PKPT02

Pharmacokinetic Parameter Summary – Plasma/Serum/Blood PK Parameters (Stats in Rows)

Standard Table – Plasma
Data Setup

Code

# lyt creation
lyt <- basic_table() %>%
  split_cols_by(
    var = "ARMCD",
    split_fun = trim_levels_in_group("ARMCD"),
    split_label = "Treatment Arm"
  ) %>%
  split_rows_by(
    var = "PKPARAM",
    label_pos = "topleft",
    split_label = "PK Parameter"
  ) %>%
  tern::analyze_vars(
    vars = "AVAL",
    .stats = c("n", "mean_sd", "cv", "geom_mean", "geom_cv", "median", "range"),
    .formats = c(
      n = "xx.",
      mean_sd = format_sigfig(3, "xx (xx)"),
      cv = "xx.x",
      geom_mean = format_sigfig(3),
      geom_cv = "xx.x",
      median = format_sigfig(3),
      range = format_sigfig(3, "xx - xx")
    )
  )

Plasma Drug X

Preview
Try this using WebR

Code

adpp0 <- adpp %>%
  filter(PPCAT == "Plasma Drug X") %>%
  h_pkparam_sort() %>%
  mutate(PKPARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")"))) %>%
  mutate(PKPARAM = reorder(PKPARAM, TLG_ORDER))

result <- build_table(lyt, df = adpp0)
main_title(result) <- paste("Summary of", unique(adpp0$PPSPEC), "PK Parameter by Treatment Arm, PK Population")
subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(adpp0$AVISIT))
result

Summary of Plasma PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug X 
Visit: CYCLE 1 DAY 1

———————————————————————————————————————————————————
PK Parameter                ARM A         ARM C    
———————————————————————————————————————————————————
Cmax (ug/mL)                                       
  n                          134           132     
  Mean (SD)              30.2 (6.24)   30.0 (5.46) 
  CV (%)                    20.6           18.2    
  Geometric Mean            29.6           29.5    
  CV % Geometric Mean       21.0           18.9    
  Median                    29.9           29.8    
  Min - Max              17.5 - 48.7   15.9 - 47.6 
AUCinf obs (day*ug/mL)                             
  n                          134           132     
  Mean (SD)              203 (37.7)     195 (37.8) 
  CV (%)                    18.6           19.4    
  Geometric Mean             199           192     
  CV % Geometric Mean       18.7           20.1    
  Median                     197           196     
  Min - Max               125 - 311     103 - 315  
CL obs (ml/day/kg)                                 
  n                          134           132     
  Mean (SD)              5.04 (1.04)   5.01 (0.985)
  CV (%)                    20.6           19.7    
  Geometric Mean            4.93           4.91    
  CV % Geometric Mean       22.4           21.1    
  Median                    5.08           4.97    
  Min - Max              2.25 - 7.39   2.10 - 7.49

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

adpp1 <- adpp %>%
  filter(PPCAT == "Plasma Drug Y") %>%
  h_pkparam_sort() %>%
  mutate(PKPARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")"))) %>%
  mutate(PKPARAM = reorder(PKPARAM, TLG_ORDER))

result <- build_table(lyt, df = adpp1)
main_title(result) <- paste("Summary of", unique(adpp1$PPSPEC), "PK Parameter by Treatment Arm, PK Population")
subtitles(result) <- paste("Analyte:", unique(adpp1$PPCAT), "\nVisit:", unique(adpp1$AVISIT))
result

Summary of Plasma PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug Y 
Visit: CYCLE 1 DAY 1

—————————————————————————————————————
PK Parameter                ARM C    
—————————————————————————————————————
Cmax (ug/mL)                         
  n                          132     
  Mean (SD)              29.9 (5.55) 
  CV (%)                     18.6    
  Geometric Mean             29.4    
  CV % Geometric Mean        20.1    
  Median                     29.7    
  Min - Max              14.1 - 43.4 
AUCinf obs (day*ug/mL)               
  n                          132     
  Mean (SD)               199 (37.9) 
  CV (%)                     19.1    
  Geometric Mean             195     
  CV % Geometric Mean        18.9    
  Median                     195     
  Min - Max               126 - 318  
CL obs (ml/day/kg)                   
  n                          132     
  Mean (SD)              4.96 (0.895)
  CV (%)                     18.1    
  Geometric Mean             4.87    
  CV % Geometric Mean        18.7    
  Median                     4.94    
  Min - Max              2.99 - 7.21

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)

adpp <- random.cdisc.data::cadpp
adpp <- adpp %>% filter(PPSPEC == "Plasma", AVISIT == "CYCLE 1 DAY 1")

Reproducibility

Timestamp

[1] "2024-11-02 18:36:39 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 ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
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 broom               1.0.7   2024-09-26 [1] CRAN (R 4.4.1)
 checkmate           2.3.2   2024-07-29 [1] CRAN (R 4.4.1)
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 dplyr             * 1.1.4   2023-11-17 [1] CRAN (R 4.4.1)
 evaluate            1.0.1   2024-10-10 [1] CRAN (R 4.4.1)
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 glue                1.8.0   2024-09-30 [1] CRAN (R 4.4.1)
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 knitr               1.48    2024-07-07 [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)
 magrittr          * 2.0.3   2022-03-30 [1] CRAN (R 4.4.1)
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 pillar              1.9.0   2023-03-22 [1] CRAN (R 4.4.1)
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 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  2024-11-02 [1] https://insightsengineering.r-universe.dev (R 4.4.1)
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 rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.4.1)
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 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)
 tern              * 0.9.6   2024-09-24 [1] CRAN (R 4.4.1)
 testthat            3.2.1.1 2024-04-14 [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)
 xfun                0.49    2024-10-31 [1] CRAN (R 4.4.1)
 yaml                2.3.10  2024-07-26 [1] CRAN (R 4.4.1)

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

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

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Plasma Drug X

Plasma Drug Y

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file