Package 'teal.reporter'

Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.
Authors: Dawid Kaledkowski [aut, cre] , Kartikeya Kirar [aut] , Marcin Kosinski [aut], Maciej Nasinski [aut], Konrad Pagacz [aut], Mahmoud Hallal [aut], Chendi Liao [rev], Dony Unardi [rev], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <[email protected]>
License: Apache License 2.0
Version: 0.3.1
Built: 2024-09-15 03:46:42 UTC
Source: https://github.com/insightsengineering/teal.reporter

Help Index

Add card button module

Description

[Experimental]

Provides a button to add views/cards to a report.

For more details see the vignette: vignette("simpleReporter", "teal.reporter").

Usage

add_card_button_ui(id)

add_card_button_srv(id, reporter, card_fun)

Arguments

id

(character(1)) this shiny module's id.
reporter

(Reporter) instance.
card_fun

(function) which returns a ReportCard instance. See Details.

Details

The card_fun function is designed to create a new ReportCard instance and optionally customize it:

  • The card parameter allows for specifying a custom or default ReportCard instance.

  • Use the comment parameter to add a comment to the card via card$append_text() - if card_fun does not have the comment parameter, then comment from ⁠Add Card UI⁠ module will be added at the end of the content of the card.

  • The label parameter enables customization of the card's name and its content through card$append_text()- if card_fun does not have the label parameter, then card name will be set to the name passed in ⁠Add Card UI⁠ module, but no text will be added to the content of the card.

This module supports using a subclass of ReportCard for added flexibility. A subclass instance should be passed as the default value of the card argument in the card_fun function. See below: 

CustomReportCard <- R6::R6Class(
  classname = "CustomReportCard",
  inherit = teal.reporter::ReportCard
)

custom_function <- function(card = CustomReportCard$new()) {
  card
}

Value

NULL.

Parse a named list to yaml header for an Rmd file

Description

[Experimental]

Converts a named list into a yaml header for Rmd, handling output types and arguments as defined in the rmarkdown package. This function simplifies the process of generating yaml headers.

Usage

as_yaml_auto(
  input_list,
  as_header = TRUE,
  convert_logi = TRUE,
  multi_output = FALSE,
  silent = FALSE
)

Arguments

input_list

(⁠named list⁠) non nested with slots names and their values compatible with Rmd yaml header.
as_header

(logical(1)) optionally wrap with result with the internal md_header(), default TRUE.
convert_logi

(logical(1)) convert a character values to logical, if they are recognized as quoted yaml logical values , default TRUE.
multi_output

(logical(1)) multi output slots in the input argument, default FALSE.
silent

(logical(1)) suppress messages and warnings, default FALSE.

Details

This function processes a non-nested (flat) named list into a yaml header for an Rmd document. It supports all standard Rmd yaml header fields, including author, date, title, subtitle, abstract, keywords, subject, description, category, and lang. Additionally, it handles output field types and arguments as defined in the rmarkdown package.

Value

character with rmd_yaml_header class, result of yaml::as.yaml, optionally wrapped with internal md_header().

Note

Only non-nested lists are automatically parsed. Nested lists require direct processing with yaml::as.yaml.

Examples

# nested so using yaml::as.yaml directly
as_yaml_auto(
  list(author = "", output = list(pdf_document = list(toc = TRUE)))
)

# auto parsing for a flat list, like shiny input
input <- list(author = "", output = "pdf_document", toc = TRUE, keep_tex = TRUE)
as_yaml_auto(input)

as_yaml_auto(list(author = "", output = "pdf_document", toc = TRUE, keep_tex = "TRUE"))

as_yaml_auto(list(
  author = "", output = "pdf_document", toc = TRUE, keep_tex = TRUE,
  wrong = 2
))

as_yaml_auto(list(author = "", output = "pdf_document", toc = TRUE, keep_tex = 2),
  silent = TRUE
)

input <- list(author = "", output = "pdf_document", toc = TRUE, keep_tex = "True")
as_yaml_auto(input)
as_yaml_auto(input, convert_logi = TRUE, silent = TRUE)
as_yaml_auto(input, silent = TRUE)
as_yaml_auto(input, convert_logi = FALSE, silent = TRUE)

as_yaml_auto(
  list(
    author = "", output = "pdf_document",
    output = "html_document", toc = TRUE, keep_tex = TRUE
  ),
  multi_output = TRUE
)
as_yaml_auto(
  list(
    author = "", output = "pdf_document",
    output = "html_document", toc = "True", keep_tex = TRUE
  ),
  multi_output = TRUE
)

Download report button module

Description

[Experimental]

Provides a button that triggers downloading a report.

For more information, refer to the vignette: vignette("simpleReporter", "teal.reporter").

Usage

download_report_button_ui(id)

download_report_button_srv(
  id,
  reporter,
  global_knitr = getOption("teal.reporter.global_knitr"),
  rmd_output = c(html = "html_document", pdf = "pdf_document", powerpoint =
    "powerpoint_presentation", word = "word_document"),
  rmd_yaml_args = list(author = "NEST", title = "Report", date =
    as.character(Sys.Date()), output = "html_document", toc = FALSE)
)

Arguments

id

(character(1)) this shiny module's id.
reporter

(Reporter) instance.
global_knitr

(list) of knitr parameters (passed to knitr::opts_chunk$set) for customizing the rendering process.
rmd_output

(character) vector with rmarkdown output types, by default all possible pdf_document, html_document, powerpoint_presentation, and word_document. If vector is named then those names will appear in the UI.
rmd_yaml_args

(⁠named list⁠) with Rmd yaml header fields and their default values. This list will result in the custom subset of UI inputs for the download reporter functionality. Default list(author = "NEST", title = "Report", date = Sys.Date(), output = "html_document", toc = FALSE). The list must include at least "output" field. The default value for "output" has to be in the rmd_output argument.

Details

To access the default values for the global_knitr parameter, use getOption('teal.reporter.global_knitr'). These defaults include:

  • echo = TRUE

  • tidy.opts = list(width.cutoff = 60)

  • tidy = TRUE if formatR package is installed, FALSE otherwise

Value

NULL.

Print method for the yaml_header class

Description

[Experimental]

Usage

## S3 method for class 'rmd_yaml_header'
print(x, ...)

Arguments

x

(rmd_yaml_header) class object.
...

optional text.

Value

NULL.

Examples

input <- list(author = "", output = "pdf_document", toc = TRUE, keep_tex = TRUE)
out <- as_yaml_auto(input)
out
print(out)

ReportCard: An R6 class for building report elements

Description

[Experimental]

This R6 class that supports creating a report card containing text, plot, table and metadata blocks that can be appended and rendered to form a report output from a shiny app.

Methods

Public methods

Method new()

Initialize a ReportCard object.

Usage
ReportCard$new()
Returns

Object of class ReportCard, invisibly.

Examples
card <- ReportCard$new()

Method append_table()

Appends a table to this ReportCard.

Usage
ReportCard$append_table(table)
Arguments
table

A (data.frame or rtables or TableTree or ElementaryTable or listing_df) that can be coerced into a table.

Returns

self, invisibly.

Examples
card <- ReportCard$new()$append_table(iris)

Method append_plot()

Appends a plot to this ReportCard.

Usage
ReportCard$append_plot(plot, dim = NULL)
Arguments
plot

(ggplot or grob or trellis) plot object.

dim

(numeric(2)) width and height in pixels.

Returns

self, invisibly.

Examples
library(ggplot2)

card <- ReportCard$new()$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

Method append_text()

Appends a text paragraph to this ReportCard.

Usage
ReportCard$append_text(text, style = TextBlock$new()$get_available_styles()[1])
Arguments
text

(character) The text content to add.

style

(character(1)) the style of the paragraph. One of: default, header, verbatim

Returns

self, invisibly.

Examples
card <- ReportCard$new()$append_text("A paragraph of default text")

Method append_rcode()

Appends an R code chunk to ReportCard.

Usage
ReportCard$append_rcode(text, ...)
Arguments
text

(character) The R code to include.

...

Additional rmarkdown parameters for formatting the R code chunk.

Returns

self, invisibly.

Examples
card <- ReportCard$new()$append_rcode("2+2", echo = FALSE)

Method append_content()

Appends a generic ContentBlock to this ReportCard.

Usage
ReportCard$append_content(content)
Arguments
content

(ContentBlock) object.

Returns

self, invisibly.

Examples
NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter")
card <- ReportCard$new()$append_content(NewpageBlock$new())

Method get_content()

Get all content blocks from this ReportCard.

Usage
ReportCard$get_content()
Returns

list() list of TableBlock, TextBlock and PictureBlock.

Examples
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2")

card$get_content()

Method reset()

Clears all content and metadata from ReportCard.

Usage
ReportCard$reset()
Returns

self, invisibly.

Method get_metadata()

Get the metadata associated with ReportCard.

Usage
ReportCard$get_metadata()
Returns

⁠named list⁠ list of elements.

Examples
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2")

card$get_metadata()

Method append_metadata()

Appends metadata to this ReportCard.

Usage
ReportCard$append_metadata(key, value)
Arguments
key

(character(1)) string specifying the metadata key.

value

value associated with the metadata key.

Returns

self, invisibly.

Examples
library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()
card$get_metadata()

Method get_name()

Get the name of the ReportCard.

Usage
ReportCard$get_name()
Returns

character a card name.

Examples
ReportCard$new()$set_name("NAME")$get_name()

Method set_name()

Set the name of the ReportCard.

Usage
ReportCard$set_name(name)
Arguments
name

(character(1)) a card name.

Returns

self, invisibly.

Examples
ReportCard$new()$set_name("NAME")$get_name()

Method to_list()

Convert the ReportCard to a list, including content and metadata.

Usage
ReportCard$to_list(output_dir)
Arguments
output_dir

(character) with a path to the directory where files will be copied.

Returns

(⁠named list⁠) a ReportCard representation.

Examples
library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()

card$to_list(tempdir())

Method from_list()

Reconstructs the ReportCard from a list representation.

Usage
ReportCard$from_list(card, output_dir)
Arguments
card

(⁠named list⁠) a ReportCard representation.

output_dir

(character) with a path to the directory where a file will be copied.

Returns

self, invisibly.

Examples
library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()

ReportCard$new()$from_list(card$to_list(tempdir()), tempdir())

Method clone()

The objects of this class are cloneable with this method.

Usage
ReportCard$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `ReportCard$new`
## ------------------------------------------------

card <- ReportCard$new()


## ------------------------------------------------
## Method `ReportCard$append_table`
## ------------------------------------------------

card <- ReportCard$new()$append_table(iris)


## ------------------------------------------------
## Method `ReportCard$append_plot`
## ------------------------------------------------

library(ggplot2)

card <- ReportCard$new()$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)


## ------------------------------------------------
## Method `ReportCard$append_text`
## ------------------------------------------------

card <- ReportCard$new()$append_text("A paragraph of default text")


## ------------------------------------------------
## Method `ReportCard$append_rcode`
## ------------------------------------------------

card <- ReportCard$new()$append_rcode("2+2", echo = FALSE)


## ------------------------------------------------
## Method `ReportCard$append_content`
## ------------------------------------------------

NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter")
card <- ReportCard$new()$append_content(NewpageBlock$new())


## ------------------------------------------------
## Method `ReportCard$get_content`
## ------------------------------------------------

card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2")

card$get_content()



## ------------------------------------------------
## Method `ReportCard$get_metadata`
## ------------------------------------------------

card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2")

card$get_metadata()


## ------------------------------------------------
## Method `ReportCard$append_metadata`
## ------------------------------------------------

library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()
card$get_metadata()


## ------------------------------------------------
## Method `ReportCard$get_name`
## ------------------------------------------------

ReportCard$new()$set_name("NAME")$get_name()

## ------------------------------------------------
## Method `ReportCard$set_name`
## ------------------------------------------------

ReportCard$new()$set_name("NAME")$get_name()

## ------------------------------------------------
## Method `ReportCard$to_list`
## ------------------------------------------------

library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()

card$to_list(tempdir())


## ------------------------------------------------
## Method `ReportCard$from_list`
## ------------------------------------------------

library(ggplot2)

card <- ReportCard$new()$append_text("Some text")$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)$append_text("Some text")$append_metadata(key = "lm",
                  value = lm(Ozone ~ Solar.R, airquality))
card$get_content()

ReportCard$new()$from_list(card$to_list(tempdir()), tempdir())

Reporter: An R6 class for managing report cards

Description

[Experimental]

This R6 class is designed to store and manage report cards, facilitating the creation, manipulation, and serialization of report-related data.

Methods

Public methods

Method new()

Initialize a Reporter object.

Usage
Reporter$new()
Returns

Object of class Reporter, invisibly.

Examples
reporter <- Reporter$new()

Method append_cards()

Append one or more ReportCard objects to the Reporter.

Usage
Reporter$append_cards(cards)
Arguments
cards

(ReportCard) or a list of such objects

Returns

self, invisibly.

Examples
library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))

Method get_cards()

Retrieves all ReportCard objects contained in the Reporter.

Usage
Reporter$get_cards()
Returns

A (list) of ReportCard objects.

Examples
library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
 ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))
reporter$get_cards()

Method get_blocks()

Compiles and returns all content blocks from the ReportCard in the Reporter.

Usage
Reporter$get_blocks(sep = NewpageBlock$new())
Arguments
sep

An optional separator to insert between each content block. Default is a NewpageBlock$new()object.

Returns

list() list of TableBlock, TextBlock, PictureBlock and NewpageBlock.

Examples
library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
 ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))
reporter$get_blocks()

Method reset()

Resets the Reporter, removing all ReportCard objects and metadata.

Usage
Reporter$reset()
Returns

self, invisibly.

Method remove_cards()

Removes specific ReportCard objects from the Reporter by their indices.

Usage
Reporter$remove_cards(ids = NULL)
Arguments
ids

(integer(id)) the indexes of cards

Returns

self, invisibly.

Method swap_cards()

Swaps the positions of two ReportCard objects within the Reporter.

Usage
Reporter$swap_cards(start, end)
Arguments
start

(integer) the index of the first card

end

(integer) the index of the second card

Returns

self, invisibly.

Method get_reactive_add_card()

Gets the current value of the reactive variable for adding cards.

Usage
Reporter$get_reactive_add_card()
Returns

reactive_add_card current numeric value of the reactive variable.

Examples
library(shiny)

isolate(Reporter$new()$get_reactive_add_card())

Method get_metadata()

Get the metadata associated with this Reporter.

Usage
Reporter$get_metadata()
Returns

⁠named list⁠ of metadata to be appended.

Examples
reporter <- Reporter$new()$append_metadata(list(sth = "sth"))
reporter$get_metadata()

Method append_metadata()

Appends metadata to this Reporter.

Usage
Reporter$append_metadata(meta)
Arguments
meta

(⁠named list⁠) of metadata to be appended.

Returns

self, invisibly.

Examples
reporter <- Reporter$new()$append_metadata(list(sth = "sth"))
reporter$get_metadata()

Method from_reporter()

Reinitializes a Reporter instance by copying the report cards and metadata from another Reporter.

Usage
Reporter$from_reporter(reporter)
Arguments
reporter

(Reporter) instance to copy from.

Returns

self, invisibly.

Examples
reporter <- Reporter$new()
reporter$from_reporter(reporter)

Method to_list()

Convert a Reporter to a list and transfer any associated files to specified directory.

Usage
Reporter$to_list(output_dir)
Arguments
output_dir

(character(1)) a path to the directory where files will be copied.

Returns

⁠named list⁠ representing the Reporter instance, including version information, metadata, and report cards.

Examples
reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "testdir")
dir.create(tmp_dir)
reporter$to_list(tmp_dir)

Method from_list()

Reinitializes a Reporter from a list representation and associated files in a specified directory.

Usage
Reporter$from_list(rlist, output_dir)
Arguments
rlist

(⁠named list⁠) representing a Reporter instance.

output_dir

(character(1)) a path to the directory from which files will be copied.

Returns

self, invisibly.

Examples
reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "testdir")
unlink(tmp_dir, recursive = TRUE)
dir.create(tmp_dir)
reporter$from_list(reporter$to_list(tmp_dir), tmp_dir)

Method to_jsondir()

Serializes the Reporter to a JSON file and copies any associated files to a specified directory.

Usage
Reporter$to_jsondir(output_dir)
Arguments
output_dir

(character(1)) a path to the directory where files will be copied, JSON and statics.

Returns

output_dir argument.

Examples
reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "jsondir")
dir.create(tmp_dir)
reporter$to_jsondir(tmp_dir)

Method from_jsondir()

Reinitializes a Reporter from a JSON file and files in a specified directory.

Usage
Reporter$from_jsondir(output_dir)
Arguments
output_dir

(character(1)) a path to the directory with files, JSON and statics.

Returns

self, invisibly.

Examples
reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "jsondir")
dir.create(tmp_dir)
unlink(list.files(tmp_dir, recursive = TRUE))
reporter$to_jsondir(tmp_dir)
reporter$from_jsondir(tmp_dir)

Method clone()

The objects of this class are cloneable with this method.

Usage
Reporter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

The function has to be used in the shiny reactive context.

Examples

## ------------------------------------------------
## Method `Reporter$new`
## ------------------------------------------------

reporter <- Reporter$new()


## ------------------------------------------------
## Method `Reporter$append_cards`
## ------------------------------------------------

library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))

## ------------------------------------------------
## Method `Reporter$get_cards`
## ------------------------------------------------

library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
 ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))
reporter$get_cards()

## ------------------------------------------------
## Method `Reporter$get_blocks`
## ------------------------------------------------

library(ggplot2)
library(rtables)

card1 <- ReportCard$new()

card1$append_text("Header 2 text", "header2")
card1$append_text("A paragraph of default text", "header2")
card1$append_plot(
 ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
)

card2 <- ReportCard$new()

card2$append_text("Header 2 text", "header2")
card2$append_text("A paragraph of default text", "header2")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)
card2$append_table(iris)

reporter <- Reporter$new()
reporter$append_cards(list(card1, card2))
reporter$get_blocks()


## ------------------------------------------------
## Method `Reporter$get_reactive_add_card`
## ------------------------------------------------

library(shiny)

isolate(Reporter$new()$get_reactive_add_card())

## ------------------------------------------------
## Method `Reporter$get_metadata`
## ------------------------------------------------

reporter <- Reporter$new()$append_metadata(list(sth = "sth"))
reporter$get_metadata()


## ------------------------------------------------
## Method `Reporter$append_metadata`
## ------------------------------------------------

reporter <- Reporter$new()$append_metadata(list(sth = "sth"))
reporter$get_metadata()


## ------------------------------------------------
## Method `Reporter$from_reporter`
## ------------------------------------------------

reporter <- Reporter$new()
reporter$from_reporter(reporter)

## ------------------------------------------------
## Method `Reporter$to_list`
## ------------------------------------------------

reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "testdir")
dir.create(tmp_dir)
reporter$to_list(tmp_dir)

## ------------------------------------------------
## Method `Reporter$from_list`
## ------------------------------------------------

reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "testdir")
unlink(tmp_dir, recursive = TRUE)
dir.create(tmp_dir)
reporter$from_list(reporter$to_list(tmp_dir), tmp_dir)

## ------------------------------------------------
## Method `Reporter$to_jsondir`
## ------------------------------------------------

reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "jsondir")
dir.create(tmp_dir)
reporter$to_jsondir(tmp_dir)

## ------------------------------------------------
## Method `Reporter$from_jsondir`
## ------------------------------------------------

reporter <- Reporter$new()
tmp_dir <- file.path(tempdir(), "jsondir")
dir.create(tmp_dir)
unlink(list.files(tmp_dir, recursive = TRUE))
reporter$to_jsondir(tmp_dir)
reporter$from_jsondir(tmp_dir)

Report previewer module

Description

[Experimental]

Module offers functionalities to visualize, manipulate, and interact with report cards that have been added to a report. It includes a previewer interface to see the cards and options to modify the report before downloading.

For more details see the vignette: vignette("previewerReporter", "teal.reporter").

Usage

reporter_previewer_ui(id)

reporter_previewer_srv(
  id,
  reporter,
  global_knitr = getOption("teal.reporter.global_knitr"),
  rmd_output = c(html = "html_document", pdf = "pdf_document", powerpoint =
    "powerpoint_presentation", word = "word_document"),
  rmd_yaml_args = list(author = "NEST", title = "Report", date =
    as.character(Sys.Date()), output = "html_document", toc = FALSE)
)

Arguments

id

(character(1)) shiny module instance id.
reporter

(Reporter) instance.
global_knitr

(list) of knitr parameters (passed to knitr::opts_chunk$set) for customizing the rendering process.
rmd_output

(character) vector with rmarkdown output types, by default all possible pdf_document, html_document, powerpoint_presentation, and word_document. If vector is named then those names will appear in the UI.
rmd_yaml_args

(⁠named list⁠) with Rmd yaml header fields and their default values. This list will result in the custom subset of UI inputs for the download reporter functionality. Default list(author = "NEST", title = "Report", date = Sys.Date(), output = "html_document", toc = FALSE). The list must include at least "output" field. The default value for "output" has to be in the rmd_output argument.

Details

To access the default values for the global_knitr parameter, use getOption('teal.reporter.global_knitr'). These defaults include:

  • echo = TRUE

  • tidy.opts = list(width.cutoff = 60)

  • tidy = TRUE if formatR package is installed, FALSE otherwise

Value

NULL.

Reset report button module

Description

[Experimental]

Provides a button that triggers resetting the report content.

For more information, refer to the vignette: vignette("simpleReporter", "teal.reporter").

Usage

reset_report_button_ui(id, label = NULL)

reset_report_button_srv(id, reporter)

Arguments

id

(character(1)) shiny module instance id.
label

(character(1)) label before the icon. By default NULL.
reporter

(Reporter) instance.

Value

NULL.

Get document output arguments from the rmarkdown package

Description

[Experimental]

Retrieves the arguments for a specified document output type from the rmarkdown package.

Usage

rmd_output_arguments(output_name, default_values = FALSE)

Arguments

output_name

(character) rmarkdown output name.
default_values

(logical(1)) if to return a default values for each argument.

Examples

rmd_output_arguments("pdf_document")
rmd_output_arguments("pdf_document", TRUE)

Get document output types from the rmarkdown package

Description

[Experimental]

Retrieves vector of available document output types from the rmarkdown package, such as pdf_document, html_document, etc.

Usage

rmd_outputs()

Value

character vector.

Examples

rmd_outputs()

Simple reporter module

Description

[Experimental]

Module provides compact UI and server functions for managing a report in a shiny app. This module combines functionalities for adding cards to a report, downloading the report, and resetting report content.

For more details see the vignette: vignette("simpleReporter", "teal.reporter").

Usage

simple_reporter_ui(id)

simple_reporter_srv(
  id,
  reporter,
  card_fun,
  global_knitr = getOption("teal.reporter.global_knitr"),
  rmd_output = c(html = "html_document", pdf = "pdf_document", powerpoint =
    "powerpoint_presentation", word = "word_document"),
  rmd_yaml_args = list(author = "NEST", title = "Report", date =
    as.character(Sys.Date()), output = "html_document", toc = FALSE)
)

Arguments

id

(character(1)) shiny module instance id.
reporter

(Reporter) instance.
card_fun

(function) which returns a ReportCard instance, the function has a card argument and an optional comment argument.
global_knitr

(list) a global knitr parameters for customizing the rendering process.
rmd_output

(character) vector with rmarkdown output types, by default all possible pdf_document, html_document, powerpoint_presentation, and word_document. If vector is named then those names will appear in the UI.
rmd_yaml_args

(⁠named list⁠) with Rmd yaml header fields and their default values. This list will result in the custom subset of UI inputs for the download reporter functionality. Default list(author = "NEST", title = "Report", date = Sys.Date(), output = "html_document", toc = FALSE). The list must include at least "output" field. The default value for "output" has to be in the rmd_output argument.

Details

To access the default values for the global_knitr parameter, use getOption('teal.reporter.global_knitr'). These defaults include:

  • echo = TRUE

  • tidy.opts = list(width.cutoff = 60)

  • tidy = TRUE if formatR package is installed, FALSE otherwise

Value

NULL.

Examples

library(shiny)
if (interactive()) {
  shinyApp(
    ui = fluidPage(simple_reporter_ui("simple")),
    server = function(input, output, session) {
      simple_reporter_srv("simple", Reporter$new(), function(card) card)
    }
  )
}