teal.modules.clinical (version 0.12.0)

tm_t_summary_by: teal Module: Summarize Variables by Row Groups

Description

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 = tern::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(),
  transformators = list(),
  decorators = list()
)

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.

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

(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").

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

decorators

(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Decorating Module

This module generates the following objects, which can be modified in place using decorators:

• table (TableTree - output of rtables::build_table())

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_t_summary_by(
   ..., # arguments for module
   decorators = list(
     table = teal_transform_module(...) # applied only to `table` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.modules.clinical").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

Reporting

This module returns an object of class teal_module, that contains a server function. Since the server function returns a teal_report object, this makes this module reportable, which means that the reporting functionality will be turned on automatically by the teal framework.

For more information on reporting in teal, see the vignettes:

• vignette("reportable-shiny-application", package = "teal.reporter")

• vignette("adding-support-for-reporting-to-custom-modules", package = "teal")

Examples in Shinylive

example-1

Open in Shinylive

See Also

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

Examples

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  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"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}