teal module: Missing data analysis

Usage

tm_missing_data(
  label = "Missing data",
  plot_height = c(600, 400, 5000),
  plot_width = NULL,
  parent_dataname = "ADSL",
  ggtheme = c("classic", "gray", "bw", "linedraw", "light", "dark", "minimal", "void"),
  ggplot2_args = list(`Combinations Hist` = teal.widgets::ggplot2_args(labs =
    list(caption = NULL)), `Combinations Main` = teal.widgets::ggplot2_args(labs =
    list(title = NULL))),
  pre_output = NULL,
  post_output = NULL,
  decorators = NULL
)

Arguments

label

(character(1)) Label shown in the navigation item for the module or module group. For modules() defaults to "root". See Details.

plot_height

(numeric) optional, specifies the plot height as a three-element vector of value, min, and max intended for use with a slider UI element.

plot_width

(numeric) optional, specifies the plot width as a three-element vector of value, min, and max for a slider encoding the plot width.

parent_dataname

(character(1)) Specifies the parent dataset name. Default is ADSL for CDISC data. If provided and exists, enables additional analysis "by subject". For non-CDISC data, this parameter can be ignored.

ggtheme

(character) optional, specifies the default ggplot2 theme for plots. Defaults to classic.

ggplot2_args

(ggplot2_args) optional, object created by teal.widgets::ggplot2_args() with settings for all the plots or named list of ggplot2_args objects for plot-specific settings. The argument is merged with options variable teal.ggplot2_args and default module setup.

List names should match the following: c("default", "Summary Obs", "Summary Patients", "Combinations Main", "Combinations Hist", "By Subject").

For more details see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

pre_output

(shiny.tag) optional, text or UI element to be displayed before the module's output, providing context or a title. with text placed before the output to put the output into context. For example a title.

post_output

(shiny.tag) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like shiny::helpText() are useful.

decorators

(list of teal_transform_module, named list of teal_transform_module or NULL) optional, if not NULL, decorator for tables or plots included in the module. When a named list of teal_transform_module, the decorators are applied to the respective output objects.

Otherwise, the decorators are applied to all objects, which is equivalent as using the name default.

See section "Decorating tm_missing_data" below for more details.

Value

Object of class teal_module to be used in teal applications.

Decorating tm_missing_data

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

• summary_plot (grob created with ggplot2::ggplotGrob())

• combination_plot (grob created with ggplot2::ggplotGrob())

• by_subject_plot (ggplot2)

• table (DT::datatable())

Decorators can be applied to all outputs or only to specific objects using a named list of teal_transform_module objects. The "default" name is reserved for decorators that are applied to all outputs. See code snippet below:

tm_missing_data(
   ..., # arguments for module
   decorators = list(
     default = list(teal_transform_module(...)), # applied to all outputs
     summary_plot = list(teal_transform_module(...)), # applied only to `summary_plot` output
     combination_plot = list(teal_transform_module(...)) # applied only to `combination_plot` output
     by_subject_plot = list(teal_transform_module(...)) # applied only to `by_subject_plot` output
     table = list(teal_transform_module(...)) # applied only to `table` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-modules-output", package = "teal") or the teal::teal_transform_module() documentation.

Examples in Shinylive

example-1

Open in Shinylive

example-2

Open in Shinylive

Examples

# general example data
data <- teal_data()
data <- within(data, {
  require(nestcolor)

  add_nas <- function(x) {
    x[sample(seq_along(x), floor(length(x) * runif(1, .05, .17)))] <- NA
    x
  }

  iris <- iris
  mtcars <- mtcars

  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

app <- init(
  data = data,
  modules = modules(
    tm_missing_data()
  )
)
#> Initializing tm_missing_data
#> Warning: 'package:rlang' may not be available when loading
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}
# CDISC example data
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- teal.data::rADSL
  ADRS <- rADRS
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_missing_data()
  )
)
#> Initializing tm_missing_data
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}