template_smq: Template: Adverse Events Table by Standardized MedDRA Query

In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

Template: Adverse Events Table by Standardized MedDRA Query

Description

Creates a valid expression to generate an adverse events table by Standardized MedDRA Query.

Usage

template_smq(
  dataname,
  parentname,
  arm_var,
  llt = "AEDECOD",
  add_total = TRUE,
  total_label = default_total_label(),
  sort_criteria = c("freq_desc", "alpha"),
  drop_arm_levels = TRUE,
  na_level = default_na_str(),
  smq_varlabel = "Standardized MedDRA Query",
  baskets = c("SMQ01NAM", "SMQ02NAM", "CQ01NAM"),
  id_var = "USUBJID",
  basic_table_args = teal.widgets::basic_table_args()
)

Arguments

dataname	(character) analysis data used in teal module.
parentname	(character) parent analysis data used in teal module, usually this refers to ADSL.
arm_var	(character) variable names that can be used as arm_var.
llt	(character) name of the variable with low level term for events.
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").
sort_criteria	(character) how to sort the final table. Default option freq_desc sorts on column sort_freq_col by decreasing number of patients with event. Alternative option alpha sorts events alphabetically.
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.
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").
smq_varlabel	(character) label to use for new column SMQ created by tern::h_stack_by_baskets().
baskets	(character) names of the selected standardized/customized queries variables.
id_var	(character) the variable name for subject id.
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 list of expressions to generate a table or plot object.

See Also

tm_t_smq()

teal.modules.clinical documentation built on April 4, 2025, 12:35 a.m.