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teal Module: Adverse Events Table by Standardized MedDRA Query

Source: R/tm_t_smq.R
tm_t_smq.Rd

This module produces an adverse events table by Standardized MedDRA Query.

Usage 

tm_t_smq(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  llt,
  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,
  scopes,
  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.

id_var

(teal.transform::choices_selected())
object specifying the variable name for subject id.

llt

(teal.transform::choices_selected())
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

(teal.transform::choices_selected())
object with all available choices and preselected options for standardized/customized queries.

scopes

(teal.transform::choices_selected())
object with all available choices for the scopes of standardized queries.

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

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

Examples 

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADAE <- tmc_ex_adae

  names_baskets <- grep("^(SMQ|CQ).*NAM$", names(ADAE), value = TRUE)
  names_scopes <- grep("^SMQ.*SC$", names(ADAE), value = TRUE)

  cs_baskets <- choices_selected(
    choices = variable_choices(ADAE, subset = names_baskets),
    selected = names_baskets
  )

  cs_scopes <- choices_selected(
    choices = variable_choices(ADAE, subset = names_scopes),
    selected = names_scopes,
    fixed = TRUE
  )
})

datanames <- c("ADSL", "ADAE")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_t_smq(
      label = "Adverse Events by SMQ Table",
      dataname = "ADAE",
      arm_var = choices_selected(
        choices = variable_choices(data[["ADSL"]], subset = c("ARM", "SEX")),
        selected = "ARM"
      ),
      add_total = FALSE,
      baskets = data[["cs_baskets"]],
      scopes = data[["cs_scopes"]],
      llt = choices_selected(
        choices = variable_choices(data[["ADAE"]], subset = c("AEDECOD")),
        selected = "AEDECOD"
      )
    )
  )
)
#> [INFO] 2024-02-26 01:42:47.1248 pid:1518 token:[] teal.modules.clinical Initializing tm_t_smq
if (interactive()) {
  shinyApp(app$ui, app$server)
}