teal.modules.clinical (version 0.9.0)

template_smq: 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()
)

Value

a list of expressions to generate a table or plot object.

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

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

tm_t_smq()