teal Module: Summarize Variables by Row Groups

This module produces a table to summarize variables by row groups.

Usage

tm_t_summary_by(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  by_vars,
  summarize_vars,
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  paramcd = NULL,
  add_total = TRUE,
  total_label = default_total_label(),
  parallel_vars = FALSE,
  row_groups = FALSE,
  useNA = c("ifany", "no"),
  na_level = default_na_str(),
  numeric_stats = c("n", "mean_sd", "median", "range"),
  denominator = teal.transform::choices_selected(c("n", "N", "omit"), "omit", fixed =
    TRUE),
  drop_arm_levels = TRUE,
  drop_zero_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.
by_vars: (teal.transform::choices_selected())
object with all available choices and preselected option for variable names used to split the summary by rows.
summarize_vars: (teal.transform::choices_selected())
names of the variables that should be summarized.
id_var: (teal.transform::choices_selected())
object specifying the variable name for subject id.
paramcd: (teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.
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").
parallel_vars: (logical)
whether summarized variables should be arranged in columns. Can only be set to TRUE if all chosen analysis variables are numeric.
row_groups: (logical)
whether summarized variables should be arranged in row groups.
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.
drop_zero_levels: (logical)
whether rows with zero counts in all columns should be removed from the table.
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.

Examples

ADSL <- tmc_ex_adsl
ADLB <- tmc_ex_adlb

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADLB = ADLB,
    code = "
      ADSL <- tmc_ex_adsl
      ADLB <- tmc_ex_adlb
    "
  ),
  modules = modules(
    tm_t_summary_by(
      label = "Summary by Row Groups Table",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      add_total = TRUE,
      by_vars = choices_selected(
        choices = variable_choices(ADLB, c("PARAM", "AVISIT")),
        selected = c("AVISIT")
      ),
      summarize_vars = choices_selected(
        choices = variable_choices(ADLB, c("AVAL", "CHG")),
        selected = c("AVAL")
      ),
      useNA = "ifany",
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = "ALT"
      )
    )
  )
)
#> [INFO] 2024-02-26 01:42:47.9308 pid:1518 token:[] teal.modules.clinical Initializing tm_t_summary_by
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Usage

Arguments

Value

See also

Examples