TSFECG02

Categorized Corrected QT Interval Values Over Time

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Output

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# Program Name:              tsfecg02

# Prep Environment

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

# Define script level parameters:

tblid <- "TSFECG02"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

popfl <- "SAFFL"
trtvar <- "TRT01A"
ctrl_grp <- "Placebo"

selparamcd <- c("QTC", "QTCBAG", "QTCFAG")
selvisit <- c(
  "Baseline",
  "Month 1",
  "Month 3",
  "Month 6",
  "Month 9",
  "Month 12"
)

# Process Data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(.data[[popfl]] == "Y") %>%
  select(
    USUBJID,
    all_of(c(popfl, trtvar)),
    SEX_DECODE,
    AGEGR1,
    RACE_DECODE,
    ETHNIC_DECODE
  )

adsl$colspan_trt <- factor(
  ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"),
  levels = c("Active Study Agent", " ")
)


filtered_adeg <- pharmaverseadamjnj::adeg %>%
  filter(PARAMCD %in% selparamcd) %>%
  filter(AVISIT %in% selvisit) %>%
  filter(ANL02FL == "Y") %>%
  filter(!is.na(AVALCAT1)) %>%
  select(
    STUDYID,
    USUBJID,
    PARAMCD,
    PARAM,
    AVALCAT1,
    AVALCA1N,
    AVISIT,
    ANL02FL,
    APOBLFL,
    ABLFL,
    ONTRTFL
  ) %>%
  inner_join(adsl)

## main analysis variable is AVALCAT1 : these have the same levels for all selected parameters
## no need to create an map dataframe for usage in layout

colspan_trt_map <- create_colspan_map(
  adsl,
  non_active_grp = ctrl_grp,
  non_active_grp_span_lbl = " ",
  active_grp_span_lbl = "Active Study Agent",
  colspan_var = "colspan_trt",
  trt_var = trtvar
)

ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp)

# Define layout and build table:

extra_args_rr <- list(
  method = "wald",
  denom = "n_df",
  .stats = c("denom", "count_unique_fraction")
)
# extra_args_rr2 <- list(method = "wald", denom = "n_df", .stats = c("denom",  "count_unique_denom_fraction")) # version with explicit denominator (usefull for testing purpose)

lyt <- basic_table(
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(trtvar) %>%
  split_rows_by(
    "PARAM",
    label_pos = "topleft",
    child_labels = "default",
    split_label = "QTc Interval",
    section_div = " ",
    ## ensure only selected params are included
    split_fun = drop_split_levels
  ) %>%
  split_rows_by(
    "AVISIT",
    label_pos = "topleft",
    child_labels = "default",
    split_label = "Study Visit",
    section_div = " ",
    ## ensure only the selected visits are included
    split_fun = drop_split_levels
  ) %>%
  analyze(
    "AVALCAT1",
    a_freq_j,
    extra_args = extra_args_rr,
    show_labels = "hidden",
    indent_mod = 0L
  ) %>%
  append_topleft(c("   Criteria, n (%)"))


result <- build_table(lyt, filtered_adeg, alt_counts_df = adsl)

# Post-Processing:

result <- remove_col_count(result)

# 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)

TSFECG02: Categorized Corrected QT Interval Values Over Time; Safety Analysis Set (Study jjcs - core)
QTc Interval	Active Study Agent
Study Visit	Xanomeline High Dose	Xanomeline Low Dose	Placebo
Criteria, n (%)	N=53	N=73	N=59
QT Interval, Corrected (msec)
Baseline
N	53	73	59
≤450	42 (79.2%)	54 (74.0%)	42 (71.2%)
>450 to ≤480	5 (9.4%)	10 (13.7%)	8 (13.6%)
>480 to ≤500	3 (5.7%)	3 (4.1%)	3 (5.1%)
>500	3 (5.7%)	6 (8.2%)	6 (10.2%)
Month 1
N	53	71	58
≤450	43 (81.1%)	50 (70.4%)	42 (72.4%)
>450 to ≤480	5 (9.4%)	2 (2.8%)	8 (13.8%)
>480 to ≤500	1 (1.9%)	7 (9.9%)	3 (5.2%)
>500	4 (7.5%)	12 (16.9%)	5 (8.6%)
Month 3
N	53	53	56
≤450	40 (75.5%)	37 (69.8%)	46 (82.1%)
>450 to ≤480	4 (7.5%)	6 (11.3%)	5 (8.9%)
>480 to ≤500	2 (3.8%)	3 (5.7%)	3 (5.4%)
>500	7 (13.2%)	7 (13.2%)	2 (3.6%)
Month 6
N	51	47	51
≤450	36 (70.6%)	35 (74.5%)	43 (84.3%)
>450 to ≤480	9 (17.6%)	3 (6.4%)	2 (3.9%)
>480 to ≤500	3 (5.9%)	3 (6.4%)	1 (2.0%)
>500	3 (5.9%)	6 (12.8%)	5 (9.8%)
Month 9
N	41	42	51
≤450	31 (75.6%)	32 (76.2%)	41 (80.4%)
>450 to ≤480	4 (9.8%)	4 (9.5%)	4 (7.8%)
>480 to ≤500	1 (2.4%)	2 (4.8%)	3 (5.9%)
>500	5 (12.2%)	4 (9.5%)	3 (5.9%)
Month 12
N	37	35	48
≤450	25 (67.6%)	26 (74.3%)	35 (72.9%)
>450 to ≤480	4 (10.8%)	4 (11.4%)	5 (10.4%)
>480 to ≤500	2 (5.4%)	1 (2.9%)	4 (8.3%)
>500	6 (16.2%)	4 (11.4%)	4 (8.3%)
QTcB Interval, Aggregate  (msec)
Baseline
N	53	73	59
≤450	37 (69.8%)	58 (79.5%)	46 (78.0%)
>450 to ≤480	4 (7.5%)	8 (11.0%)	4 (6.8%)
>480 to ≤500	5 (9.4%)	3 (4.1%)	4 (6.8%)
>500	7 (13.2%)	4 (5.5%)	5 (8.5%)
Month 1
N	53	71	58
≤450	38 (71.7%)	60 (84.5%)	41 (70.7%)
>450 to ≤480	8 (15.1%)	3 (4.2%)	10 (17.2%)
>480 to ≤500	4 (7.5%)	5 (7.0%)	3 (5.2%)
>500	3 (5.7%)	3 (4.2%)	4 (6.9%)
Month 3
N	53	53	56
≤450	41 (77.4%)	38 (71.7%)	47 (83.9%)
>450 to ≤480	6 (11.3%)	4 (7.5%)	4 (7.1%)
>480 to ≤500	2 (3.8%)	6 (11.3%)	2 (3.6%)
>500	4 (7.5%)	5 (9.4%)	3 (5.4%)
Month 6
N	51	47	51
≤450	37 (72.5%)	40 (85.1%)	42 (82.4%)
>450 to ≤480	6 (11.8%)	2 (4.3%)	3 (5.9%)
>480 to ≤500	5 (9.8%)	3 (6.4%)	3 (5.9%)
>500	3 (5.9%)	2 (4.3%)	3 (5.9%)
Month 9
N	41	42	51
≤450	33 (80.5%)	33 (78.6%)	41 (80.4%)
>450 to ≤480	4 (9.8%)	5 (11.9%)	3 (5.9%)
>480 to ≤500	2 (4.9%)	1 (2.4%)	4 (7.8%)
>500	2 (4.9%)	3 (7.1%)	3 (5.9%)
Month 12
N	37	35	48
≤450	33 (89.2%)	29 (82.9%)	37 (77.1%)
>450 to ≤480	1 (2.7%)	3 (8.6%)	8 (16.7%)
>480 to ≤500	2 (5.4%)	2 (5.7%)	1 (2.1%)
>500	1 (2.7%)	1 (2.9%)	2 (4.2%)
QTcF Interval, Aggregate  (msec)
Baseline
N	53	73	59
≤450	44 (83.0%)	59 (80.8%)	42 (71.2%)
>450 to ≤480	2 (3.8%)	6 (8.2%)	9 (15.3%)
>480 to ≤500	4 (7.5%)	2 (2.7%)	5 (8.5%)
>500	3 (5.7%)	6 (8.2%)	3 (5.1%)
Month 1
N	53	71	58
≤450	42 (79.2%)	57 (80.3%)	49 (84.5%)
>450 to ≤480	3 (5.7%)	8 (11.3%)	1 (1.7%)
>480 to ≤500	5 (9.4%)	2 (2.8%)	2 (3.4%)
>500	3 (5.7%)	4 (5.6%)	6 (10.3%)
Month 3
N	53	53	56
≤450	42 (79.2%)	40 (75.5%)	43 (76.8%)
>450 to ≤480	3 (5.7%)	4 (7.5%)	2 (3.6%)
>480 to ≤500	6 (11.3%)	4 (7.5%)	5 (8.9%)
>500	2 (3.8%)	5 (9.4%)	6 (10.7%)
Month 6
N	51	47	51
≤450	42 (82.4%)	37 (78.7%)	36 (70.6%)
>450 to ≤480	4 (7.8%)	2 (4.3%)	7 (13.7%)
>480 to ≤500	2 (3.9%)	1 (2.1%)	3 (5.9%)
>500	3 (5.9%)	7 (14.9%)	5 (9.8%)
Month 9
N	41	42	51
≤450	32 (78.0%)	36 (85.7%)	38 (74.5%)
>450 to ≤480	2 (4.9%)	1 (2.4%)	3 (5.9%)
>480 to ≤500	3 (7.3%)	3 (7.1%)	4 (7.8%)
>500	4 (9.8%)	2 (4.8%)	6 (11.8%)
Month 12
N	37	35	48
≤450	30 (81.1%)	27 (77.1%)	38 (79.2%)
>450 to ≤480	2 (5.4%)	4 (11.4%)	7 (14.6%)
>480 to ≤500	3 (8.1%)	0	2 (4.2%)
>500	2 (5.4%)	4 (11.4%)	1 (2.1%)
Note: N is the number of subjects with a non-missing value for the ECG parameter at the specified time point.

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