TSIEX09

Distribution of Subjects by Study Treatment Lot

Output

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Code

# Program Name:              tsiex09.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSIEX09"
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(STUDYID, USUBJID, all_of(trtvar), all_of(popfl))

adex <- pharmaverseadamjnj::adex %>%
  select(USUBJID, ATRT, EXLOT)

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")) %>%
  mutate(ATRT = stringr::str_to_sentence(ATRT)) %>%
  mutate(trttxt = paste0(ATRT, " lots"))

ex$trttxt2 <- factor(ex$trttxt)

# Puts placebo last - this line can be removed if you do not have a placebo treatment arm
ex$trttxt2 <- forcats::fct_relevel(ex$trttxt2, "Placebo lots", after = Inf)

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:

extra_args1 <- list(
  .stats = "count_unique_fraction",
  denom = "n_parentdf",
  # trick to get 0 for Placebo column for non Placebo lots
  denom_by = "STUDYID"
)

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 %>%
  # trick to get 0 for Placebo column for non Placebo lots
  # we do not want to show this split_rows group label - therefor set child_labels to hidden
  split_rows_by("STUDYID", child_labels = "hidden") %>%
  split_rows_by(
    "trttxt2",
    split_label = "Study Treatment",
    split_fun = trim_levels_in_group("STUDYID"),
    label_pos = "topleft",
    indent_mod = 0L,
    section_div = c(" ")
  ) %>%
  analyze(
    "EXLOT",
    afun = a_freq_j,
    extra_args = extra_args1,
    indent_mod = 0L,
    show_labels = "hidden"
  ) %>%
  append_topleft("  Lot, n (%)")

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")

TSIEX09: Distribution of Subjects by Study Treatment Lot; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
Study Treatment	Xanomeline High Dose	Xanomeline Low Dose	Combined	Placebo
Lot, n (%)	N=53	N=73	N=126	N=59
Xanomeline lots
XXX-YYY-ZZZ-002	30 (56.6%)	31 (42.5%)	61 (48.4%)	0
XXX-YYY-ZZZ-003	26 (49.1%)	28 (38.4%)	54 (42.9%)	0
XXX-YYY-ZZZ-004	20 (37.7%)	38 (52.1%)	58 (46.0%)	0
XXX-YYY-ZZZ-005	25 (47.2%)	29 (39.7%)	54 (42.9%)	0

Placebo lots
XXX-YYY-ZZZ-002	0	0	0	32 (54.2%)
XXX-YYY-ZZZ-003	0	0	0	28 (47.5%)
XXX-YYY-ZZZ-004	0	0	0	33 (55.9%)
XXX-YYY-ZZZ-005	0	0	0	32 (54.2%)

Note: Subjects may be counted in multiple lots, if applicable.

Download RTF file

--- title: TSIEX09 subtitle: Distribution of Subjects by Study Treatment Lot --- ------------------------------------------------------------------------ {{< 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: tsiex09.R # Prep Environment library(envsetup) library(tern) library(dplyr) library(rtables) library(junco) # Define script level parameters: # - Define output ID and file location tblid <- "TSIEX09" 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(STUDYID, USUBJID, all_of(trtvar), all_of(popfl)) adex <- pharmaverseadamjnj::adex %>% select(USUBJID, ATRT, EXLOT) adsl$colspan_trt <- factor( ifelse(adsl[[trtvar]] == "Placebo", " ", "Active Study Agent"), levels = c("Active Study Agent", " ") ) # join data together ex <- adex %>% inner_join(., adsl, by = c("USUBJID")) %>% mutate(ATRT = stringr::str_to_sentence(ATRT)) %>% mutate(trttxt = paste0(ATRT, " lots")) ex$trttxt2 <- factor(ex$trttxt) # Puts placebo last - this line can be removed if you do not have a placebo treatment arm ex$trttxt2 <- forcats::fct_relevel(ex$trttxt2, "Placebo lots", after = Inf) 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: extra_args1 <- list( .stats = "count_unique_fraction", denom = "n_parentdf", # trick to get 0 for Placebo column for non Placebo lots denom_by = "STUDYID" ) 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 %>% # trick to get 0 for Placebo column for non Placebo lots # we do not want to show this split_rows group label - therefor set child_labels to hidden split_rows_by("STUDYID", child_labels = "hidden") %>% split_rows_by( "trttxt2", split_label = "Study Treatment", split_fun = trim_levels_in_group("STUDYID"), label_pos = "topleft", indent_mod = 0L, section_div = c(" ") ) %>% analyze( "EXLOT", afun = a_freq_j, extra_args = extra_args1, indent_mod = 0L, show_labels = "hidden" ) %>% append_topleft(" Lot, n (%)") 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')`) ::::