PKPT07

Table of Mean Dose-Normalized Selected Pharmacokinetic Parameters (Stats in Columns)

Standard Table – Urine
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                                                                                                                        
  RENALCLD (L/hr/mg)   134   0.00487   0.000965    19.8       0.00477              21.2           0.00497   0.00238   0.00726
ARM C                                                                                                                        
  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                                                                                                                       
  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)
library(stringr)

adpp <- random.cdisc.data::cadpp
adpp <- adpp %>%
  filter(AVISIT == "CYCLE 1 DAY 1", str_detect(tolower(PARAM), regex("norm by dose", ignore_case = TRUE)))

Reproducibility

Timestamp

[1] "2024-11-02 18:36:07 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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 evaluate            1.0.1   2024-10-10 [1] CRAN (R 4.4.1)
 fansi               1.0.6   2023-12-08 [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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 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