TPK01A

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

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Code

# Program Name:              tpk01a

# Prep environment:

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

# Define script level parameters:

tblid <- "TPK01a"
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

# 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, 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 = "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 = "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 = fileid, orientation = "portrait")

TPK01a: [Matrix] [Active Study Agent/Analyte] Concentrations ([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
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00
Geometric mean	NA	NA	NA
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	NA	NA	NA
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 1 - 5 Min Post-dose
N	72	96	168
Mean (SD)	0.10 (0.00)	0.10 (0.01)	0.10 (0.01)
Median	0.10	0.10	0.10
Geometric mean	0.10	0.10	0.10
Min, max	0.09, 0.11	0.09, 0.11	0.09, 0.11
CV (%)	4.9	5.3	5.1
Interquartile range	0.10, 0.10	0.10, 0.10	0.10, 0.10

Day 1 - 30 Min Post-dose
N	72	96	168
Mean (SD)	0.54 (0.02)	0.55 (0.03)	0.55 (0.03)
Median	0.54	0.54	0.54
Geometric mean	0.54	0.55	0.54
Min, max	0.50, 0.60	0.50, 0.60	0.50, 0.60
CV (%)	4.4	4.8	4.6
Interquartile range	0.52, 0.56	0.53, 0.57	0.52, 0.56

Day 1 - 1h Post-dose
N	72	96	168
Mean (SD)	0.93 (0.04)	0.93 (0.04)	0.93 (0.04)
Median	0.93	0.93	0.93
Geometric mean	0.93	0.93	0.93
Min, max	0.86, 1.02	0.85, 1.01	0.85, 1.02
CV (%)	4.0	4.4	4.2
Interquartile range	0.90, 0.95	0.90, 0.96	0.90, 0.96

Day 1 - 1.5h Post-dose
N	72	96	168
Mean (SD)	1.20 (0.04)	1.20 (0.05)	1.20 (0.05)
Median	1.20	1.20	1.20
Geometric mean	1.20	1.20	1.20
Min, max	1.12, 1.31	1.11, 1.29	1.11, 1.31
CV (%)	3.7	4.0	3.9
Interquartile range	1.17, 1.22	1.16, 1.24	1.17, 1.23

Day 1 - 2h Post-dose
N	72	96	168
Mean (SD)	1.39 (0.05)	1.39 (0.05)	1.39 (0.05)
Median	1.38	1.39	1.39
Geometric mean	1.39	1.39	1.39
Min, max	1.31, 1.50	1.29, 1.49	1.29, 1.50
CV (%)	3.4	3.7	3.6
Interquartile range	1.36, 1.41	1.35, 1.43	1.35, 1.43

Day 1 - 4h Post-dose
N	72	96	168
Mean (SD)	1.73 (0.05)	1.74 (0.05)	1.74 (0.05)
Median	1.73	1.74	1.73
Geometric mean	1.73	1.74	1.73
Min, max	1.65, 1.84	1.64, 1.83	1.64, 1.84
CV (%)	3.0	3.2	3.1
Interquartile range	1.69, 1.78	1.69, 1.79	1.69, 1.78

Day 1 - 0-6h Post-dose
N	72	96	168
Mean (SD)	26.85 (1.51)	26.72 (1.44)	26.78 (1.47)
Median	26.80	26.63	26.67
Geometric mean	26.81	26.68	26.74
Min, max	24.49, 29.19	24.53, 29.25	24.49, 29.25
CV (%)	5.6	5.4	5.5
Interquartile range	25.46, 28.28	25.56, 28.01	25.52, 28.17

Day 1 - 6h Post-dose
N	72	96	168
Mean (SD)	1.82 (0.05)	1.82 (0.05)	1.82 (0.05)
Median	1.82	1.82	1.82
Geometric mean	1.82	1.82	1.82
Min, max	1.74, 1.92	1.73, 1.91	1.73, 1.92
CV (%)	3.0	3.0	3.0
Interquartile range	1.77, 1.87	1.77, 1.88	1.77, 1.87

Day 1 - 8h Post-dose
N	72	96	168
Mean (SD)	1.84 (0.05)	1.84 (0.05)	1.84 (0.05)
Median	1.84	1.84	1.84
Geometric mean	1.84	1.84	1.84
Min, max	1.76, 1.94	1.75, 1.94	1.75, 1.94
CV (%)	3.0	3.0	3.0
Interquartile range	1.79, 1.90	1.79, 1.90	1.79, 1.90

Day 1 - 6-12h Post-dose
N	72	96	168
Mean (SD)	22.67 (1.69)	22.52 (1.61)	22.58 (1.64)
Median	22.62	22.43	22.47
Geometric mean	22.60	22.47	22.53
Min, max	20.01, 25.27	20.06, 25.34	20.01, 25.34
CV (%)	7.4	7.1	7.3
Interquartile range	21.11, 24.26	21.23, 23.97	21.18, 24.15

Day 1 - 12h Post-dose
N	72	96	168
Mean (SD)	0.55 (0.03)	0.55 (0.03)	0.55 (0.03)
Median	0.55	0.55	0.55
Geometric mean	0.55	0.55	0.55
Min, max	0.49, 0.62	0.49, 0.62	0.49, 0.62
CV (%)	6.2	5.4	5.7
Interquartile range	0.53, 0.58	0.53, 0.57	0.53, 0.57

Day 1 - 16h Post-dose
N	72	96	168
Mean (SD)	0.16 (0.02)	0.16 (0.02)	0.16 (0.02)
Median	0.17	0.16	0.16
Geometric mean	0.16	0.16	0.16
Min, max	0.13, 0.20	0.13, 0.20	0.13, 0.20
CV (%)	11.0	10.0	10.4
Interquartile range	0.15, 0.18	0.15, 0.18	0.15, 0.18

Day 1 - 12-24h Post-dose
N	72	96	168
Mean (SD)	14.30 (2.04)	14.13 (1.95)	14.20 (1.99)
Median	14.26	14.02	14.07
Geometric mean	14.15	13.99	14.06
Min, max	11.07, 17.44	11.13, 17.52	11.07, 17.52
CV (%)	14.3	13.8	14.0
Interquartile range	12.41, 16.24	12.56, 15.88	12.50, 16.10

Day 2 - 24h Post-dose
N	72	96	168
Mean (SD)	0.01 (0.00)	0.01 (0.00)	0.01 (0.00)
Median	0.01	0.01	0.01
Geometric mean	0.01	0.01	0.01
Min, max	0.01, 0.02	0.01, 0.02	0.01, 0.02
CV (%)	20.9	19.7	20.2
Interquartile range	0.01, 0.02	0.01, 0.02	0.01, 0.02

Day 2 - Pre-dose
N	72	94	166
Mean (SD)	0.01 (0.00)	0.01 (0.00)	0.01 (0.00)
Median	0.01	0.01	0.01
Geometric mean	0.01	0.01	0.01
Min, max	0.01, 0.02	0.01, 0.02	0.01, 0.02
CV (%)	20.9	19.7	20.2
Interquartile range	0.01, 0.02	0.01, 0.02	0.01, 0.02

Day 2 - 36h Post-dose
N	72	96	168
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 2 - 24-48h Post-dose
N	72	96	168
Mean (SD)	0.28 (0.53)	0.22 (0.49)	0.25 (0.50)
Median	0.00	0.00	0.00
Geometric mean	0.02	0.01	0.02
Min, max	0.00, 1.78	0.00, 1.89	0.00, 1.89
CV (%)	191.0	217.2	204.4
Interquartile range	0.00, 0.18	0.00, 0.00	0.00, 0.00

Day 3 - 48h Post-dose
N	72	96	168
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0
Interquartile range	0.00, 0.00	0.00, 0.00	0.00, 0.00

Day 3 - Pre-dose
N	72	92	164
Mean (SD)	0.00 (0.00)	0.00 (0.00)	0.00 (0.00)
Median	0.00	0.00	0.00
Geometric mean	0.01	0.01	0.01
Min, max	0.00, 0.00	0.00, 0.00	0.00, 0.00
CV (%)	0.0	0.0	0.0
Interquartile range	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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