TPK01B

Matrix Active Study Agent/Analyte Concentrations (units) Over Time

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Output

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# Program Name:              tpk01b

# Prep environment:

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

# Define script level parameters:

tblid <- "TPK01b"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
popfl <- "PKFL"
trtvar <- "TRT01A"

trt_grps <- c("Xanomeline High Dose", "Xanomeline Low Dose")

for (i in seq_along(trt_grps)) {
  trt_grp <- trt_grps[i]
  path <- paste0(fileid, "part", i)
  
  ##############################################################################
  # Process data:
  ##############################################################################
  
  adsl <- pharmaverseadamjnj::adsl |>
    filter(.data[[popfl]] == "Y") |>
    select(USUBJID, all_of(trtvar), PKFL) |>
    filter(.data[[trtvar]] == trt_grp) |>
    mutate(colspan = "Observed")
  
  adpc <- pharmaverseadamjnj::adpc |>
    filter(PARAMCD == "XAN") |>
    select(USUBJID, all_of(trtvar), AVISIT, ATPT, AVAL) |>
    filter(.data[[trtvar]] == trt_grp) |>
    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 = trtvar,
      show_colcounts = TRUE,
      colcount_format = "N=xx",
      split_fun = drop_split_levels
    ) |>
    
    split_cols_by("colspan") |>
    
    split_rows_by(
      var = "AVISIT_ATPT",
      split_label = "Time Point",
      label_pos = "topleft",
      child_labels = "hidden"
    ) |>
    
    analyze_vars_in_cols(
      vars = "AVAL",
      .stats = c(
        "n",
        "mean",
        "sd",
        "median",
        "min",
        "max",
        "cv",
        "geom_mean"
      ),
      .labels = c(
        n = "N",
        mean = "Mean",
        sd = "SD",
        median = "Med",
        min = "Min",
        max = "Max",
        cv = "% CV",
        geom_mean = "Geometric Mean"
      ),
      .formats = c(
        n = jjcsformat_xx("xx"),
        mean = jjcsformat_xx("xx.xx"),
        sd = jjcsformat_xx("xx.xx"),
        median = jjcsformat_xx("xx.xx"),
        min = jjcsformat_xx("xx.xx"),
        max = jjcsformat_xx("xx.xx"),
        cv = jjcsformat_xx("xx.x"),
        geom_mean = jjcsformat_xx("xx.xx")
      )
    )
  
  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 = path, orientation = "landscape")
}

TPK01b: [Matrix] [Active Study Agent/Analyte] Concentrations ([units]) Over Time; Pharmacokinetics Analysis Set (Study jjcs - core)
	Xanomeline Low Dose
	N=96
	Observed
Time Point	N	Mean	SD	Med	Min	Max	% CV	Geometric Mean
Day 1 - Pre-dose	96	0.00	0.00	0.00	0.00	0.00	NA	NA
Day 1 - 5 Min Post-dose	96	0.10	0.01	0.10	0.09	0.11	5.3	0.10
Day 1 - 30 Min Post-dose	96	0.55	0.03	0.54	0.50	0.60	4.8	0.55
Day 1 - 1h Post-dose	96	0.93	0.04	0.93	0.85	1.01	4.4	0.93
Day 1 - 1.5h Post-dose	96	1.20	0.05	1.20	1.11	1.29	4.0	1.20
Day 1 - 2h Post-dose	96	1.39	0.05	1.39	1.29	1.49	3.7	1.39
Day 1 - 4h Post-dose	96	1.74	0.05	1.74	1.64	1.83	3.2	1.74
Day 1 - 0-6h Post-dose	96	26.72	1.44	26.63	24.53	29.25	5.4	26.68
Day 1 - 6h Post-dose	96	1.82	0.05	1.82	1.73	1.91	3.0	1.82
Day 1 - 8h Post-dose	96	1.84	0.05	1.84	1.75	1.94	3.0	1.84
Day 1 - 6-12h Post-dose	96	22.52	1.61	22.43	20.06	25.34	7.1	22.47
Day 1 - 12h Post-dose	96	0.55	0.03	0.55	0.49	0.62	5.4	0.55
Day 1 - 16h Post-dose	96	0.16	0.02	0.16	0.13	0.20	10.0	0.16
Day 1 - 12-24h Post-dose	96	14.13	1.95	14.02	11.13	17.52	13.8	13.99
Day 2 - 24h Post-dose	96	0.01	0.00	0.01	0.01	0.02	19.7	0.01
Day 2 - Pre-dose	94	0.01	0.00	0.01	0.01	0.02	19.7	0.01
Day 2 - 36h Post-dose	96	0.00	0.00	0.00	0.00	0.00	0.0	0.01
Day 2 - 24-48h Post-dose	96	0.22	0.49	0.00	0.00	1.89	217.2	0.01
Day 3 - 48h Post-dose	96	0.00	0.00	0.00	0.00	0.00	0.0	0.01
Day 3 - Pre-dose	92	0.00	0.00	0.00	0.00	0.00	0.0	0.01
Note: Incongruous samples are not included in this summary.
Note: Concentrations below the lowest quantifiable concentration (ie, [xx.x ng/mL]) will be treated as zero in calculating the summary statistics.

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