Package 'teal.reporter' reference manual

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:	0.3.1.9021
Built:	2024-12-17 12:40:30 UTC
Source:	https://github.com/insightsengineering/teal.reporter

Add card button module

Description

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)
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

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
)
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
)
# 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

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)
)
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

Usage

## S3 method for class 'rmd_yaml_header'
print(x, ...)
## 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)
input <- list(author = "", output = "pdf_document", toc = TRUE, keep_tex = TRUE)
out <- as_yaml_auto(input)
out
print(out)

Server to Load `Reporter`

Description

Server to load ReporterCard(s) to the Reporter

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

Usage

report_load_srv(id, reporter)
report_load_srv(id, reporter)

Arguments

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

Value

shiny::moduleServer

User Interface to Load `Reporter`

Description

Button to upload ReporterCard(s) to the Reporter.

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

Usage

report_load_ui(id)
report_load_ui(id)

Arguments

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

Value

shiny::tagList

`ReportCard`: An `R6` class for building report elements

Description

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.

For more information about the various blocks, refer to the vignette: vignette("teal-reporter-blocks-overview", "teal.reporter").

Methods

Public methods

ReportCard$new()
ReportCard$append_table()
ReportCard$append_html()
ReportCard$append_plot()
ReportCard$append_text()
ReportCard$append_rcode()
ReportCard$append_content()
ReportCard$get_content()
ReportCard$reset()
ReportCard$get_metadata()
ReportCard$append_metadata()
ReportCard$get_name()
ReportCard$set_name()
ReportCard$to_list()
ReportCard$from_list()
ReportCard$clone()

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_html()`

Appends a html content to this ReportCard.

Usage

ReportCard$append_html(content)

Arguments

content: An object that can be rendered as a HTML content.

Returns

self, invisibly.

Examples

card <- ReportCard$new()$append_html(shiny::div("HTML Content"))

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.

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.

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.

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.

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


library(ggplot2)

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


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()


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())


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

card <- ReportCard$new()


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

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


## ------------------------------------------------
## Method `ReportCard$append_html`
## ------------------------------------------------

card <- ReportCard$new()$append_html(shiny::div("HTML Content"))


## ------------------------------------------------
## 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$get_name`
## ------------------------------------------------

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

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

ReportCard$new()$set_name("NAME")$get_name()
library(ggplot2)

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


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()


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())


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

card <- ReportCard$new()


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

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


## ------------------------------------------------
## Method `ReportCard$append_html`
## ------------------------------------------------

card <- ReportCard$new()$append_html(shiny::div("HTML Content"))


## ------------------------------------------------
## 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$get_name`
## ------------------------------------------------

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

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

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

`Reporter`: An `R6` class for managing report cards

Description

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

Methods

Public methods

Reporter$new()
Reporter$append_cards()
Reporter$get_cards()
Reporter$get_blocks()
Reporter$reset()
Reporter$remove_cards()
Reporter$swap_cards()
Reporter$get_reactive_add_card()
Reporter$get_metadata()
Reporter$append_metadata()
Reporter$from_reporter()
Reporter$to_list()
Reporter$from_list()
Reporter$to_jsondir()
Reporter$from_jsondir()
Reporter$set_id()
Reporter$get_id()
Reporter$clone()

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.

Method `get_cards()`

Retrieves all ReportCard objects contained in the Reporter.

Usage

Reporter$get_cards()

Returns

A (list) of ReportCard objects.

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.

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

invisibly self

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 `set_id()`

Set the Reporter id Optionally add id to a Reporter which will be compared when it is rebuilt from a list. The id is added to the downloaded file name.

Usage

Reporter$set_id(id)

Arguments

id: (character(1)) a Report id.

Returns

self, invisibly.

Method `get_id()`

Get the Reporter id

Usage

Reporter$get_id()

Returns

character(1) the Reporter id.

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.

if Report has an id when converting to JSON then It will be compared to the currently available one.

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))


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()


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$new`
## ------------------------------------------------

reporter <- Reporter$new()


## ------------------------------------------------
## 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)
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))


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()


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$new`
## ------------------------------------------------

reporter <- Reporter$new()


## ------------------------------------------------
## 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

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.

Cards are saved by the shiny bookmarking mechanism.

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),
  previewer_buttons = c("download", "load", "reset")
)
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),
  previewer_buttons = c("download", "load", "reset")
)

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.
`previewer_buttons`	(`character`) set of modules to include with `c("download", "load", "reset")` possible values and `"download"` is required. Default `c("download", "load", "reset")`

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

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)
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

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

Usage

rmd_output_arguments(output_name, default_values = FALSE)
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)
rmd_output_arguments("pdf_document")
rmd_output_arguments("pdf_document", TRUE)

Get document output types from the `rmarkdown` package

Description

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

Usage

rmd_outputs()
rmd_outputs()

Value

character vector.

Examples

rmd_outputs()
rmd_outputs()

Simple reporter module

Description

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)
)
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

if (interactive()) {
  library(shiny)

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

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

Package 'teal.reporter'

Help Index

Add card button module

Description

Usage

Arguments

Details

Value

Parse a named list to yaml header for an Rmd file

Description

Usage

Arguments

Details

Value

Note

Examples

Download report button module

Description

Usage

Arguments

Details

Value

Print method for the yaml_header class

Description

Usage

Arguments

Value

Examples

Server to Load Reporter

Description

Usage

Arguments

Value

User Interface to Load Reporter

Description

Usage

Arguments

Value

ReportCard: An R6 class for building report elements

Description

Methods

Public methods

Method new()

Usage

Returns

Examples

Method append_table()

Usage

Arguments

Returns

Examples

Method append_html()

Usage

Arguments

Returns

Examples

Method append_plot()

Usage

Arguments

Returns

Method append_text()

Usage

Arguments

Returns

Examples

Method append_rcode()

Usage

Arguments

Returns

Examples

Method append_content()

Usage

Arguments

Returns

Examples

Method get_content()

Usage

Returns

Examples

Method reset()

Parse a named list to `yaml` header for an `Rmd` file

Print method for the `yaml_header` class

Server to Load `Reporter`

User Interface to Load `Reporter`

`ReportCard`: An `R6` class for building report elements

Method `new()`

Method `append_table()`

Method `append_html()`

Method `append_plot()`

Method `append_text()`

Method `append_rcode()`

Method `append_content()`

Method `get_content()`

Method `reset()`

Method `get_metadata()`

Method `append_metadata()`

Method `get_name()`

Method `set_name()`

Method `to_list()`

Method `from_list()`

Method `clone()`

`Reporter`: An `R6` class for managing report cards

Method `new()`

Method `append_cards()`

Method `get_cards()`

Method `get_blocks()`

Method `reset()`

Method `remove_cards()`

Method `swap_cards()`

Method `get_reactive_add_card()`

Method `get_metadata()`

Method `append_metadata()`