.2%)   13/113 (11.5%)   16/112 (14.3%)
            Low                          3/15 (20%)      2/21 (9.5%)       5/20 (25%)  
            Total                      33/134 (24.6%)   15/134 (11.2%)   21/132 (15.9%)
  High                                                                                 
            Not high                   17/114 (14.9%)   11/112 (9.8%)    16/115 (13.9%)
            High                         2/20 (10%)      6/22 (27.3%)     3/17 (17.6%) 
            Total                      19/134 (14.2%)   17/134 (12.7%)   19/132 (14.4%)
WEEK 5 DAY 36                                                                          
  Low                                                                                  
            Not low                    17/119 (14.3%)   19/113 (16.8%)   16/112 (14.3%)
            Low                         2/15 (13.3%)     3/21 (14.3%)      5/20 (25%)  
            Total                      19/134 (14.2%)   22/134 (16.4%)   21/132 (15.9%)
  High                                                                                 
            Not high                   19/114 (16.7%)   17/112 (15.2%)   11/115 (9.6%) 
            High                         4/20 (20%)      6/22 (27.3%)     2/17 (11.8%) 
            Total                      23/134 (17.2%)   23/134 (17.2%)   13/132 (9.8%)

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

# The following code generates one large table for multiple lab tests.
# If separate tables are needed for each lab test per GDSR standard, use the code for "single lab test".

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_rows_by("PARAM", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adlb_f$PARAM)) %>%
  split_rows_by("AVISIT", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adlb_f$AVISIT)) %>%
  count_abnormal_by_baseline(
    "ANRIND",
    abnormal = c(Low = "LOW", High = "HIGH"),
    .indent_mods = 4L
  ) %>%
  append_varlabels(adlb_f, "ANRIND", indent = 2L) %>%
  append_topleft("      Baseline Status")

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

result

Parameter                                                                                
  Visit                                                                                  
    Analysis Reference Range Indicator     A: Drug X        B: Placebo     C: Combination
      Baseline Status                       (N=134)          (N=134)          (N=132)    
—————————————————————————————————————————————————————————————————————————————————————————
Alanine Aminotransferase Measurement                                                     
  WEEK 1 DAY 8                                                                           
    Low                                                                                  
              Not low                    19/113 (16.8%)   13/117 (11.1%)   14/123 (11.4%)
              Low                         2/21 (9.5%)      1/17 (5.9%)      1/9 (11.1%)  
              Total                      21/134 (15.7%)   14/134 (10.4%)   15/132 (11.4%)
    High                                                                                 
              Not high                       0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
  WEEK 2 DAY 15                                                                          
    Low                                                                                  
              Not low                     17/113 (15%)    13/117 (11.1%)   13/123 (10.6%)
              Low                         2/21 (9.5%)      2/17 (11.8%)     4/9 (44.4%)  
              Total                      19/134 (14.2%)   15/134 (11.2%)   17/132 (12.9%)
    High                                                                                 
              Not high                       0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
  WEEK 3 DAY 22                                                                          
    Low                                                                                  
              Not low                    10/113 (8.8%)    20/117 (17.1%)   21/123 (17.1%)
              Low                          4/21 (19%)      4/17 (23.5%)     2/9 (22.2%)  
              Total                      14/134 (10.4%)   24/134 (17.9%)   23/132 (17.4%)
    High                                                                                 
              Not high                       0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
  WEEK 4 DAY 29                                                                          
    Low                                                                                  
              Not low                    15/113 (13.3%)   19/117 (16.2%)   18/123 (14.6%)
              Low                         2/21 (9.5%)      3/17 (17.6%)     1/9 (11.1%)  
              Total                      17/134 (12.7%)   22/134 (16.4%)   19/132 (14.4%)
    High                                                                                 
              Not high                       0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
  WEEK 5 DAY 36                                                                          
    Low                                                                                  
              Not low                     17/113 (15%)    23/117 (19.7%)   18/123 (14.6%)
              Low                             0/21         1/17 (5.9%)      1/9 (11.1%)  
              Total                      17/134 (12.7%)   24/134 (17.9%)   19/132 (14.4%)
    High                                                                                 
              Not high                       0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
C-Reactive Protein Measurement                                                           
  WEEK 1 DAY 8                                                                           
    Low                                                                                  
              Not low                    16/119 (13.4%)   22/113 (19.5%)   24/112 (21.4%)
              Low                         2/15 (13.3%)     2/21 (9.5%)       7/20 (35%)  
              Total                      18/134 (13.4%)   24/134 (17.9%)   31/132 (23.5%)
    High                                                                                 
              Not high                   21/114 (18.4%)   20/112 (17.9%)   17/115 (14.8%)
              High                         2/20 (10%)      4/22 (18.2%)     3/17 (17.6%) 
              Total                      23/134 (17.2%)   24/134 (17.9%)   20/132 (15.2%)
  WEEK 2 DAY 15                                                                          
    Low                                                                                  
              Not low                    26/119 (21.8%)   20/113 (17.7%)   12/112 (10.7%)
              Low                         2/15 (13.3%)     3/21 (14.3%)      4/20 (20%)  
              Total                      28/134 (20.9%)   23/134 (17.2%)   16/132 (12.1%)
    High                                                                                 
              Not high                   15/114 (13.2%)   17/112 (15.2%)    15/115 (13%) 
              High                         2/20 (10%)      4/22 (18.2%)     4/17 (23.5%) 
              Total                      17/134 (12.7%)   21/134 (15.7%)   19/132 (14.4%)
  WEEK 3 DAY 22                                                                          
    Low                                                                                  
              Not low                    15/119 (12.6%)   21/113 (18.6%)   18/112 (16.1%)
              Low                             0/15         3/21 (14.3%)         0/20     
              Total                      15/134 (11.2%)   24/134 (17.9%)   18/132 (13.6%)
    High                                                                                 
              Not high                   22/114 (19.3%)   18/112 (16.1%)   17/115 (14.8%)
              High                         2/20 (10%)      5/22 (22.7%)     1/17 (5.9%)  
              Total                      24/134 (17.9%)   23/134 (17.2%)   18/132 (13.6%)
  WEEK 4 DAY 29                                                                          
    Low                                                                                  
              Not low                    30/119 (25.2%)   13/113 (11.5%)   16/112 (14.3%)
              Low                          3/15 (20%)      2/21 (9.5%)       5/20 (25%)  
              Total                      33/134 (24.6%)   15/134 (11.2%)   21/132 (15.9%)
    High                                                                                 
              Not high                   17/114 (14.9%)   11/112 (9.8%)    16/115 (13.9%)
              High                         2/20 (10%)      6/22 (27.3%)     3/17 (17.6%) 
              Total                      19/134 (14.2%)   17/134 (12.7%)   19/132 (14.4%)
  WEEK 5 DAY 36                                                                          
    Low                                                                                  
              Not low                    17/119 (14.3%)   19/113 (16.8%)   16/112 (14.3%)
              Low                         2/15 (13.3%)     3/21 (14.3%)      5/20 (25%)  
              Total                      19/134 (14.2%)   22/134 (16.4%)   21/132 (15.9%)
    High                                                                                 
              Not high                   19/114 (16.7%)   17/112 (15.2%)   11/115 (9.6%) 
              High                         4/20 (20%)      6/22 (27.3%)     2/17 (11.8%) 
              Total                      23/134 (17.2%)   23/134 (17.2%)   13/132 (9.8%) 
Immunoglobulin A Measurement                                                             
  WEEK 1 DAY 8                                                                           
    Low                                                                                  
              Not low                        0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
    High                                                                                 
              Not high                   18/119 (15.1%)   20/116 (17.2%)   14/113 (12.4%)
              High                        1/15 (6.7%)      5/18 (27.8%)     4/19 (21.1%) 
              Total                      19/134 (14.2%)   25/134 (18.7%)   18/132 (13.6%)
  WEEK 2 DAY 15                                                                          
    Low                                                                                  
              Not low                        0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
    High                                                                                 
              Not high                   16/119 (13.4%)   13/116 (11.2%)   12/113 (10.6%)
              High                        1/15 (6.7%)      1/18 (5.6%)      2/19 (10.5%) 
              Total                      17/134 (12.7%)   14/134 (10.4%)   14/132 (10.6%)
  WEEK 3 DAY 22                                                                          
    Low                                                                                  
              Not low                        0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
    High                                                                                 
              Not high                   17/119 (14.3%)   15/116 (12.9%)   21/113 (18.6%)
              High                            0/15         1/18 (5.6%)      1/19 (5.3%)  
              Total                      17/134 (12.7%)   16/134 (11.9%)   22/132 (16.7%)
  WEEK 4 DAY 29                                                                          
    Low                                                                                  
              Not low                        0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
    High                                                                                 
              Not high                    19/119 (16%)    16/116 (13.8%)   19/113 (16.8%)
              High                        4/15 (26.7%)     5/18 (27.8%)     3/19 (15.8%) 
              Total                      23/134 (17.2%)   21/134 (15.7%)   22/132 (16.7%)
  WEEK 5 DAY 36                                                                          
    Low                                                                                  
              Not low                        0/134            0/134            0/132     
              Total                          0/134            0/134            0/132     
    High                                                                                 
              Not high                   16/119 (13.4%)   21/116 (18.1%)   20/113 (17.7%)
              High                        1/15 (6.7%)      3/18 (16.7%)         0/19     
              Total                      17/134 (12.7%)   24/134 (17.9%)   20/132 (15.2%)

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(tern)
library(dplyr)

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)
# Please note that df_explict_na has a na_level argument defaulting to "<Missing>",
# Please don't change the na_level to anything other than NA, empty string or the default "<Missing>".

adlb_f <- adlb %>%
  dplyr::filter(ABLFL != "Y") %>%
  dplyr::filter(!(AVISIT %in% c("SCREENING", "BASELINE"))) %>%
  dplyr::mutate(AVISIT = droplevels(AVISIT)) %>%
  var_relabel(AVISIT = "Visit")

adlb_f_crp <- adlb_f %>% dplyr::filter(PARAMCD == "CRP")

Reproducibility

Timestamp

[1] "2024-12-21 17:44:22 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     2024-12-21
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ 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
 checkmate           2.3.2   2024-07-29 [1] RSPM
 cli                 3.6.3   2024-06-21 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.4.1)
 colorspace          2.1-1   2024-07-26 [1] RSPM
 curl                6.0.1   2024-11-14 [1] RSPM
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.1   2024-10-10 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 forcats             1.0.0   2023-01-29 [1] RSPM
 formatters        * 0.5.9   2024-09-12 [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
 jsonlite            1.8.9   2024-09-20 [1] RSPM
 knitr               1.49    2024-11-08 [1] RSPM
 lattice             0.22-6  2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr          * 2.0.3   2022-03-30 [1] RSPM
 Matrix              1.7-1   2024-10-18 [1] RSPM
 munsell             0.5.1   2024-04-01 [1] RSPM
 pillar              1.10.0  2024-12-17 [1] RSPM
 pkgcache            2.2.3   2024-09-12 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.4   2024-03-16 [1] RSPM
 ps                  1.8.1   2024-10-28 [1] RSPM
 purrr               1.0.2   2023-08-10 [1] RSPM
 R6                  2.5.1   2021-08-19 [1] RSPM
 random.cdisc.data   0.3.16  2024-10-10 [1] RSPM
 rbibutils           2.3     2024-10-04 [1] RSPM
 Rdpack              2.6.2   2024-11-15 [1] RSPM
 rlang               1.1.4   2024-06-04 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 rtables           * 0.6.10  2024-09-20 [1] RSPM
 scales              1.3.0   2023-11-28 [1] RSPM
 sessioninfo         1.2.2   2021-12-06 [1] any (@1.2.2)
 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 [1] RSPM
 tern              * 0.9.6   2024-09-24 [1] RSPM
 testthat            3.2.2   2024-12-10 [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                0.49    2024-10-31 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

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

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

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Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file