PKPT04

Pharmacokinetic Parameter Summary – Urine PK Parameters (Stats in Rows)

Output

Standard Table
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 Urine PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug X 
Visit: CYCLE 1 DAY 1

———————————————————————————————————————————————————————————————
PK Parameter                  ARM A                ARM C       
———————————————————————————————————————————————————————————————
Ae (mg)                                                        
  n                            268                  264        
  Mean (SD)                1.55 (0.338)         1.54 (0.298)   
  CV (%)                       21.8                 19.4       
  Geometric Mean               1.51                 1.51       
  CV % Geometric Mean          23.0                 20.3       
  Median                       1.55                 1.55       
  Min - Max                0.702 - 2.46         0.850 - 2.21   
Fe (%)                                                         
  n                            268                  264        
  Mean (SD)                15.7 (3.35)          16.1 (3.10)    
  CV (%)                       21.3                 19.3       
  Geometric Mean               15.3                 15.8       
  CV % Geometric Mean          22.2                 20.2       
  Median                       15.8                 16.0       
  Min - Max                8.15 - 24.5          8.50 - 24.4    
CLR (L/hr)                                                     
  n                            134                  132        
  Mean (SD)              0.0492 (0.00961)     0.0502 (0.0105)  
  CV (%)                       19.5                 20.9       
  Geometric Mean              0.0482               0.0491      
  CV % Geometric Mean          21.0                 21.9       
  Median                      0.0491               0.0498      
  Min - Max              0.0249 - 0.0751      0.0251 - 0.0856  
RENALCLD (L/hr/mg)                                             
  n                            134                  132        
  Mean (SD)             0.00487 (0.000965)   0.00511 (0.000934)
  CV (%)                       19.8                 18.3       
  Geometric Mean             0.00477              0.00502      
  CV % Geometric Mean          21.2                 19.7       
  Median                     0.00497              0.00515      
  Min - Max             0.00238 - 0.00726    0.00236 - 0.00741

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

—————————————————————————————————————————
PK Parameter                  ARM C      
—————————————————————————————————————————
Ae (mg)                                  
  n                            264       
  Mean (SD)               1.60 (0.315)   
  CV (%)                      19.7       
  Geometric Mean              1.56       
  CV % Geometric Mean         21.4       
  Median                      1.60       
  Min - Max               0.857 - 2.26   
Fe (%)                                   
  n                            264       
  Mean (SD)                15.8 (3.08)   
  CV (%)                      19.4       
  Geometric Mean              15.5       
  CV % Geometric Mean         20.2       
  Median                      15.7       
  Min - Max                8.31 - 23.8   
CLR (L/hr)                               
  n                            132       
  Mean (SD)              0.0497 (0.0101) 
  CV (%)                      20.3       
  Geometric Mean             0.0486      
  CV % Geometric Mean         22.0       
  Median                     0.0491      
  Min - Max              0.0184 - 0.0776 
RENALCLD (L/hr/mg)                       
  n                            132       
  Mean (SD)             0.00509 (0.00103)
  CV (%)                      20.3       
  Geometric Mean             0.00499     
  CV % Geometric Mean         21.4       
  Median                     0.00502     
  Min - Max             0.00236 - 0.00794

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 == "Urine", AVISIT == "CYCLE 1 DAY 1")

Reproducibility

Timestamp

[1] "2024-11-20 09:48:33 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     2024-11-20
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
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 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
 fansi               1.0.6   2023-12-08 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.9   2024-09-12 [1] RSPM
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 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              1.9.0   2023-03-22 [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            3.7-0   2024-06-05 [2] CRAN (R 4.4.1)
 tern              * 0.9.6   2024-09-24 [1] RSPM
 testthat            3.2.1.1 2024-04-14 [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
 utf8                1.2.4   2023-10-22 [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

Plasma Drug X

Plasma Drug Y

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file