TSFECG03

Categorized Change From Baseline to Maximum On-treatment Corrected QT Interval

Output

Preview

Code

# Program Name:              tsfecg03

# Prep Environment

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

# Define script level parameters:

tblid <- "TSFECG03"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

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

ad_domain <- "adeg"

selvisit <- c(
  "Baseline",
  "Month 1",
  "Month 3",
  "Month 6",
  "Month 9",
  "Month 12",
  "Month 15",
  "Month 18",
  "Month 24"
)

## selection of QTC parameters
selparamcd <- c("QTCFAG", "QTCBAG", "QTCS", "QTCLAG")

# initial read of data

adeg_complete <- pharmaverseadamjnj::adeg

### available QTC parameters in study
selparamcd <- intersect(selparamcd, unique(adeg_complete$PARAMCD))


catvar <- "CHGCAT1"
## all parameters have the same levels for CHGCAT1 -- there is no need to create a map dataframe

# Process Data:

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


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

adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))


adeg <- adeg_complete %>%
  filter(PARAMCD %in% selparamcd) %>%
  # filter(AVISIT %in% selvisit) %>%
  ### Maximum On-treatment
  ### note: by filter ANL03FL, this table is restricted to On-treatment values, per definition of ANL03FL
  ### therefor, no need to add ONTRTFL in filter
  ### if derivation of ANL03FL is not restricted to ONTRTFL records, adding ONTRTFL here will not give the correct answer either
  ### as mixing worst with other period is not giving the proper selection !!!
  filter(ANL03FL == "Y") %>%
  select(
    USUBJID,
    ONTRTFL,
    TRTEMFL,
    PARAM,
    PARAMCD,
    AVISITN,
    AVISIT,
    AVAL,
    BASE,
    CHG,
    CRIT1,
    CRIT1FL,
    CRIT2,
    CRIT2FL,
    all_of(catvar),
    ONTRTFL,
    TRTEMFL,
    ANL01FL,
    ANL02FL
  ) %>%
  inner_join(., adsl)


check1 <- adeg %>%
  group_by(TRT01A, PARAMCD, AVISIT) %>%
  summarize(n = n_distinct(USUBJID))

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")
)


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_fun = add_combo_levels(combodf)
  ) %>%
  ### if risk diff columns are wanted - re-enable next 2 split_cols_by lines
  # split_cols_by("rrisk_header", nested = FALSE) %>%
  # split_cols_by(trtvar, labels_var = "rrisk_label",
  #               split_fun = remove_split_levels(ctrl_grp))  %>%

  split_rows_by(
    "PARAM",
    split_label = "QTc Interval",
    label_pos = "topleft",
    split_fun = drop_split_levels,
    section_div = " "
  ) %>%
  analyze(
    c("CHGCAT1"),
    a_freq_j,
    extra_args = extra_args_rr,
    show_labels = "hidden",
    indent_mod = 1L
  ) %>%
  append_topleft("   Criteria, n (%)")

result <- build_table(lyt, adeg, 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)

TSFECG03: Categorized Change From Baseline to Maximum On-treatment Corrected QT Interval; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
QTc Interval	Xanomeline High Dose	Xanomeline Low Dose	Placebo
Criteria, n (%)	N=53	N=73	N=59
QTcB Interval, Aggregate (msec)
N	53	53	56
≤30	30 (56.6%)	29 (54.7%)	37 (66.1%)
>30 to ≤60	5 (9.4%)	3 (5.7%)	2 (3.6%)
>60	18 (34.0%)	21 (39.6%)	17 (30.4%)

QTcF Interval, Aggregate (msec)
N	53	53	56
≤30	31 (58.5%)	25 (47.2%)	28 (50.0%)
>30 to ≤60	4 (7.5%)	3 (5.7%)	8 (14.3%)
>60	18 (34.0%)	25 (47.2%)	20 (35.7%)

Note: On-treatment is defined as QTc interval values obtained after the first dose and within [30 days] following treatment discontinuation.
Note: N is the number of subjects with at least 1 non-missing change from baseline value for the ECG parameter over the specified time period.

Download RTF file

--- title: TSFECG03 subtitle: Categorized Change From Baseline to Maximum On-treatment Corrected QT Interval --- ------------------------------------------------------------------------ {{< include ../../_utils/envir_hook.qmd >}} ```{r setup, echo = FALSE, warning = FALSE, message = FALSE} options(docx.add_datetime = FALSE, tidytlg.add_datetime = FALSE) envsetup_config_name <- "default" # Path to the combined config file envsetup_file_path <- file.path("../..", "envsetup.yml") Sys.setenv(ENVSETUP_ENVIRON = '') library(envsetup) loaded_config <- config::get(config = envsetup_config_name, file = envsetup_file_path) envsetup::rprofile(loaded_config) dpscomp <- compound dpspdr <- paste(protocol,dbrelease,rpteff,sep="__") aptcomp <- compound aptpdr <- paste(protocol,dbrelease,rpteff,sep="__") ###### Study specific updates (formerly in envre) dpscomp <- "standards" dpspdr <- "jjcs__NULL__jjcs - core" apt <- FALSE library(junco) default_str_map <- rbind(default_str_map, c("&ctcae", "5.0")) ``` ## Output :::: panel-tabset ## {{< fa regular file-lines sm fw >}} Preview ```{r variant1, results='hide', warning = FALSE, message = FALSE} # Program Name: tsfecg03 # Prep Environment library(envsetup) library(tern) library(dplyr) library(rtables) library(junco) # Define script level parameters: tblid <- "TSFECG03" fileid <- tblid titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map popfl <- "SAFFL" trtvar <- "TRT01A" ctrl_grp <- "Placebo" ad_domain <- "adeg" selvisit <- c( "Baseline", "Month 1", "Month 3", "Month 6", "Month 9", "Month 12", "Month 15", "Month 18", "Month 24" ) ## selection of QTC parameters selparamcd <- c("QTCFAG", "QTCBAG", "QTCS", "QTCLAG") # initial read of data adeg_complete <- pharmaverseadamjnj::adeg ### available QTC parameters in study selparamcd <- intersect(selparamcd, unique(adeg_complete$PARAMCD)) catvar <- "CHGCAT1" ## all parameters have the same levels for CHGCAT1 -- there is no need to create a map dataframe # Process Data: adsl <- pharmaverseadamjnj::adsl %>% filter(.data[[popfl]] == "Y") %>% select(USUBJID, all_of(c(popfl, trtvar))) adsl$colspan_trt <- factor( ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"), levels = c("Active Study Agent", " ") ) adsl$rrisk_header <- "Risk Difference (%) (95% CI)" adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp)) adeg <- adeg_complete %>% filter(PARAMCD %in% selparamcd) %>% # filter(AVISIT %in% selvisit) %>% ### Maximum On-treatment ### note: by filter ANL03FL, this table is restricted to On-treatment values, per definition of ANL03FL ### therefor, no need to add ONTRTFL in filter ### if derivation of ANL03FL is not restricted to ONTRTFL records, adding ONTRTFL here will not give the correct answer either ### as mixing worst with other period is not giving the proper selection !!! filter(ANL03FL == "Y") %>% select( USUBJID, ONTRTFL, TRTEMFL, PARAM, PARAMCD, AVISITN, AVISIT, AVAL, BASE, CHG, CRIT1, CRIT1FL, CRIT2, CRIT2FL, all_of(catvar), ONTRTFL, TRTEMFL, ANL01FL, ANL02FL ) %>% inner_join(., adsl) check1 <- adeg %>% group_by(TRT01A, PARAMCD, AVISIT) %>% summarize(n = n_distinct(USUBJID)) 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") ) 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_fun = add_combo_levels(combodf) ) %>% ### if risk diff columns are wanted - re-enable next 2 split_cols_by lines # split_cols_by("rrisk_header", nested = FALSE) %>% # split_cols_by(trtvar, labels_var = "rrisk_label", # split_fun = remove_split_levels(ctrl_grp)) %>% split_rows_by( "PARAM", split_label = "QTc Interval", label_pos = "topleft", split_fun = drop_split_levels, section_div = " " ) %>% analyze( c("CHGCAT1"), a_freq_j, extra_args = extra_args_rr, show_labels = "hidden", indent_mod = 1L ) %>% append_topleft(" Criteria, n (%)") result <- build_table(lyt, adeg, 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) ``` ```{r result1, echo=FALSE, message=FALSE, warning=FALSE, test = list(result_v1 = "result")} tt_to_flextable_j(result, tblid, string_map = string_map) ``` [Download RTF file](`r paste0(tolower(tblid), '.rtf')`) ::::