Teal Module: Shift by Arm

Usage

tm_t_shift_by_arm(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  paramcd,
  visit_var,
  aval_var,
  base_var,
  treatment_flag_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
    "ONTRTFL"), selected = "ONTRTFL", fixed = TRUE),
  treatment_flag =
    teal.transform::choices_selected(teal.transform::value_choices(dataname, "ONTRTFL"),
    selected = "Y", fixed = TRUE),
  useNA = c("ifany", "no"),
  na_level = "<Missing>",
  add_total = FALSE,
  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

(choices_selected or data_extract_spec)
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.

paramcd

(choices_selected or data_extract_spec)
variable value designating the studied parameter.

visit_var

(choices_selected or data_extract_spec)
object with all available choices and preselected option for variable names that can be used as visit variable. Must be a factor in dataname.

aval_var

(choices_selected or data_extract_spec)
object with all available choices and preselected option for the analysis variable.

base_var

(character)
the variable name for the baseline reference range indicator.

treatment_flag_var

(choices_selected or data_extract_spec)
on treatment flag variable.

treatment_flag

(choices_selected] or data_extract_spec)
value indicating on treatment records in treatment_flag_var.

useNA

(character)
whether missing data (NA) should be displayed as a level.

na_level

(string)
used to replace all NA or empty values in character or factor variables in the data.

add_total

(logical)
whether to include row with total number of patients.

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").

Examples

library(dplyr)
library(tern)
library(scda)
synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
adsl <- synthetic_cdisc_data_latest$adsl
adeg <- synthetic_cdisc_data_latest$adeg

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", adsl,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADSL <- synthetic_cdisc_data_latest$adsl"
    ),
    cdisc_dataset("ADEG", adeg,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADEG <- synthetic_cdisc_data_latest$adeg"
    )
  ),
  modules = modules(
    tm_t_shift_by_arm(
      label = "Shift by Arm Table",
      dataname = "ADEG",
      arm_var = choices_selected(
        variable_choices(adsl, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        value_choices(adeg, "PARAMCD"),
        selected = "HR"
      ),
      visit_var = choices_selected(
        value_choices(adeg, "AVISIT"),
        selected = "POST-BASELINE MINIMUM"
      ),
      aval_var = choices_selected(
        variable_choices(adeg, subset = "ANRIND"),
        selected = "ANRIND", fixed = TRUE
      ),
      base_var = choices_selected(
        variable_choices(adeg, subset = "BNRIND"),
        selected = "BNRIND", fixed = TRUE
      ),
      useNA = "ifany"
    )
  )
)
#> [INFO] 2022-10-14 09:11:09.9519 pid:3139 token:[] teal.modules.clinical Initializing tm_t_shift_by_arm
if (FALSE) {
shinyApp(app$ui, app$server)
}