teal Module: Summary of Variables

Usage

tm_t_summary(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  summarize_vars,
  add_total = TRUE,
  total_label = default_total_label(),
  useNA = c("ifany", "no"),
  na_level = default_na_str(),
  numeric_stats = c("n", "mean_sd", "mean_ci", "median", "median_ci", "quantiles",
    "range", "geom_mean"),
  denominator = c("N", "n", "omit"),
  drop_arm_levels = TRUE,
  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.

arm_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as arm_var. It defines the grouping variable(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.

summarize_vars

(teal.transform::choices_selected())
names of the variables that should be summarized.

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").

useNA

(character)
whether missing data (NA) should be displayed as a level.

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").

numeric_stats

(character)
names of statistics to display for numeric summary variables. Available statistics are n, mean_sd, mean_ci, median, median_ci, quantiles, range, and geom_mean.

denominator

(character)
chooses how percentages are calculated. With option N, the reference population from the column total is used as the denominator. With option n, the number of non-missing records in this row and column intersection is used as the denominator. If omit is chosen, then the percentage is omitted.

drop_arm_levels

(logical)
whether to drop unused levels of arm_var. If TRUE, arm_var levels are set to those used in the dataname dataset. If FALSE, arm_var levels are set to those used in the parentname dataset. If dataname and parentname are the same, then drop_arm_levels is set to TRUE and user input for this parameter is ignored.

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").

Value

a teal_module object.

See also

Examples

# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data.
ADSL <- tmc_ex_adsl
ADSL$EOSDY[1] <- NA_integer_

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    code = "
      ADSL <- tmc_ex_adsl
      ADSL$EOSDY[1] <- NA_integer_
    "
  ),
  modules = modules(
    tm_t_summary(
      label = "Demographic Table",
      dataname = "ADSL",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      add_total = TRUE,
      summarize_vars = choices_selected(
        c("SEX", "RACE", "BMRKR2", "EOSDY", "DCSREAS", "AGE"),
        c("SEX", "RACE")
      ),
      useNA = "ifany"
    )
  )
)
#> [INFO] 2024-02-26 01:42:47.5735 pid:1518 token:[] teal.modules.clinical Initializing tm_t_summary
if (interactive()) {
  shinyApp(app$ui, app$server)
}