teal Module: Multiple Events by Term

Usage

tm_t_mult_events(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  seq_var,
  hlt,
  llt,
  add_total = TRUE,
  total_label = default_total_label(),
  na_level = default_na_str(),
  event_type = "event",
  drop_arm_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 in the results table.

seq_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as analysis sequence number variable. Used for counting the unique number of events.

hlt

(teal.transform::choices_selected())
name of the variable with high level term for events.

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").

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").

event_type

(character)
type of event that is summarized (e.g. adverse event, treatment). Default is "event".

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.

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").

Value

a teal_module object.

See also

Examples in Shinylive

example-1

Open in Shinylive

Examples

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADCM <- tmc_ex_adcm
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys

ADSL <- data[["ADSL"]]
ADCM <- data[["ADCM"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_mult_events(
      label = "Concomitant Medications by Medication Class and Preferred Name",
      dataname = "ADCM",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      seq_var = choices_selected("CMSEQ", selected = "CMSEQ", fixed = TRUE),
      hlt = choices_selected(
        choices = variable_choices(ADCM, c("ATC1", "ATC2", "ATC3", "ATC4")),
        selected = c("ATC1", "ATC2", "ATC3", "ATC4")
      ),
      llt = choices_selected(
        choices = variable_choices(ADCM, c("CMDECOD")),
        selected = c("CMDECOD")
      ),
      add_total = TRUE,
      event_type = "treatment"
    )
  )
)
#> Initializing tm_t_mult_events
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}