Teal Module: SMQ Table

Adverse Events Table by Standardized MedDRA Query.

Usage

tm_t_smq(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
  llt,
  add_total = TRUE,
  sort_criteria = c("freq_desc", "alpha"),
  drop_arm_levels = TRUE,
  na_level = "<Missing>",
  smq_varlabel = "Standardized MedDRA Query",
  baskets,
  scopes,
  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.

id_var

(choices_selected or data_extract_spec)
object specifying the variable name for subject id.

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.

sort_criteria

(character)
how to sort the final table. Default option freq_desc sorts by decreasing total number of patients with event. Alternative option alpha sorts events alphabetically.

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.

na_level

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

smq_varlabel

(character)
label of the new column SMQ created by tern::h_stack_by_baskets().

baskets

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
object with all available choices and preselected options for Standardized/Customized queries

scopes

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
object with all available choices for the scopes of Standardized queries.

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(scda)

synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
adsl <- synthetic_cdisc_data_latest$adsl
adae <- synthetic_cdisc_data_latest$adae

names_baskets <- grep("^(SMQ|CQ).*NAM$", names(adae), value = TRUE)
names_scopes <- grep("^SMQ.*SC$", names(adae), value = TRUE)

cs_baskets <- choices_selected(
  choices = variable_choices(adae, subset = names_baskets),
  selected = names_baskets
)

cs_scopes <- choices_selected(
  choices = variable_choices(adae, subset = names_scopes),
  selected = names_scopes,
  fixed = TRUE
)

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", adsl,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADSL <- synthetic_cdisc_data_latest$adsl"
    ),
    cdisc_dataset("ADAE", adae,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADAE <- synthetic_cdisc_data_latest$adae"
    )
  ),
  modules = modules(
    tm_t_smq(
      label = "Adverse events by `SMQ` Table",
      dataname = "ADAE",
      arm_var = choices_selected(
        choices = variable_choices(adsl, subset = c("ARM", "SEX")),
        selected = "ARM"
      ),
      add_total = FALSE,
      baskets = cs_baskets,
      scopes = cs_scopes,
      llt = choices_selected(
        choices = variable_choices(adae, subset = c("AEDECOD")),
        selected = "AEDECOD"
      )
    )
  )
)
#> [INFO] 2022-10-14 09:11:17.9984 pid:3139 token:[] teal.modules.clinical Initializing tm_t_smq
if (FALSE) {
shinyApp(app$ui, app$server)
}