TPK02

Matrix Active Study Agent/Analyte Concentrations (units) Over Time by Body Weight Quartiles

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Code

# Program Name:              tpk02

# Prep environment:

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

# Define script level parameters:

tblid <- "TPK02"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
popfl <- "PKFL"
trtvar <- "TRT01A"

# Flags indicating whether to include certain statistics in the table
add_geometric_mean <- TRUE
add_cv <- TRUE
add_interquartile_range <- TRUE

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") |>
    filter(.data[[trtvar]] == trt_grp) |>
    select(USUBJID, all_of(trtvar), WGTGR1, PKFL) |>
    mutate(colspan = "[Body Weight (kg)] [Quartiles]")
  
  adpc <- pharmaverseadamjnj::adpc |>
    filter(PARAMCD == "XAN") |>
    filter(.data[[trtvar]] == trt_grp) |>
    select(USUBJID, all_of(trtvar), AVISIT, ATPT, AVAL) |>
    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_cols_by("WGTGR1") |>
    
    split_rows_by(
      var = "AVISIT_ATPT",
      split_label = "Time Point",
      label_pos = "topleft",
      section_div = " "
    ) |>
    
    analyze(
      vars = "AVAL",
      afun = a_summary,
      extra_args = list(
        .stats = c(
          "n",
          "mean_sd",
          "median",
          if (add_geometric_mean) "geom_mean" else NULL, 
          "range",
          if (add_cv) "cv" else NULL,
          if (add_interquartile_range) "quantiles" else NULL
        ),
        .labels = c(
          n = "N",
          mean_sd = "Mean (SD)",
          median = "Median",
          geom_mean = "Geometric mean",
          range = "Min, max",
          cv = "CV (%)",
          quantiles = "Interquartile range"
        ),
        .formats = c(
          mean_sd = jjcsformat_xx("xx.xx (xx.xx)"),
          median = jjcsformat_xx("xx.xx"),
          geom_mean = jjcsformat_xx("xx.xx"),
          range = jjcsformat_xx("xx.xx, xx.xx"),
          cv = jjcsformat_xx("xx.x"),
          quantiles = jjcsformat_xx("xx.xx, xx.xx")
        ),
        .indent_mods = c(
          n = 0,
          mean_sd = 1,
          median = 1,
          geom_mean = 1,
          range = 1,
          cv = 1,
          quantiles = 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 = path, orientation = "portrait")
}

TPK02: [Matrix] [Active Study Agent/Analyte] Concentrations ([units]) Over Time by [Body Weight] [Quartiles]; Pharmacokinetics Analysis Set (Study jjcs - core)
	Xanomeline Low Dose
	N=96
	[Body Weight (kg)] [Quartiles]
Time Point	<30	≥30 to <60	≥60 to <90	≥90
Day 1 - Pre-dose
N	19	17	19	41
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00	0.00
Geometric mean	NA	NA	NA	NA
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	NA	NA	NA	NA
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 1 - 5 Min Post-dose
N	19	17	19	41
Mean (SD)	0.10 (0.01)	0.10 (0.01)	0.10 (0.01)	0.10 (0.01)
Median	0.10	0.10	0.10	0.10
Geometric mean	0.10	0.10	0.10	0.10
Min, max	0.09, 0.11	0.09, 0.11	0.09, 0.11	0.09, 0.11
CV (%)	5.5	5.3	5.0	5.4
Interquartile range	0.10, 0.10	0.10, 0.10	0.10, 0.11	0.10, 0.11

Day 1 - 30 Min Post-dose
N	19	17	19	41
Mean (SD)	0.54 (0.03)	0.55 (0.03)	0.55 (0.02)	0.55 (0.03)
Median	0.54	0.54	0.54	0.55
Geometric mean	0.54	0.55	0.55	0.55
Min, max	0.50, 0.60	0.50, 0.59	0.50, 0.59	0.50, 0.60
CV (%)	5.1	4.9	4.5	4.9
Interquartile range	0.52, 0.56	0.53, 0.56	0.54, 0.57	0.53, 0.57

Day 1 - 1h Post-dose
N	19	17	19	41
Mean (SD)	0.92 (0.04)	0.93 (0.04)	0.93 (0.04)	0.93 (0.04)
Median	0.92	0.93	0.93	0.93
Geometric mean	0.92	0.93	0.93	0.93
Min, max	0.86, 1.01	0.86, 0.99	0.86, 1.00	0.85, 1.01
CV (%)	4.8	4.4	4.0	4.4
Interquartile range	0.89, 0.96	0.90, 0.96	0.92, 0.96	0.90, 0.97

Day 1 - 1.5h Post-dose
N	19	17	19	41
Mean (SD)	1.19 (0.05)	1.20 (0.05)	1.21 (0.04)	1.20 (0.05)
Median	1.19	1.20	1.21	1.20
Geometric mean	1.19	1.20	1.21	1.20
Min, max	1.11, 1.29	1.12, 1.27	1.12, 1.28	1.11, 1.29
CV (%)	4.5	4.0	3.6	4.0
Interquartile range	1.15, 1.24	1.16, 1.23	1.19, 1.24	1.17, 1.24

Day 1 - 2h Post-dose
N	19	17	19	41
Mean (SD)	1.38 (0.06)	1.39 (0.05)	1.40 (0.05)	1.39 (0.05)
Median	1.37	1.39	1.40	1.39
Geometric mean	1.38	1.39	1.40	1.39
Min, max	1.30, 1.49	1.31, 1.47	1.31, 1.48	1.29, 1.49
CV (%)	4.3	3.8	3.3	3.7
Interquartile range	1.33, 1.43	1.35, 1.43	1.37, 1.43	1.36, 1.44

Day 1 - 4h Post-dose
N	19	17	19	41
Mean (SD)	1.73 (0.07)	1.74 (0.06)	1.75 (0.05)	1.74 (0.05)
Median	1.70	1.73	1.75	1.74
Geometric mean	1.73	1.73	1.75	1.74
Min, max	1.65, 1.83	1.66, 1.82	1.66, 1.82	1.64, 1.83
CV (%)	3.9	3.2	2.7	3.1
Interquartile range	1.67, 1.79	1.69, 1.77	1.72, 1.79	1.70, 1.78

Day 1 - 0-6h Post-dose
N	19	17	19	41
Mean (SD)	26.99 (1.30)	26.68 (1.48)	26.87 (1.56)	26.55 (1.45)
Median	27.03	26.33	26.59	26.62
Geometric mean	26.96	26.65	26.83	26.51
Min, max	24.64, 28.88	24.59, 28.82	24.60, 29.15	24.53, 29.25
CV (%)	4.8	5.5	5.8	5.5
Interquartile range	25.92, 28.09	25.43, 28.45	25.50, 28.30	25.43, 27.51

Day 1 - 6h Post-dose
N	19	17	19	41
Mean (SD)	1.82 (0.07)	1.82 (0.06)	1.83 (0.05)	1.82 (0.05)
Median	1.77	1.81	1.85	1.82
Geometric mean	1.81	1.82	1.83	1.82
Min, max	1.74, 1.91	1.74, 1.91	1.75, 1.90	1.73, 1.90
CV (%)	3.8	3.0	2.6	2.9
Interquartile range	1.75, 1.89	1.79, 1.85	1.80, 1.88	1.78, 1.87

Day 1 - 8h Post-dose
N	19	17	19	41
Mean (SD)	1.84 (0.07)	1.84 (0.06)	1.85 (0.05)	1.84 (0.05)
Median	1.79	1.84	1.86	1.84
Geometric mean	1.84	1.84	1.85	1.84
Min, max	1.76, 1.93	1.76, 1.94	1.78, 1.92	1.75, 1.92
CV (%)	3.7	3.0	2.6	2.8
Interquartile range	1.77, 1.91	1.81, 1.88	1.81, 1.90	1.80, 1.89

Day 1 - 6-12h Post-dose
N	19	17	19	41
Mean (SD)	22.83 (1.45)	22.48 (1.65)	22.69 (1.75)	22.33 (1.62)
Median	22.87	22.10	22.39	22.42
Geometric mean	22.78	22.42	22.62	22.27
Min, max	20.19, 24.93	20.12, 24.86	20.14, 25.23	20.06, 25.34
CV (%)	6.4	7.4	7.7	7.3
Interquartile range	21.63, 24.05	21.08, 24.46	21.16, 24.29	21.08, 23.41

Day 1 - 12h Post-dose
N	19	17	19	41
Mean (SD)	0.55 (0.03)	0.55 (0.03)	0.56 (0.03)	0.55 (0.03)
Median	0.55	0.55	0.55	0.54
Geometric mean	0.55	0.55	0.55	0.54
Min, max	0.49, 0.61	0.50, 0.59	0.51, 0.62	0.50, 0.62
CV (%)	5.4	5.5	5.9	5.2
Interquartile range	0.54, 0.57	0.53, 0.57	0.54, 0.58	0.53, 0.57

Day 1 - 16h Post-dose
N	19	17	19	41
Mean (SD)	0.17 (0.02)	0.16 (0.02)	0.17 (0.02)	0.16 (0.02)
Median	0.17	0.16	0.16	0.16
Geometric mean	0.17	0.16	0.17	0.16
Min, max	0.13, 0.19	0.14, 0.19	0.14, 0.20	0.14, 0.20
CV (%)	9.1	10.2	11.0	9.9
Interquartile range	0.16, 0.18	0.15, 0.18	0.15, 0.18	0.15, 0.17

Day 1 - 12-24h Post-dose
N	19	17	19	41
Mean (SD)	14.50 (1.76)	14.07 (2.00)	14.32 (2.12)	13.89 (1.97)
Median	14.56	13.62	13.97	14.01
Geometric mean	14.39	13.94	14.18	13.75
Min, max	11.28, 17.03	11.20, 16.95	11.22, 17.39	11.13, 17.52
CV (%)	12.2	14.2	14.8	14.2
Interquartile range	13.04, 15.98	12.38, 16.47	12.47, 16.27	12.37, 15.21

Day 2 - 24h Post-dose
N	19	17	19	41
Mean (SD)	0.02 (0.00)	0.01 (0.00)	0.02 (0.00)	0.01 (0.00)
Median	0.01	0.01	0.01	0.01
Geometric mean	0.01	0.01	0.01	0.01
Min, max	0.01, 0.02	0.01, 0.02	0.01, 0.02	0.01, 0.02
CV (%)	17.3	20.2	21.5	20.1
Interquartile range	0.01, 0.02	0.01, 0.02	0.01, 0.02	0.01, 0.02

Day 2 - Pre-dose
N	19	16	19	40
Mean (SD)	0.02 (0.00)	0.01 (0.00)	0.02 (0.00)	0.01 (0.00)
Median	0.01	0.01	0.01	0.01
Geometric mean	0.01	0.01	0.01	0.01
Min, max	0.01, 0.02	0.01, 0.02	0.01, 0.02	0.01, 0.02
CV (%)	17.3	19.5	21.5	20.3
Interquartile range	0.01, 0.02	0.01, 0.02	0.01, 0.02	0.01, 0.02

Day 2 - 36h Post-dose
N	19	17	19	41
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0	0.0
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 2 - 24-48h Post-dose
N	19	17	19	41
Mean (SD)	0.18 (0.40)	0.24 (0.41)	0.30 (0.57)	0.20 (0.52)
Median	0.00	0.00	0.00	0.00
Geometric mean	0.01	0.02	0.02	0.01
Min, max	0.00, 1.24	0.00, 1.13	0.00, 1.71	0.00, 1.89
CV (%)	220.2	167.0	190.7	260.5
Interquartile range	0.00, 0.00	0.00, 0.49	0.00, 0.23	0.00, 0.00

Day 3 - 48h Post-dose
N	19	17	19	41
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0	0.0
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 3 - Pre-dose
N	18	16	19	39
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0	0.0
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00	0.00, 0.00

Note: Incongruous samples are not included in this summary.
Note: Concentrations below the lowest quantifiable concentration (ie, [x.xx ng/mL]) will be treated as zero in calculating the summary statistics.

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