EGT01

ECG Results and Change from Baseline by Visit

Code
# Define the split function
split_fun <- drop_split_levels

afun <- function(x, .var, .spl_context, ...) {
  n_fun <- sum(!is.na(x), na.rm = TRUE)
  if (n_fun == 0) {
    mean_sd_fun <- c(NA, NA)
    median_fun <- NA
    min_max_fun <- c(NA, NA)
  } else {
    mean_sd_fun <- c(mean(x, na.rm = TRUE), sd(x, na.rm = TRUE))
    median_fun <- median(x, na.rm = TRUE)
    min_max_fun <- c(min(x), max(x))
  }
  is_chg <- .var == "CHG"
  is_baseline <- .spl_context$value[which(.spl_context$split == "AVISIT")] == "BASELINE"
  if (is_baseline && is_chg) n_fun <- mean_sd_fun <- median_fun <- min_max_fun <- NULL

  in_rows(
    "n" = n_fun,
    "Mean (SD)" = mean_sd_fun,
    "Median" = median_fun,
    "Min - Max" = min_max_fun,
    .formats = list("n" = "xx", "Mean (SD)" = "xx.xx (xx.xx)", "Median" = "xx.xx", "Min - Max" = "xx.xx - xx.xx"),
    .format_na_strs = list("n" = "NE", "Mean (SD)" = "NE (NE)", "Median" = "NE", "Min - Max" = "NE - NE")
  )
}

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ACTARM") %>%
  split_rows_by("PARAM", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adeg_f$PARAM)) %>%
  split_rows_by("AVISIT", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adeg_f$AVISIT)) %>%
  split_cols_by_multivar(
    vars = c("AVAL", "CHG"),
    varlabels = c("Value at Visit", "Change from\nBaseline")
  ) %>%
  analyze_colvars(afun = afun)

result <- build_table(lyt, adeg_f, alt_counts_df = adsl)
result
                                 A: Drug X                              B: Placebo                            C: Combination            
                                         Change from                             Change from                             Change from    
Parameter           Value at Visit         Baseline         Value at Visit         Baseline         Value at Visit         Baseline     
  Analysis Visit       (N=134)             (N=134)             (N=134)             (N=134)             (N=132)             (N=132)      
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Heart Rate                                                                                                                              
  BASELINE                                                                                                                              
    n                    134                                     134                                     132                            
    Mean (SD)       71.45 (17.93)                           69.83 (20.72)                           69.34 (20.95)                       
    Median              72.70                                   73.35                                   71.96                           
    Min - Max       9.09 - 106.91                           13.49 - 115.52                          11.63 - 115.49                      
  WEEK 1 DAY 8                                                                                                                          
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       70.19 (20.27)       -1.26 (25.97)       69.43 (20.80)       -0.40 (29.73)       68.65 (18.06)       -0.69 (27.81)   
    Median              70.70               -2.20               70.46               -0.52               68.57               -0.76       
    Min - Max       8.53 - 127.50       -50.97 - 89.16      16.85 - 129.14      -68.18 - 88.38      16.87 - 115.60      -68.25 - 67.20  
  WEEK 2 DAY 15                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       70.32 (19.56)       -1.13 (26.26)       71.11 (20.56)        1.28 (31.35)       69.19 (18.06)       -0.15 (28.61)   
    Median              70.88               -1.10               72.52               -0.31               69.30               -1.55       
    Min - Max       17.14 - 116.32      -85.03 - 67.52      9.22 - 120.54       -73.07 - 81.44      29.62 - 120.50      -67.75 - 66.29  
  WEEK 3 DAY 22                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       68.25 (20.17)       -3.20 (28.66)       68.95 (20.56)       -0.88 (30.14)       70.88 (20.28)        1.54 (27.28)   
    Median              68.79               -2.17               67.80                1.19               70.12                0.14       
    Min - Max       13.33 - 131.73      -81.20 - 72.57      23.98 - 130.41     -73.03 - 103.31      20.91 - 116.79      -64.51 - 72.52  
  WEEK 4 DAY 29                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       70.06 (18.41)       -1.38 (26.59)       71.60 (20.34)        1.77 (30.26)       71.02 (20.59)        1.68 (29.60)   
    Median              69.33               -4.54               72.21               -0.88               70.52                3.81       
    Min - Max       22.30 - 116.51      -58.07 - 77.32      17.53 - 129.06      -64.32 - 85.34      10.35 - 117.30     -65.91 - 105.67  
  WEEK 5 DAY 36                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       66.41 (19.74)       -5.04 (27.11)       71.25 (18.92)        1.42 (27.08)       71.26 (18.56)        1.92 (29.59)   
    Median              65.40               -6.83               70.86                0.64               73.29                1.74       
    Min - Max       23.89 - 110.38      -73.26 - 57.24      25.86 - 125.73      -71.15 - 67.37      23.89 - 117.19      -58.23 - 68.86  
QT Duration                                                                                                                             
  BASELINE                                                                                                                              
    n                    134                                     134                                     132                            
    Mean (SD)      336.83 (117.96)                          351.00 (98.44)                         352.60 (105.11)                      
    Median              344.41                                  351.48                                  347.96                          
    Min - Max       86.98 - 665.40                          98.90 - 641.92                         105.68 - 628.14                      
  WEEK 1 DAY 8                                                                                                                          
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      342.57 (101.09)      5.74 (159.94)      363.95 (102.34)      12.94 (140.73)     359.42 (105.16)      6.83 (147.13)   
    Median              347.26              -1.78               356.54              13.73               363.84               8.69       
    Min - Max       91.63 - 591.42     -346.44 - 452.75    114.92 - 656.45     -317.53 - 416.35     51.91 - 611.88     -473.19 - 358.00 
  WEEK 2 DAY 15                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       353.24 (93.93)      16.41 (162.10)      345.93 (96.78)      -5.08 (152.51)      335.69 (98.61)     -16.91 (138.45)  
    Median              351.10              16.72               346.83              -9.68               320.96              -22.27      
    Min - Max      138.01 - 587.30     -414.07 - 389.16    146.42 - 556.07     -440.28 - 364.76    104.91 - 562.34     -326.55 - 325.27 
  WEEK 3 DAY 22                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      370.12 (101.57)      33.28 (152.78)     343.41 (102.58)      -7.59 (138.80)      346.95 (94.96)      -5.65 (144.65)  
    Median              378.21              39.59               335.12              -15.89              352.15               9.11       
    Min - Max      118.14 - 615.18     -391.72 - 520.09     63.37 - 566.51     -311.28 - 293.76    126.09 - 580.81     -412.11 - 410.01 
  WEEK 4 DAY 29                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       345.77 (95.97)      8.94 (145.65)      354.38 (108.29)      3.37 (142.39)      341.36 (106.75)     -11.24 (145.65)  
    Median              340.13               5.58               346.70              -17.13              352.30              -11.87      
    Min - Max      110.12 - 616.58     -393.34 - 456.04     80.82 - 687.69     -439.90 - 364.80     4.95 - 570.61      -480.94 - 330.67 
  WEEK 5 DAY 36                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)       358.90 (97.69)      22.07 (155.68)      338.65 (99.26)     -12.36 (130.46)      349.30 (95.77)      -3.30 (136.00)  
    Median              351.96               5.89               344.17               0.40               350.32              12.68       
    Min - Max       88.38 - 661.12     -353.30 - 539.84     31.25 - 563.90     -338.85 - 352.75    119.02 - 581.83     -311.45 - 295.53 
RR Duration                                                                                                                             
  BASELINE                                                                                                                              
    n                    134                                     134                                     132                            
    Mean (SD)      1028.42 (286.38)                        1027.48 (324.00)                        1074.62 (277.33)                     
    Median             1041.86                                 1047.27                                 1080.87                          
    Min - Max      34.33 - 1783.71                          5.29 - 1877.19                         289.60 - 1617.06                     
  WEEK 1 DAY 8                                                                                                                          
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      990.15 (318.74)     -38.26 (446.40)     1061.59 (269.14)     34.10 (401.76)     1039.64 (284.39)    -34.98 (406.04)  
    Median              963.88              -86.50             1061.50              66.91              1014.78              -97.83      
    Min - Max      110.82 - 2014.56   -1014.82 - 1389.40   276.83 - 1711.99    -942.16 - 993.82    498.21 - 1937.47    -958.61 - 908.90 
  WEEK 2 DAY 15                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      1013.37 (304.13)    -15.05 (425.81)     1109.40 (318.23)     81.92 (453.11)     1045.21 (277.51)    -29.41 (380.84)  
    Median             1040.69              40.49              1117.76              69.27              1034.64              -15.33      
    Min - Max      164.19 - 1677.10   -1216.10 - 1053.15   160.73 - 2048.73   -1127.10 - 1148.61   252.84 - 1722.33    -859.27 - 871.54 
  WEEK 3 DAY 22                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      1013.99 (304.99)    -14.43 (406.53)     1118.35 (296.53)     90.86 (409.57)     1036.59 (268.52)    -38.03 (421.48)  
    Median             1027.23              -50.54             1134.60              52.03              1030.72              -60.72      
    Min - Max      357.04 - 1798.65   -882.94 - 1080.26    97.14 - 1825.43    -887.06 - 1166.15    446.02 - 1713.38    -984.79 - 902.37 
  WEEK 4 DAY 29                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      1033.31 (313.92)     4.89 (483.15)      1079.76 (298.94)     52.28 (429.25)     1027.55 (295.86)    -47.07 (378.23)  
    Median             1050.40               5.60              1051.61              69.55              1023.36              -49.52      
    Min - Max      54.33 - 1979.43    -1345.93 - 1195.41   347.94 - 1762.04   -826.43 - 1191.83    341.62 - 2144.86   -1002.03 - 1048.66
  WEEK 5 DAY 36                                                                                                                         
    n                    134                 134                 134                 134                 132                 132        
    Mean (SD)      1072.33 (282.90)     43.92 (379.05)     1058.45 (271.01)     30.97 (436.03)     1029.04 (271.21)    -45.58 (405.53)  
    Median             1067.33              55.87              1068.95              33.61              1065.26              -34.40      
    Min - Max      352.97 - 2000.56   -1028.79 - 1418.57   208.83 - 1794.73   -978.97 - 1365.13    436.28 - 1794.07   -962.18 - 1329.88

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)

# Data should be filtered for the studied Parameter (`PARAM`) and the
# Analysis Visit (`AVISIT`). According to the GDSR template, the values for
# the `AVISIT` reported in the EGT01 standard may be:
# 'POST-BASELINE MAXIMUM', 'POST-BASELINE MINIMUM', 'POST-BASELINE LAST'.

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)

adeg_f <- adeg %>%
  filter(ANL01FL == "Y") %>%
  filter(PARAM %in% c("Heart Rate", "QT Duration", "RR Duration"))

teal 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

  # 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)
})
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_summary_by(
      label = "ECG Results and Change from Baseline by Visit",
      dataname = "ADEG",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      by_vars = choices_selected(
        choices = variable_choices(ADEG, c("PARAM", "AVISIT")),
        selected = c("AVISIT")
      ),
      summarize_vars = choices_selected(
        choices = variable_choices(ADEG, c("AVAL", "CHG")),
        selected = c("AVAL")
      ),
      useNA = "ifany",
      paramcd = choices_selected(
        choices = value_choices(ADEG, "PARAMCD", "PARAM"),
        selected = "HR"
      ),
      parallel_vars = TRUE
    )
  ),
  filter = teal_slices(teal_slice("ADEG", "AVAL", selected = NULL))
)

shinyApp(app$ui, app$server)

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

  # 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)
})
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_summary_by(
      label = "ECG Results and Change from Baseline by Visit",
      dataname = "ADEG",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      by_vars = choices_selected(
        choices = variable_choices(ADEG, c("PARAM", "AVISIT")),
        selected = c("AVISIT")
      ),
      summarize_vars = choices_selected(
        choices = variable_choices(ADEG, c("AVAL", "CHG")),
        selected = c("AVAL")
      ),
      useNA = "ifany",
      paramcd = choices_selected(
        choices = value_choices(ADEG, "PARAMCD", "PARAM"),
        selected = "HR"
      ),
      parallel_vars = TRUE
    )
  ),
  filter = teal_slices(teal_slice("ADEG", "AVAL", selected = NULL))
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-02 18:22:39 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 ───────────────────────────────────────────────────────────────────
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 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)
 viridisLite             0.4.2       2023-05-02 [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

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