teal Module: Exposure Table for Risk management plan

The module produces an exposure table for risk management plan.

Usage

tm_t_exposure(
  label,
  dataname,
  parentname = ifelse(inherits(col_by_var, "data_extract_spec"),
    teal.transform::datanames_input(col_by_var), "ADSL"),
  row_by_var,
  col_by_var,
  paramcd = teal.transform::choices_selected(choices =
    teal.transform::value_choices(dataname, "PARAMCD", "PARAM"), selected = "TDURD"),
  paramcd_label = "PARAM",
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  parcat,
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "AVAL"), selected = "AVAL", fixed = TRUE),
  avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "AVALU"), selected = "AVALU", fixed = TRUE),
  add_total,
  total_label = default_total_label(),
  add_total_row = TRUE,
  total_row_label = "Total number of patients and patient time*",
  na_level = default_na_str(),
  pre_output = NULL,
  post_output = NULL,
  basic_table_args = teal.widgets::basic_table_args()
)

Arguments

label: (character)
menu item label of the module in the teal app.
dataname: (character)
analysis data used in teal module.
parentname: (character)
parent analysis data used in teal module, usually this refers to ADSL.
row_by_var: (teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used to split rows.
col_by_var: (teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used to split columns.
paramcd: (teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.
paramcd_label: (character)
the column from the dataset where the value will be used to label the argument paramcd.
id_var: (teal.transform::choices_selected())
object specifying the variable name for subject id.
parcat: (teal.transform::choices_selected())
object with all available choices and preselected option for parameter category values.
aval_var: (teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.
avalu_var: (teal.transform::choices_selected())
object with all available choices and preselected option for the analysis unit variable.
add_total: (logical)
whether to include column with total number of patients.
total_label: (string)
string to display as total column/row label if column/row is enabled (see add_total). Defaults to "All Patients". To set a new default total_label to apply in all modules, run set_default_total_label("new_default").
add_total_row: (flag)
whether a "total" level should be added after the others which includes all the levels that constitute the split. A custom label can be set for this level via the total_row_label argument.
total_row_label: (character)
string to display as total row label if row is enabled (see add_total_row).
na_level: (string)
used to replace all NA or empty values in character or factor variables in the data. Defaults to "<Missing>". To set a default na_level to apply in all modules, run set_default_na_str("new_default").
pre_output: (shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.
post_output: (shiny.tag) optional,
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.
basic_table_args: (basic_table_args) optional
object created by teal.widgets::basic_table_args() with settings for the module table. The argument is merged with option teal.basic_table_args and with default module arguments (hard coded in the module body). For more details, see the vignette: vignette("custom-basic-table-arguments", package = "teal.widgets").

Value

a teal_module object.

Examples

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADEX <- tmc_ex_adex

  set.seed(1, kind = "Mersenne-Twister")
  labels <- col_labels(ADEX, fill = FALSE)
  ADEX <- ADEX %>%
    distinct(USUBJID, .keep_all = TRUE) %>%
    mutate(
      PARAMCD = "TDURD",
      PARAM = "Overall duration (days)",
      AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
      AVALU = "Days"
    ) %>%
    bind_rows(ADEX)
  col_labels(ADEX) <- labels
})

datanames <- c("ADSL", "ADEX")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_t_exposure(
      label = "Duration of Exposure Table",
      dataname = "ADEX",
      paramcd = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARAMCD", "PARAM"),
        selected = "TDURD"
      ),
      col_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("SEX", "ARM")),
        selected = "SEX"
      ),
      row_by_var = choices_selected(
        choices = variable_choices(data[["ADEX"]], subset = c("RACE", "REGION1", "STRATA1", "SEX")),
        selected = "RACE"
      ),
      parcat = choices_selected(
        choices = value_choices(data[["ADEX"]], "PARCAT2"),
        selected = "Drug A"
      ),
      add_total = FALSE
    )
  ),
  filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)
#> Initializing tm_t_exposure
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Usage

Arguments

Value

See also

Examples