This module produces a summary table of worst grades per subject by visit and parameter.
Usage
tm_t_shift_by_grade(
label,
dataname,
parentname = ifelse(inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var), "ADSL"),
arm_var,
visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
subset = "AVISIT"), selected = "AVISIT", fixed = TRUE),
paramcd,
worst_flag_var =
teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")), selected = "WGRLOVFL"),
worst_flag_indicator =
teal.transform::choices_selected(teal.transform::value_choices(dataname, "WGRLOVFL"),
selected = "Y", fixed = TRUE),
anl_toxgrade_var =
teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
c("ATOXGR")), selected = c("ATOXGR"), fixed = TRUE),
base_toxgrade_var =
teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =
c("BTOXGR")), selected = c("BTOXGR"), fixed = TRUE),
id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
subset = "USUBJID"), selected = "USUBJID", fixed = TRUE),
add_total = FALSE,
total_label = default_total_label(),
drop_arm_levels = TRUE,
pre_output = NULL,
post_output = NULL,
na_level = default_na_str(),
code_missing_baseline = FALSE,
basic_table_args = teal.widgets::basic_table_args(),
transformators = list(),
decorators = list()
)
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 toADSL
.- arm_var
(
teal.transform::choices_selected()
)
object with all available choices and preselected option for variable names that can be used asarm_var
. It defines the grouping variable in the results table.- visit_var
(
teal.transform::choices_selected()
)
object with all available choices and preselected option for variable names that can be used asvisit
variable. Must be a factor indataname
.- paramcd
(
teal.transform::choices_selected()
)
object with all available choices and preselected option for the parameter code variable fromdataname
.- worst_flag_var
(
teal.transform::choices_selected()
)
object with all available choices and preselected option for variable names that can be used as worst flag variable.- worst_flag_indicator
(
teal.transform::choices_selected()
)
value indicating worst grade.- anl_toxgrade_var
(
teal.transform::choices_selected()
)
variable for analysis toxicity grade.- base_toxgrade_var
(
teal.transform::choices_selected()
)
variable for baseline toxicity grade.- id_var
(
teal.transform::choices_selected()
)
object specifying the variable name for subject id.- add_total
(
logical
)
whether to include column with total number of patients.- total_label
(
string
)
string to display as total column/row label if column/row is enabled (seeadd_total
). Defaults to"All Patients"
. To set a new defaulttotal_label
to apply in all modules, runset_default_total_label("new_default")
.- drop_arm_levels
(
logical
)
whether to drop unused levels ofarm_var
. IfTRUE
,arm_var
levels are set to those used in thedataname
dataset. IfFALSE
,arm_var
levels are set to those used in theparentname
dataset. Ifdataname
andparentname
are the same, thendrop_arm_levels
is set toTRUE
and user input for this parameter is ignored.- 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 theshiny::helpText()
elements are useful.- na_level
(
string
)
used to replace allNA
or empty values in character or factor variables in the data. Defaults to"<Missing>"
. To set a defaultna_level
to apply in all modules, runset_default_na_str("new_default")
.- code_missing_baseline
(
logical
)
whether missing baseline grades should be counted as grade 0.- basic_table_args
(
basic_table_args
) optional
object created byteal.widgets::basic_table_args()
with settings for the module table. The argument is merged with optionteal.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")
.- transformators
(
list
ofteal_transform_module
) that will be applied to transform module's data input. To learn more checkvignette("transform-input-data", package = "teal")
.- decorators
-
(named
list
of lists ofteal_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
(TableTree
- output ofrtables::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_shift_by_grade(
..., # 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.
See also
The TLG Catalog where additional example apps implementing this module can be found.
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_shift_by_grade(
label = "Grade Laboratory Abnormality Table",
dataname = "ADLB",
arm_var = choices_selected(
choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
selected = "ARM"
),
paramcd = choices_selected(
choices = value_choices(ADLB, "PARAMCD", "PARAM"),
selected = "ALT"
),
worst_flag_var = choices_selected(
choices = variable_choices(ADLB, subset = c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")),
selected = c("WGRLOVFL")
),
worst_flag_indicator = choices_selected(
value_choices(ADLB, "WGRLOVFL"),
selected = "Y", fixed = TRUE
),
anl_toxgrade_var = choices_selected(
choices = variable_choices(ADLB, subset = c("ATOXGR")),
selected = c("ATOXGR"),
fixed = TRUE
),
base_toxgrade_var = choices_selected(
choices = variable_choices(ADLB, subset = c("BTOXGR")),
selected = c("BTOXGR"),
fixed = TRUE
),
add_total = FALSE
)
),
filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y"))
)
#> Initializing tm_t_shift_by_grade
if (interactive()) {
shinyApp(app$ui, app$server)
}