TSIEX07

Dose Levels Over Time

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Code

# Program Name:              tsiex07.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSIEX07"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map


trtvar <- "TRT01A"
popfl <- "SAFFL"

dose_order <- c("60", "120", "180", "240", "300", "480", "720", "960", "Total")

# Process Data:

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

adex <- pharmaverseadamjnj::adex %>%
  filter(!grepl("UNSCHEDULED", AVISIT, ignore.case = TRUE)) %>%
  filter(!is.na(ADOSE)) %>%
  mutate(ADOSEC = as.factor(ADOSE)) %>%
  select(USUBJID, ADOSEC, 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)

# Create Total column manually as we cannot use the table layout option since patients can
# appear in multiple dose level columns

extot_ <- adex %>%
  group_by(USUBJID, AVISIT) %>%
  slice(1) %>%
  mutate(ADOSEC = "Total") %>%
  ungroup()

extot <- bind_rows(adex, extot_)

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

ex$colspan_trt <- factor(
  ifelse(ex$ADOSEC == "Total", " ", "Active Study Agent"),
  levels = c("Active Study Agent", " ")
)

ex$ADOSEC <- factor(ex$ADOSEC, levels = dose_order)

# Create dataset to be used for column counts
adex_unique <- ex %>%
  group_by(USUBJID, ADOSEC) %>%
  slice(1) %>%
  ungroup()

# 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_in_group("ADOSEC")) %>%
  split_cols_by("ADOSEC") %>%
  tern::count_occurrences(
    "AVISIT",
    .stats = "count_fraction_fixed_dp",
    .formats = c("count_fraction_fixed_dp" = jjcsformat_count_fraction),
    var_labels = " ",
    show_labels = "hidden"
  ) %>%
  append_topleft("Time Point, n (%)")

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

# 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 = "landscape")

TSIEX07: Dose Levels Over Time; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
	60	120	240	300	480	720	960	Total
Time Point, n (%)	N=3	N=3	N=3	N=8	N=26	N=98	N=51	N=125
Baseline	1 (33.3%)	2 (66.7%)	3 (100.0%)	3 (37.5%)	13 (50.0%)	94 (95.9%)	9 (17.6%)	125 (100.0%)
Week 2	1 (33.3%)	1 (33.3%)	0	3 (37.5%)	3 (11.5%)	2 (2.0%)	41 (80.4%)	104 (83.2%)
Week 24	2 (66.7%)	0	0	2 (25.0%)	12 (46.2%)	17 (17.3%)	2 (3.9%)	35 (28.0%)

Download RTF file

--- title: TSIEX07 subtitle: Dose Levels 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: tsiex07.R # Prep Environment library(envsetup) library(tern) library(dplyr) library(rtables) library(junco) # Define script level parameters: # - Define output ID and file location tblid <- "TSIEX07" fileid <- tblid tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map trtvar <- "TRT01A" popfl <- "SAFFL" dose_order <- c("60", "120", "180", "240", "300", "480", "720", "960", "Total") # Process Data: # Read in required data adsl <- pharmaverseadamjnj::adsl %>% filter(!!rlang::sym(popfl) == "Y" & !!rlang::sym(trtvar) != "Placebo") %>% select(USUBJID, all_of(trtvar), all_of(popfl)) adex <- pharmaverseadamjnj::adex %>% filter(!grepl("UNSCHEDULED", AVISIT, ignore.case = TRUE)) %>% filter(!is.na(ADOSE)) %>% mutate(ADOSEC = as.factor(ADOSE)) %>% select(USUBJID, ADOSEC, 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$AVISIT, levels = avisit_levs) # Create Total column manually as we cannot use the table layout option since patients can # appear in multiple dose level columns extot_ <- adex %>% group_by(USUBJID, AVISIT) %>% slice(1) %>% mutate(ADOSEC = "Total") %>% ungroup() extot <- bind_rows(adex, extot_) # join data together ex <- extot %>% inner_join(., adsl, by = c("USUBJID")) ex$colspan_trt <- factor( ifelse(ex$ADOSEC == "Total", " ", "Active Study Agent"), levels = c("Active Study Agent", " ") ) ex$ADOSEC <- factor(ex$ADOSEC, levels = dose_order) # Create dataset to be used for column counts adex_unique <- ex %>% group_by(USUBJID, ADOSEC) %>% slice(1) %>% ungroup() # 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_in_group("ADOSEC")) %>% split_cols_by("ADOSEC") %>% tern::count_occurrences( "AVISIT", .stats = "count_fraction_fixed_dp", .formats = c("count_fraction_fixed_dp" = jjcsformat_count_fraction), var_labels = " ", show_labels = "hidden" ) %>% append_topleft("Time Point, n (%)") result <- build_table(lyt, ex, alt_counts_df = adex_unique) # 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 = "landscape") ``` ```{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')`) ::::