PKPT05

Summary of Urinary PK Parameters by Treatment Arm (Stats in Columns)

Output

Standard Table
Data Setup

Code

# lyt creation
lyt <- basic_table() %>%
  split_rows_by(
    var = "ARMCD",
    split_fun = trim_levels_in_group("ARMCD"),
    label_pos = "topleft",
    split_label = "Treatment Arm"
  ) %>%
  split_rows_by(
    var = "PKPARAM",
    label_pos = "topleft",
    split_label = "PK Parameter",
    child_labels = "hidden"
  ) %>%
  analyze_vars_in_cols(
    vars = "AVAL",
    .stats = c(
      "n", "mean", "sd", "cv",
      "geom_mean", "geom_cv", "median",
      "min", "max"
    ),
    .labels = c(
      n = "n",
      mean = "Mean",
      sd = "SD",
      cv = "CV (%)",
      geom_mean = "Geometric Mean",
      geom_cv = "CV % Geometric Mean",
      median = "Median",
      min = "Minimum",
      max = "Maximum"
    ),
    .formats = c(
      n = "xx.",
      mean = format_sigfig(3),
      sd = format_sigfig(3),
      cv = "xx.x",
      median = format_sigfig(3),
      geom_mean = format_sigfig(3),
      geom_cv = "xx.x",
      min = format_sigfig(3),
      max = format_sigfig(3)
    )
  )

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

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

————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Treatment Arm                                                                                                               
  PK Parameter          n     Mean       SD      CV (%)   Geometric Mean   CV % Geometric Mean   Median    Minimum   Maximum
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ARM C                                                                                                                       
  Ae (mg)              264    1.60      0.315     19.7         1.56               21.4            1.60      0.857     2.26  
  Fe (%)               264    15.8      3.08      19.4         15.5               20.2            15.7      8.31      23.8  
  CLR (L/hr)           132   0.0497    0.0101     20.3        0.0486              22.0           0.0491    0.0184    0.0776 
  RENALCLD (L/hr/mg)   132   0.00509   0.00103    20.3       0.00499              21.4           0.00502   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] "2024-12-21 18:03:58 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
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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
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 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
 nestcolor           0.1.2.9017  2024-12-21 [1] https://p~
 pillar              1.10.0      2024-12-17 [1] RSPM
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 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   0.3.16.9001 2024-12-21 [1] https://p~
 rbibutils           2.3         2024-10-04 [1] RSPM
 Rdpack              2.6.2       2024-11-15 [1] RSPM
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 stringr             1.5.1       2023-11-14 [1] RSPM
 survival            3.8-3       2024-12-17 [1] RSPM
 tern              * 0.9.6.9017  2024-12-21 [1] https://p~
 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

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

`.lock` file

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Output

Plasma Drug X

Plasma Drug Y

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file