teal.modules.clinical (version 0.9.0)

tm_t_exposure: teal Module: Exposure Table for Risk management plan

Description

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()
)

Value

a teal_module object.

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

optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.

post_output

optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

basic_table_args

optional, (basic_table_args)
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").

See Also

The TLG Catalog where additional example apps implementing this module can be found.

Examples

library(dplyr)
library(formatters)

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

  set.seed(1, kind = "Mersenne-Twister")
  labels <- var_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)
  var_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"))
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}