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,
  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

(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.

seq_var

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
Analysis Sequence Number. Used for counting the unique number of events.

hlt

(choices_selected or data_extract_spec)
name of the variable with high level term for events.

llt

(choices_selected or data_extract_spec)
name of the variable with low level term for events.

add_total

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

event_type

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

drop_arm_levels

(logical)
drop the unused arm_var levels. When TRUE, arm_var levels are set to those used in the dataname dataset. When FALSE, arm_var levels are set to those used in the parantname dataset.

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(scda)

ADSL <- synthetic_cdisc_data("latest")$adsl
ADCM <- synthetic_cdisc_data("latest")$adcm
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")

app <- teal::init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'),
    cdisc_dataset("ADCM", ADCM,
      code = 'ADCM <- synthetic_cdisc_data("latest")$adcm',
      keys = adcm_keys
    )
  ),
  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("ASEQ", selected = "ASEQ", 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"
    )
  )
)
#> [INFO] 2022-10-14 09:10:56.3161 pid:3139 token:[] teal.modules.clinical Initializing tm_t_mult_events
if (FALSE) {
shinyApp(app$ui, app$server)
}