tm_t_tte | R Documentation |
This module produces a time-to-event analysis summary table, consistent with the TLG Catalog
template for TTET01
available here.
tm_t_tte(
label,
dataname,
parentname = ifelse(inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var), "ADSL"),
arm_var,
arm_ref_comp = NULL,
paramcd,
strata_var,
aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
"AVAL"), "AVAL", fixed = TRUE),
cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
"CNSR"), "CNSR", fixed = TRUE),
conf_level_coxph = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order
= TRUE),
conf_level_survfit = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95,
keep_order = TRUE),
time_points,
time_unit_var =
teal.transform::choices_selected(teal.transform::variable_choices(dataname, "AVALU"),
"AVALU", fixed = TRUE),
event_desc_var = teal.transform::choices_selected("EVNTDESC", "EVNTDESC", fixed = TRUE),
add_total = FALSE,
total_label = default_total_label(),
na_level = default_na_str(),
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args(),
transformators = list(),
decorators = list()
)
The core functionality of this module is based on tern::coxph_pairwise()
, tern::surv_timepoint()
,
and tern::surv_time()
from the tern
package.
The arm and stratification variables are taken from the parentname
data.
The following variables are used in the module:
AVAL
: time to event
CNSR
: 1 if record in AVAL
is censored, 0 otherwise
PARAMCD
: variable used to filter for endpoint (e.g. OS). After
filtering for PARAMCD
one observation per patient is expected
a teal_module
object.
This module generates the following objects, which can be modified in place using decorators:
table
(TableTree
- output of rtables::build_table()
)
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_tte( ..., # 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.
The TLG Catalog where additional example apps implementing this module can be found.
data <- teal_data()
data <- within(data, {
ADSL <- tmc_ex_adsl
ADTTE <- tmc_ex_adtte
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]
arm_ref_comp <- list(
ACTARMCD = list(
ref = "ARM B",
comp = c("ARM A", "ARM C")
),
ARM = list(
ref = "B: Placebo",
comp = c("A: Drug X", "C: Combination")
)
)
app <- init(
data = data,
modules = modules(
tm_t_tte(
label = "Time To Event Table",
dataname = "ADTTE",
arm_var = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
arm_ref_comp = arm_ref_comp,
paramcd = choices_selected(
value_choices(ADTTE, "PARAMCD", "PARAM"),
"OS"
),
strata_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
"SEX"
),
time_points = choices_selected(c(182, 243), 182),
event_desc_var = choices_selected(
variable_choices(ADTTE, "EVNTDESC"),
"EVNTDESC",
fixed = TRUE
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
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