PKPT03

Pharmacokinetic Parameter Summary of Plasma by Treatment (Stats in Columns)

Code
# lyt creation
lyt <- basic_table() %>%
  split_rows_by(
    var = "AVISIT",
    split_fun = drop_split_levels,
    split_label = "Visit",
    page_by = TRUE
  ) %>%
  split_rows_by(
    var = "ARMCD",
    split_fun = trim_levels_in_group("PARAM"),
    label_pos = "topleft",
    split_label = "Treatment Arm"
  ) %>%
  add_rowcounts(alt_counts = TRUE) %>%
  split_rows_by(
    var = "PARAM",
    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)
    ),
    na_str = "NE"
  )

Plasma Drug X

Code
result <- build_table(lyt, df = adpp_x, alt_counts_df = adsl_x_splitvars)
main_title(result) <- paste("Summary of", unique(adpp_x$PPSPEC), "PK Parameter by Treatment Arm, PK Population")
subtitles(result) <- paste("Analyte:", unique(adpp_x$PPCAT))
result <- paginate_table(result, landscape = TRUE)
result
$`CYCLE 1 DAY 1`
Summary of Plasma 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 (N=134)                                                                                                             
  Cmax (ug/mL)              0     NE     NE       NE           NE                 NE              NE       NE        NE   
  AUCinf obs (day*ug/mL)   134   203    37.7     18.6         199                18.7            197       125       311  
  CL obs (ml/day/kg)       134   5.04   1.04     20.6         4.93               22.4            5.08     2.25      7.39  
ARM C (N=132)                                                                                                             
  Cmax (ug/mL)             132   30.0   5.46     18.2         29.5               18.9            29.8     15.9      47.6  
  AUCinf obs (day*ug/mL)   132   195    37.8     19.4         192                20.1            196       103       315  
  CL obs (ml/day/kg)       132   5.01   0.985    19.7         4.91               21.1            4.97     2.10      7.49  

$`CYCLE 1 DAY 2`
Summary of Plasma PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug X
Visit: CYCLE 1 DAY 2

—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Treatment Arm                                                                                                            
  PK Parameter              n    Mean    SD    CV (%)   Geometric Mean   CV % Geometric Mean   Median   Minimum   Maximum
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ARM A (N=134)                                                                                                            
  Cmax (ug/mL)             134   29.4   6.22    21.2         28.6               24.4            29.8     10.1      43.5  
  AUCinf obs (day*ug/mL)   134   202    41.2    20.4         197                21.4            200       105       294  
  CL obs (ml/day/kg)       134   5.04   1.04    20.7         4.92               22.6            5.01     2.39      7.18  
ARM C (N=132)                                                                                                            
  Cmax (ug/mL)             132   30.4   6.03    19.9         29.7               21.7            30.5     12.4      45.5  
  AUCinf obs (day*ug/mL)   132   191    43.0    22.5         186                24.7            189      74.8       296  
  CL obs (ml/day/kg)       132   5.07   1.07    21.1         4.96               22.4            5.01     2.48      7.50

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Plasma Drug X: Remove Rows with 0s

Code
result <- build_table(lyt, df = adpp_x, alt_counts_df = adsl_x_splitvars) %>%
  prune_table()

main_title(result) <- paste("Summary of", unique(adpp_x$PPSPEC), "PK Parameter by Treatment Arm, PK Population")
subtitles(result) <- paste("Analyte:", unique(adpp_x$PPCAT))
result <- paginate_table(result, landscape = TRUE)
result
$`CYCLE 1 DAY 1`
Summary of Plasma 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 (N=134)                                                                                                             
  AUCinf obs (day*ug/mL)   134   203    37.7     18.6         199                18.7            197       125       311  
  CL obs (ml/day/kg)       134   5.04   1.04     20.6         4.93               22.4            5.08     2.25      7.39  
ARM C (N=132)                                                                                                             
  Cmax (ug/mL)             132   30.0   5.46     18.2         29.5               18.9            29.8     15.9      47.6  
  AUCinf obs (day*ug/mL)   132   195    37.8     19.4         192                20.1            196       103       315  
  CL obs (ml/day/kg)       132   5.01   0.985    19.7         4.91               21.1            4.97     2.10      7.49  

$`CYCLE 1 DAY 2`
Summary of Plasma PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug X
Visit: CYCLE 1 DAY 2

—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Treatment Arm                                                                                                            
  PK Parameter              n    Mean    SD    CV (%)   Geometric Mean   CV % Geometric Mean   Median   Minimum   Maximum
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ARM A (N=134)                                                                                                            
  Cmax (ug/mL)             134   29.4   6.22    21.2         28.6               24.4            29.8     10.1      43.5  
  AUCinf obs (day*ug/mL)   134   202    41.2    20.4         197                21.4            200       105       294  
  CL obs (ml/day/kg)       134   5.04   1.04    20.7         4.92               22.6            5.01     2.39      7.18  
ARM C (N=132)                                                                                                            
  Cmax (ug/mL)             132   30.4   6.03    19.9         29.7               21.7            30.5     12.4      45.5  
  AUCinf obs (day*ug/mL)   132   191    43.0    22.5         186                24.7            189      74.8       296  
  CL obs (ml/day/kg)       132   5.07   1.07    21.1         4.96               22.4            5.01     2.48      7.50

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Plasma Drug Y

Code
result <- build_table(lyt, df = adpp_y, alt_counts_df = adsl_y_splitvars)
main_title(result) <- paste("Summary of", unique(adpp_y$PPSPEC), "PK Parameter by Treatment Arm, PK Population")
subtitles(result) <- paste("Analyte:", unique(adpp_y$PPCAT))
result <- paginate_table(result, landscape = TRUE)
result
$`CYCLE 1 DAY 1`
Summary of Plasma 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 (N=132)                                                                                                             
  Cmax (ug/mL)             132   29.9   5.55     18.6         29.4               20.1            29.7     14.1      43.4  
  AUCinf obs (day*ug/mL)   132   199    37.9     19.1         195                18.9            195       126       318  
  CL obs (ml/day/kg)       132   4.96   0.895    18.1         4.87               18.7            4.94     2.99      7.21  

$`CYCLE 1 DAY 2`
Summary of Plasma PK Parameter by Treatment Arm, PK Population
Analyte: Plasma Drug Y
Visit: CYCLE 1 DAY 2

——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Treatment Arm                                                                                                             
  PK Parameter              n    Mean    SD     CV (%)   Geometric Mean   CV % Geometric Mean   Median   Minimum   Maximum
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ARM C (N=132)                                                                                                             
  Cmax (ug/mL)             132   30.7   6.12     19.9         30.1               21.9            31.4     12.9      48.3  
  AUCinf obs (day*ug/mL)   132   199    40.0     20.1         194                22.2            197      79.2       295  
  CL obs (ml/day/kg)       132   4.99   0.984    19.7         4.89               20.9            4.96     2.58      8.39

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Code
library(dplyr)
library(tern)

# Preprocess analysis data ----
adpp <- random.cdisc.data::cadpp
adpp <- adpp %>%
  filter(PPSPEC == "Plasma") %>%
  filter(AVISIT %in% c("CYCLE 1 DAY 1", "CYCLE 1 DAY 2")) %>%
  h_pkparam_sort() %>%
  mutate(PARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")"))) %>%
  mutate(PARAM = reorder(PARAM, TLG_ORDER))

# Preprocess subject-level data ----
adsl <- random.cdisc.data::cadsl

# Workaround needed to include (N=xx) population counts
# Repeat ADSL by the number of levels in AVISIT
# Include AVISIT and dummy PARAM as it's needed for trim_levels_in_group
adsl_tmp <- adsl %>%
  select(STUDYID, USUBJID, ARMCD) %>%
  unique() %>%
  mutate(PARAM = factor(NA_character_, levels = levels(adpp$PARAM)))

# Data for Plasma Drug X example ----
adpp_x <- adpp %>%
  filter(PPCAT == "Plasma Drug X") %>%
  # Please do not replicate mutate statement below!
  # It is used to make the random data in this example more realistic
  # as not all parameters are always available across all visits.
  mutate(
    AVAL = if_else(
      ARMCD == "ARM A" & AVISIT == "CYCLE 1 DAY 1" & PARAM == "Cmax (ug/mL)",
      NA_real_, AVAL
    )
  )

adpp_x_tmp <- adpp_x %>%
  select(STUDYID, USUBJID, ARMCD, AVISIT) %>%
  unique()

adsl_x_splitvars <- adsl_tmp %>%
  left_join(adpp_x_tmp, by = c("STUDYID", "USUBJID", "ARMCD")) %>%
  filter(!is.na(AVISIT))

# Data for Plasma Drug Y example ----
adpp_y <- adpp %>%
  filter(PPCAT == "Plasma Drug Y")

adpp_y_tmp <- adpp_y %>%
  select(STUDYID, USUBJID, ARMCD, AVISIT) %>%
  unique()

adsl_y_splitvars <- adsl_tmp %>%
  left_join(adpp_y_tmp, by = c("STUDYID", "USUBJID", "ARMCD")) %>%
  filter(!is.na(AVISIT))

Reproducibility

Timestamp

[1] "2024-11-02 18:19:44 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 ───────────────────────────────────────────────────────────────────
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 [2] /usr/local/lib/R/library

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