TPK03

Subjects With Matrix Active Study Agent/Analyte Concentrations Below the Lowest Quantification Level (LLOQ/LLOQxMRD and units) Over Time

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Output

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# Program Name:              tpk03

# Prep environment:

library(envsetup)
library(dplyr)
library(forcats)
library(rtables)
library(tern)
library(junco)

# Define script level parameters:

tblid <- "TPK03"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
popfl <- "PKFL"
trtvar <- "TRT01A"

# Process data:

adsl <- pharmaverseadamjnj::adsl |>
  filter(.data[[popfl]] == "Y") |>
  select(USUBJID, all_of(trtvar), PKFL) |>
  
  # Drop the control group
  filter(.data[[trtvar]] != "Placebo") |>
  mutate({{ trtvar }} := fct_drop(.data[[trtvar]])) |>
  
  mutate(colspan_trt = "Active Study Agent")

adpc <- pharmaverseadamjnj::adpc |>
  filter(PARAMCD == "XAN") |>
  select(USUBJID, all_of(trtvar), AVISIT, ATPT, CRIT1FL) |>
  inner_join(adsl) |>
  
  # Concatenate and reorder time points
  mutate(AVISIT_ATPT = factor(paste(AVISIT, ATPT, sep = " - "), levels = c(
    "Day 1 - Pre-dose",
    "Day 1 - 5 Min Post-dose",
    "Day 1 - 30 Min Post-dose",
    "Day 1 - 1h Post-dose",
    "Day 1 - 1.5h Post-dose",
    "Day 1 - 2h Post-dose",
    "Day 1 - 4h Post-dose",
    "Day 1 - 0-6h Post-dose",
    "Day 1 - 6h Post-dose",
    "Day 1 - 8h Post-dose",
    "Day 1 - 6-12h Post-dose",
    "Day 1 - 12h Post-dose",
    "Day 1 - 16h Post-dose",
    "Day 1 - 12-24h Post-dose",
    "Day 2 - 24h Post-dose",
    "Day 2 - Pre-dose",
    "Day 2 - 36h Post-dose",
    "Day 2 - 24-48h Post-dose",
    "Day 3 - 48h Post-dose", 
    "Day 3 - Pre-dose"
  )))

# Define layout and build table:

lyt <- basic_table() |>
  split_cols_by(
    var = "colspan_trt",
    split_fun = drop_split_levels
  ) |>
  
  split_cols_by(
    var = trtvar,
    show_colcounts = TRUE,
    colcount_format = "N=xx",
    split_fun = add_overall_level("Combined", first = FALSE)
  ) |>
  
  split_rows_by(
    var = "AVISIT_ATPT",
    split_label = "Time Point",
    label_pos = "topleft",
    section_div = " "
  ) |>
  
  analyze(
    vars = "PKFL",
    show_labels = "hidden",
    afun = a_freq_j,
    extra_args = list(
      val = "Y",
      label = "N",
      .stats = "count_unique"
    )
  ) |>
  
  analyze(
    vars = "CRIT1FL",
    show_labels = "hidden",
    afun = a_freq_j,
    extra_args = list(
      val = "Y",
      label = "Number of subjects with values below LLOQxMRD, n (%)",
      .stats = "count_unique_fraction",
      .indent_mods = 1
    )
  )

result <- build_table(lyt, df = adpc, alt_counts_df = adsl)

# Add titles and footnotes:

result <- set_titles(result, titles)

# Convert to tbl file and output table:

tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid, orientation = "portrait")

TPK03: Subjects With [Matrix] [Active Study Agent/Analyte] Concentrations Below the Lowest Quantification Level ([LLOQ/LLOQxMRD and units]) Over Time; Pharmacokinetics Analysis Set (Study jjcs - core)
	Active Study Agent
	Xanomeline High Dose	Xanomeline Low Dose	Combined
Time Point	N=72	N=96	N=168
Day 1 - Pre-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	72 (100.0%)	96 (100.0%)	168 (100.0%)
Day 1 - 5 Min Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 30 Min Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 1h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 1.5h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 2h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 4h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 0-6h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 6h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 8h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 6-12h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 12h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 16h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 1 - 12-24h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 2 - 24h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 2 - Pre-dose
N	72	94	166
Number of subjects with  values below LLOQxMRD,  n (%)	0	0	0
Day 2 - 36h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	72 (100.0%)	96 (100.0%)	168 (100.0%)
Day 2 - 24-48h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	51 (70.8%)	76 (79.2%)	127 (75.6%)
Day 3 - 48h Post-dose
N	72	96	168
Number of subjects with  values below LLOQxMRD,  n (%)	72 (100.0%)	96 (100.0%)	168 (100.0%)
Day 3 - Pre-dose
N	72	92	164
Number of subjects with  values below LLOQxMRD,  n (%)	72 (100.0%)	92 (95.8%)	164 (97.6%)
Key: MRD=minimum required dilution

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