teal Module: Events by Grade

This module produces a table to summarize events by grade.

Usage

tm_t_events_by_grade(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  hlt,
  llt,
  grade,
  grading_groups = list(`Any Grade (%)` = c("1", "2", "3", "4", "5"), `Grade 1-2 (%)` =
    c("1", "2"), `Grade 3-4 (%)` = c("3", "4"), `Grade 5 (%)` = "5"),
  col_by_grade = FALSE,
  prune_freq = 0,
  prune_diff = 0,
  add_total = TRUE,
  total_label = default_total_label(),
  na_level = default_na_str(),
  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(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.
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.
grade: (character)
name of the severity level variable.
grading_groups: (list)
named list of grading groups used when col_by_grade = TRUE.
col_by_grade: (logical)
whether to display the grading groups in nested columns.
prune_freq: (number)
threshold to use for trimming table using event incidence rate in any column.
prune_diff: (number)
threshold to use for trimming table using as criteria difference in rates between any two columns.
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").
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: 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.

Examples

data <- teal_data()
data <- within(data, {
  library(formatters)
  library(dplyr)

  ADSL <- tmc_ex_adsl
  lbls_adae <- var_labels(tmc_ex_adae)
  ADAE <- tmc_ex_adae %>%
    mutate_if(is.character, as.factor) #' be certain of having factors
  var_labels(ADAE) <- lbls_adae
})

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

app <- init(
  data = data,
  modules = modules(
    tm_t_events_by_grade(
      label = "Adverse Events by Grade Table",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      llt = choices_selected(
        choices = variable_choices(data[["ADAE"]], c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(data[["ADAE"]], c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      grade = choices_selected(
        choices = variable_choices(data[["ADAE"]], c("AETOXGR", "AESEV")),
        selected = "AETOXGR"
      )
    )
  )
)
#> [INFO] 2024-02-26 01:42:41.5284 pid:1518 token:[] teal.modules.clinical Initializing tm_t_events_by_grade
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Usage

Arguments

Value

See also

Examples