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
)

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.

Value

Object of class teal_module to be used in teal applications.

Examples

library(teal.widgets)

# module specification used in apps below
tm_missing_data_module <- tm_missing_data(
  ggplot2_args = list(
    "Combinations Hist" = ggplot2_args(
      labs = list(subtitle = "Plot produced by Missing Data Module", caption = NULL)
    ),
    "Combinations Main" = ggplot2_args(labs = list(title = NULL))
  )
)
#> [INFO] 2024-03-01 20:55:31.3330 pid:1280 token:[] teal.modules.general Initializing tm_missing_data

# 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"]])
})
datanames(data) <- c("iris", "mtcars")

app <- init(
  data = data,
  modules = modules(tm_missing_data_module)
)
#> Warning: 'package:nestcolor' may not be available when loading
if (interactive()) {
  shinyApp(app$ui, app$server)
}

# CDISC example data
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- rADSL
  ADRS <- rADRS
})
datanames(data) <- c("ADSL", "ADRS")
join_keys(data) <- default_cdisc_join_keys[datanames(data)]

app <- init(
  data = data,
  modules = modules(tm_missing_data_module)
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}