teal.modules.clinical (version 0.10.0)

tm_t_pp_laboratory: teal Module: Patient Profile Laboratory Table

Description

This module produces a patient profile laboratory table using ADaM datasets.

Usage

tm_t_pp_laboratory(
  label,
  dataname = "ADLB",
  parentname = "ADSL",
  patient_col = "USUBJID",
  timepoints = NULL,
  aval = lifecycle::deprecated(),
  aval_var = NULL,
  avalu = lifecycle::deprecated(),
  avalu_var = NULL,
  param = NULL,
  paramcd = NULL,
  anrind = NULL,
  pre_output = NULL,
  post_output = NULL,
  transformators = list(),
  decorators = list()
)

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.

patient_col

(character)
name of patient ID variable.

timepoints

(teal.transform::choices_selected())
object with all available choices and preselected option for the time variable from dataname.

aval

Please use the aval_var argument instead.

aval_var

(teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.

avalu

Please use the avalu_var argument instead.

avalu_var

(teal.transform::choices_selected())
object with all available choices and preselected option for the analysis unit variable.

param

(teal.transform::choices_selected())
object with all available choices and preselected option for the PARAM variable from dataname.

paramcd

(teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.

anrind

(teal.transform::choices_selected())
object with all available choices and preselected option for the ANRIND variable from dataname. Variable should have the following 3 levels: "HIGH", "LOW", and "NORMAL".

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.

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

decorators

(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Decorating Module

This module generates the following objects, which can be modified in place using decorators:

• table (datatables - output of DT::datatable())

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_t_pp_laboratory(
   ..., # arguments for module
   decorators = list(
     table = teal_transform_module(...) # applied only to `table` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.modules.clinical").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

Examples in Shinylive

example-1

Open in Shinylive

Examples

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_pp_laboratory(
      label = "Vitals",
      dataname = "ADLB",
      patient_col = "USUBJID",
      paramcd = choices_selected(
        choices = variable_choices(ADLB, "PARAMCD"),
        selected = "PARAMCD"
      ),
      param = choices_selected(
        choices = variable_choices(ADLB, "PARAM"),
        selected = "PARAM"
      ),
      timepoints = choices_selected(
        choices = variable_choices(ADLB, "ADY"),
        selected = "ADY"
      ),
      anrind = choices_selected(
        choices = variable_choices(ADLB, "ANRIND"),
        selected = "ANRIND"
      ),
      aval_var = choices_selected(
        choices = variable_choices(ADLB, "AVAL"),
        selected = "AVAL"
      ),
      avalu_var = choices_selected(
        choices = variable_choices(ADLB, "AVALU"),
        selected = "AVALU"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}