TSIEX06

Subjects Who Received Study Treatment Over Time

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Code

# Program Name:              tsiex06.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSIEX06"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map


trtvar <- "TRT01A"
popfl <- "SAFFL"
combined_colspan_trt <- TRUE

if (combined_colspan_trt == TRUE) {
  # Set up levels and label for the required combined columns
  add_combo <- add_combo_facet(
    "Combined",
    label = "Combined",
    levels = c("Xanomeline High Dose", "Xanomeline Low Dose")
  )

  # choose if any facets need to be removed - e.g remove the combined column for placebo
  rm_combo_from_placebo <- cond_rm_facets(
    facets = "Combined",
    ancestor_pos = NA,
    value = " ",
    split = "colspan_trt"
  )

  mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
}

# Process Data:

# Read in required data
adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  select(USUBJID, all_of(trtvar), all_of(popfl))

adex <- pharmaverseadamjnj::adex %>%
  filter(AOCCUR == "Y" & !grepl("UNSCHEDULED", AVISIT, ignore.case = TRUE)) %>%
  select(USUBJID, AOCCUR, AVISIT, AVISITN)

# Convert AVISIT to sentence case and apply levels to maintain ordering
avisit_levs <- stringr::str_to_sentence(levels(adex$AVISIT))
adex$AVISIT <- stringr::str_to_sentence(adex$AVISIT)
adex$AVISIT <- factor(adex$AVISIT, levels = avisit_levs)

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

# join data together
ex <- adex %>% inner_join(., adsl, by = c("USUBJID"))

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

# Define layout and build table:

lyt <- rtables::basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

lyt <- lyt %>%
  tern::count_occurrences(
    "AVISIT",
    .stats = "count_fraction_fixed_dp",
    .formats = c("count_fraction_fixed_dp" = jjcsformat_count_fraction),
    var_labels = "Subjects receiving study treatment, n (%)",
    show_labels = "visible"
  )

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

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table

tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid, orientation = "portrait")

TSIEX06: Subjects Who Received Study Treatment Over Time; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
	Xanomeline High Dose	Xanomeline Low Dose	Combined	Placebo
	N=53	N=73	N=126	N=59
Subjects receiving study treatment, n (%)
Baseline	30 (56.6%)	42 (57.5%)	72 (57.1%)	21 (35.6%)
Week 2	27 (50.9%)	16 (21.9%)	43 (34.1%)	28 (47.5%)
Week 24	14 (26.4%)	8 (11.0%)	22 (17.5%)	19 (32.2%)

Download RTF file

--- title: TSIEX06 subtitle: Subjects Who Received Study Treatment Over Time --- ------------------------------------------------------------------------ {{< 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: tsiex06.R # Prep Environment library(envsetup) library(tern) library(dplyr) library(rtables) library(junco) # Define script level parameters: # - Define output ID and file location tblid <- "TSIEX06" fileid <- tblid tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map trtvar <- "TRT01A" popfl <- "SAFFL" combined_colspan_trt <- TRUE if (combined_colspan_trt == TRUE) { # Set up levels and label for the required combined columns add_combo <- add_combo_facet( "Combined", label = "Combined", levels = c("Xanomeline High Dose", "Xanomeline Low Dose") ) # choose if any facets need to be removed - e.g remove the combined column for placebo rm_combo_from_placebo <- cond_rm_facets( facets = "Combined", ancestor_pos = NA, value = " ", split = "colspan_trt" ) mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo)) } # Process Data: # Read in required data adsl <- pharmaverseadamjnj::adsl %>% filter(!!rlang::sym(popfl) == "Y") %>% select(USUBJID, all_of(trtvar), all_of(popfl)) adex <- pharmaverseadamjnj::adex %>% filter(AOCCUR == "Y" & !grepl("UNSCHEDULED", AVISIT, ignore.case = TRUE)) %>% select(USUBJID, AOCCUR, AVISIT, AVISITN) # Convert AVISIT to sentence case and apply levels to maintain ordering avisit_levs <- stringr::str_to_sentence(levels(adex$AVISIT)) adex$AVISIT <- stringr::str_to_sentence(adex$AVISIT) adex$AVISIT <- factor(adex$AVISIT, levels = avisit_levs) adsl$colspan_trt <- factor( ifelse(adsl[[trtvar]] == "Placebo", " ", "Active Study Agent"), levels = c("Active Study Agent", " ") ) # join data together ex <- adex %>% inner_join(., adsl, by = c("USUBJID")) colspan_trt_map <- create_colspan_map( adsl, non_active_grp = "Placebo", non_active_grp_span_lbl = " ", active_grp_span_lbl = "Active Study Agent", colspan_var = "colspan_trt", trt_var = trtvar ) # Define layout and build table: lyt <- rtables::basic_table( top_level_section_div = " ", show_colcounts = TRUE, colcount_format = "N=xx" ) %>% split_cols_by( "colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map) ) if (combined_colspan_trt == TRUE) { lyt <- lyt %>% split_cols_by(trtvar, split_fun = mysplit) } else { lyt <- lyt %>% split_cols_by(trtvar) } lyt <- lyt %>% tern::count_occurrences( "AVISIT", .stats = "count_fraction_fixed_dp", .formats = c("count_fraction_fixed_dp" = jjcsformat_count_fraction), var_labels = "Subjects receiving study treatment, n (%)", show_labels = "visible" ) result <- build_table(lyt, ex, alt_counts_df = adsl) # Add titles and footnotes: result <- set_titles(result, tab_titles) # Convert to tbl file and output table tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid, orientation = "portrait") ``` ```{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')`) ::::