teal.modules.clinical (version 0.9.0)

tm_t_events_by_grade: teal Module: Events by Grade

Description

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()
)

Value

a teal_module object.

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").

See Also

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

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"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}