PKPT08

Pharmacokinetic Parameter Summary of Cumulative Amount of Drug Eliminated and Cumulative Percentage of Drug Recovered (Stats in Columns)

Standard Table – Plasma
Data Setup

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Code

# create layout
lyt <- basic_table() %>%
  add_overall_col("Accumulation Interval (hours)") %>%
  split_cols_by(var = "PPINT") %>%
  split_cols_by(var = "PKPARAM") %>%
  split_rows_by(
    var = "ARMCD",
    split_fun = trim_levels_in_group("ACTARM"),
    label_pos = "topleft",
    split_label = "Treatment Arm"
  ) %>%
  analyze_vars(
    vars = "AVAL",
    .stats = c(
      "n", "mean", "sd", "cv",
      "median", "min", "max"
    ),
    .labels = c(
      n = "n",
      mean = "Mean",
      sd = "SD",
      cv = "CV (%)",
      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),
      min = format_sigfig(3),
      max = format_sigfig(3)
    )
  )

adpp0 <- adpp %>%
  filter(
    AVISIT == "CYCLE 1 DAY 1",
    PPCAT == "Plasma Drug X"
  ) %>%
  h_pkparam_sort() %>%
  mutate(
    PKPARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")"))
  )

result <- build_table(lyt, df = adpp0)
main_title(result) <- paste(
  "Summary of Cumulative Amount and Percentage of", unique(adpp0$PPSPEC), "Recovered from\n",
  unique(adpp0$PPCAT), "following", unique(adpp0$REGIMEN), "Administration for",
  unique(adpp0$PPINT)[length(unique(adpp0$PPINT))], "hours, PK Population"
)
subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT), "\nVisit:", unique(adpp0$AVISIT))

cat(rtables::toString(result, indent_size = 10))

Summary of Cumulative Amount and Percentage of Urine Recovered from
 Plasma Drug X following BID Administration for 0-24 hours, PK Population
Analyte: Plasma Drug X 
Visit: CYCLE 1 DAY 1

——————————————————————————————————————————————————————————
                        Accumulation Interval (hours)     
                           0-12                0-24       
Treatment Arm       Ae (mg)    Fe (%)    Ae (mg)    Fe (%)
——————————————————————————————————————————————————————————
ARM A                                                     
          n           134        134       134       134  
          Mean        1.55      15.7       1.55      15.7 
          SD         0.339      3.35      0.339      3.35 
          CV (%)      21.9      21.4       21.9      21.4 
          Median      1.55      15.8       1.55      15.8 
          Minimum    0.702      8.15      0.702      8.15 
          Maximum     2.46      24.5       2.46      24.5 
ARM C                                                     
          n           132        132       132       132  
          Mean        1.54      16.1       1.54      16.1 
          SD         0.298      3.11      0.298      3.11 
          CV (%)      19.4      19.3       19.4      19.3 
          Median      1.55      16.0       1.55      16.0 
          Minimum    0.850      8.50      0.850      8.50 
          Maximum     2.21      24.4       2.21      24.4

Experimental use!

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Code

library(dplyr)
library(tern)

adpp <- random.cdisc.data::cadpp

adpp <- adpp %>%
  filter(PPSTINT != "NA" & PPENINT != "NA") %>%
  mutate(PPINT = factor(paste0(gsub("[PH]", "", PPSTINT), "-", gsub("[PH]", "", PPENINT))))

Reproducibility

Timestamp

[1] "2024-11-02 18:18:54 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
 backports           1.5.0       2024-05-23 [1] CRAN (R 4.4.1)
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 evaluate            1.0.1       2024-10-10 [1] CRAN (R 4.4.1)
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 lifecycle           1.0.4       2023-11-07 [1] CRAN (R 4.4.1)
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 R6                  2.5.1       2021-08-19 [1] CRAN (R 4.4.1)
 random.cdisc.data   0.3.16.9001 2024-11-02 [1] git2r (https://github.com/insightsengineering/random.cdisc.data.git@a65bfbe)
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 scales              1.3.0       2023-11-28 [1] CRAN (R 4.4.1)
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 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              * 0.9.6.9013  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.git@435fd51)
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 xfun                0.48        2024-10-03 [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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Reproducibility

Timestamp

Session Info

.lock file

`.lock` file