Help for package teal.reporter

Title:

Reporting Tools for 'shiny' Modules

Version:

0.4.0

Date:

2025-01-22

Description:

Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.

License:

Apache License 2.0

URL:

https://github.com/insightsengineering/teal.reporter, https://insightsengineering.github.io/teal.reporter/

BugReports:

https://github.com/insightsengineering/teal.reporter/issues

Imports:

bslib, checkmate (≥ 2.1.0), flextable (≥ 0.9.2), grid, htmltools (≥ 0.5.4), knitr (≥ 1.42), lifecycle (≥ 0.2.0), R6, rlistings (≥ 0.2.10), rmarkdown (≥ 2.23), rtables (≥ 0.6.11), rtables.officer (≥ 0.0.2), shiny (≥ 1.6.0), shinybusy (≥ 0.3.2), shinyWidgets (≥ 0.5.1), yaml (≥ 1.1.0), zip (≥ 1.1.0)

Suggests:

DT (≥ 0.13), formatR (≥ 1.5), formatters (≥ 0.5.10), ggplot2 (≥ 3.4.3), lattice (≥ 0.18-4), png, testthat (≥ 3.2.2), tinytex, withr (≥ 2.0.0)

VignetteBuilder:

knitr, rmarkdown

RdMacros:

lifecycle

Config/Needs/verdepcheck:

rstudio/bslib, mllg/checkmate, davidgohel/flextable, rstudio/htmltools, yihui/knitr, r-lib/lifecycle, r-lib/R6, insightsengineering/rlistings, rstudio/rmarkdown, insightsengineering/rtables, insightsengineering/rtables.officer, rstudio/shiny, dreamRs/shinybusy, dreamRs/shinyWidgets, yaml=vubiostat/r-yaml, r-lib/zip, rstudio/DT, yihui/formatR, insightsengineering/formatters, tidyverse/ggplot2, deepayan/lattice, cran/png, r-lib/testthat, rstudio/tinytex, r-lib/withr

Config/Needs/website:

insightsengineering/nesttemplate

Encoding:

UTF-8

Language:

en-US

RoxygenNote:

7.3.2

NeedsCompilation:

Packaged:

2025-01-24 17:56:27 UTC; unardid

Author:

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 <dawid.kaledkowski@roche.com>

Repository:

CRAN

Date/Publication:

2025-01-24 19:10:02 UTC

Reporting tools for `shiny` modules.

Description

A collection of tools for creating, previewing and modifying reports from shiny modules.

Author(s)

Maintainer: Dawid Kaledkowski dawid.kaledkowski@roche.com (ORCID)

Authors:

Kartikeya Kirar kartikeya.kirar@businesspartner.roche.com (ORCID)
Marcin Kosinski marcin.kosinski.mk1@roche.com
Maciej Nasinski
Konrad Pagacz
Mahmoud Hallal mahmoud.hallal@roche.com

Other contributors:

Chendi Liao chendi.liao@roche.com [reviewer]
Dony Unardi unardid@gene.com [reviewer]
F. Hoffmann-La Roche AG [copyright holder, funder]

`ContentBlock`: A building block for report content

Description

This class represents a basic content unit in a report, such as text, images, or other multimedia elements. It serves as a foundation for constructing complex report structures.

Methods

Method `set_content()`

Sets content of this ContentBlock.

Usage

ContentBlock$set_content(content)

Arguments

content: (any) R object

Returns

self, invisibly.

Examples

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$set_content("Base64 encoded picture")

Method `get_content()`

Retrieves the content assigned to this block.

Usage

ContentBlock$get_content()

Returns

object stored in a private$content field

Examples

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$get_content()

Method `from_list()`

Create the ContentBlock from a list.

Usage

ContentBlock$from_list(x)

Arguments

x: (⁠named list⁠) with two fields text and style. Use the get_available_styles method to get all possible styles.

Returns

self, invisibly.

Method `to_list()`

Convert the ContentBlock to a list.

Usage

ContentBlock$to_list()

Returns

⁠named list⁠ with a text and style.

Method `clone()`

The objects of this class are cloneable with this method.

Usage

ContentBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `ContentBlock$set_content`
## ------------------------------------------------

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$set_content("Base64 encoded picture")


## ------------------------------------------------
## Method `ContentBlock$get_content`
## ------------------------------------------------

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$get_content()

`FileBlock`

Description

FileBlock manages file-based content in a report, ensuring appropriate handling of content files.

Super class

teal.reporter::ContentBlock -> FileBlock

Methods

Public methods

FileBlock$finalize()
FileBlock$from_list()
FileBlock$to_list()
FileBlock$clone()

Inherited methods

Method `finalize()`

Finalize the FileBlock.

Usage

FileBlock$finalize()

Details

Removes the temporary file created in the constructor.

Method `from_list()`

Create the FileBlock from a list. The list should contain one named field, "basename".

Usage

FileBlock$from_list(x, output_dir)

Arguments

x: (⁠named list⁠) with one field "basename", a name of the file.
output_dir: (character) with a path to the directory where a file will be copied.

Returns

self, invisibly.

Examples

FileBlock <- getFromNamespace("FileBlock", "teal.reporter")
block <- FileBlock$new()
file_path <- tempfile(fileext = ".png")
saveRDS(iris, file_path)
block$from_list(list(basename = basename(file_path)), dirname(file_path))

Method `to_list()`

Convert the FileBlock to a list.

Usage

FileBlock$to_list(output_dir)

Arguments

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

Returns

⁠named list⁠ with a basename of the file.

Examples

FileBlock <- getFromNamespace("FileBlock", "teal.reporter")
block <- FileBlock$new()
block$to_list(tempdir())

Method `clone()`

The objects of this class are cloneable with this method.

Usage

FileBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `FileBlock$from_list`
## ------------------------------------------------

FileBlock <- getFromNamespace("FileBlock", "teal.reporter")
block <- FileBlock$new()
file_path <- tempfile(fileext = ".png")
saveRDS(iris, file_path)
block$from_list(list(basename = basename(file_path)), dirname(file_path))


## ------------------------------------------------
## Method `FileBlock$to_list`
## ------------------------------------------------

FileBlock <- getFromNamespace("FileBlock", "teal.reporter")
block <- FileBlock$new()
block$to_list(tempdir())

`HTMLBlock`

Description

Specialized FileBlock for managing HTML content in reports. It's designed to handle various HTML content, and render the report as HTML, however htmlwidgets objects can also be rendered to static document-ready format.

Super class

teal.reporter::ContentBlock -> HTMLBlock

Methods

Public methods

HTMLBlock$new()
HTMLBlock$from_list()
HTMLBlock$to_list()
HTMLBlock$clone()

Inherited methods

Method `new()`

Initialize a HTMLBlock object.

Usage

HTMLBlock$new(content)

Arguments

content: An object that can be rendered as a HTML content assigned to this HTMLBlock

Returns

Object of class HTMLBlock, invisibly.

Method `from_list()`

Create the HTMLBlock from a list.

Usage

HTMLBlock$from_list(x)

Arguments

x: (⁠named list⁠) with a single field content containing shiny.tag, shiny.tag.list or htmlwidget.

Returns

self, invisibly.

Examples

HTMLBlock <- getFromNamespace("HTMLBlock", "teal.reporter")
block <- HTMLBlock$new()
block$from_list(list(content = shiny::tags$div("test")))

Method `to_list()`

Convert the HTMLBlock to a list.

Usage

HTMLBlock$to_list()

Returns

⁠named list⁠ with a text and style.

Examples

HTMLBlock <- getFromNamespace("HTMLBlock", "teal.reporter")
block <- HTMLBlock$new(shiny::tags$div("test"))
block$to_list()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

HTMLBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `HTMLBlock$from_list`
## ------------------------------------------------

HTMLBlock <- getFromNamespace("HTMLBlock", "teal.reporter")
block <- HTMLBlock$new()
block$from_list(list(content = shiny::tags$div("test")))


## ------------------------------------------------
## Method `HTMLBlock$to_list`
## ------------------------------------------------

HTMLBlock <- getFromNamespace("HTMLBlock", "teal.reporter")
block <- HTMLBlock$new(shiny::tags$div("test"))
block$to_list()

`NewpageBlock`

Description

A ContentBlock subclass that represents a page break in a report output.

Super class

teal.reporter::ContentBlock -> NewpageBlock

Methods

Public methods

NewpageBlock$new()
NewpageBlock$clone()

Inherited methods

Method `new()`

Initialize a NewpageBlock object.

Usage

NewpageBlock$new()

Details

Returns a NewpageBlock object with no content and the default style.

Returns

Object of class NewpageBlock, invisibly.

Examples

NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter")
block <- NewpageBlock$new()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

NewpageBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `NewpageBlock$new`
## ------------------------------------------------

NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter")
block <- NewpageBlock$new()

`PictureBlock`

Description

Specialized FileBlock for managing picture content in reports. It's designed to handle plots from packages such as ggplot2, grid, or lattice. It can save plots to files, set titles and specify dimensions.

Super classes

teal.reporter::ContentBlock -> teal.reporter::FileBlock -> PictureBlock

Methods

Public methods

PictureBlock$new()
PictureBlock$set_content()
PictureBlock$set_title()
PictureBlock$get_title()
PictureBlock$set_dim()
PictureBlock$get_dim()
PictureBlock$clone()

Inherited methods

Method `new()`

Initialize a PictureBlock object.

Usage

PictureBlock$new(plot)

Arguments

plot: (ggplot or grid) a picture in this PictureBlock

Returns

Object of class PictureBlock, invisibly.

Method `set_content()`

Sets the content of this PictureBlock.

Usage

PictureBlock$set_content(content)

Arguments

content: (ggplot or grob or trellis) a picture in this PictureBlock

Details

Raises error if argument is not a ggplot, grob or trellis plot.

Returns

self, invisibly.

Method `set_title()`

Sets the title of this PictureBlock.

Usage

PictureBlock$set_title(title)

Arguments

title: (character(1)) a string assigned to this PictureBlock

Details

Raises error if argument is not character(1).

Returns

self, invisibly.

Examples

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_title("Title")

Method `get_title()`

Get the title of this PictureBlock.

Usage

PictureBlock$get_title()

Returns

The content of this PictureBlock.

Examples

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$get_title()

Method `set_dim()`

Sets the dimensions of this PictureBlock.

Usage

PictureBlock$set_dim(dim)

Arguments

dim: (numeric(2)) figure dimensions (width and height) in pixels.

Returns

self, invisibly.

Examples

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_dim(c(800, 600))

Method `get_dim()`

Get PictureBlock dimensions as a numeric vector.

Usage

PictureBlock$get_dim()

Returns

numeric the array of 2 numeric values representing width and height in pixels.

Examples

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$get_dim()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

PictureBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


library(ggplot2)
library(lattice)

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_content(ggplot(iris))

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_content(bwplot(1))

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_content(ggplotGrob(ggplot(iris)))


## ------------------------------------------------
## Method `PictureBlock$set_title`
## ------------------------------------------------

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_title("Title")


## ------------------------------------------------
## Method `PictureBlock$get_title`
## ------------------------------------------------

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$get_title()


## ------------------------------------------------
## Method `PictureBlock$set_dim`
## ------------------------------------------------

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$set_dim(c(800, 600))


## ------------------------------------------------
## Method `PictureBlock$get_dim`
## ------------------------------------------------

PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter")
block <- PictureBlock$new()
block$get_dim()

`RcodeBlock`

Description

Specialized ContentBlock designed to embed R code in reports.

Super class

teal.reporter::ContentBlock -> RcodeBlock

Methods

Public methods

RcodeBlock$new()
RcodeBlock$set_content()
RcodeBlock$set_params()
RcodeBlock$get_params()
RcodeBlock$get_available_params()
RcodeBlock$from_list()
RcodeBlock$to_list()
RcodeBlock$clone()

Inherited methods

teal.reporter::ContentBlock$get_content()

Method `new()`

Initialize a RcodeBlock object.

Usage

RcodeBlock$new(content = character(0), ...)

Arguments

content: (character(1) or character(0)) a string assigned to this RcodeBlock
...: any rmarkdown R chunk parameter and it value.

Details

Returns a RcodeBlock object with no content and no parameters.

Returns

Object of class RcodeBlock, invisibly.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()

Method `set_content()`

Sets content of this RcodeBlock.

Usage

RcodeBlock$set_content(content)

Arguments

content: (any) R object

Returns

self, invisibly.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$set_content("a <- 1")

Method `set_params()`

Sets the parameters of this RcodeBlock.

Usage

RcodeBlock$set_params(params)

Arguments

params: (list) any rmarkdown R chunk parameter and its value.

Details

Configures rmarkdown chunk parameters for the R code block, influencing its rendering and execution behavior.

Returns

self, invisibly.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$set_params(list(echo = TRUE))

Method `get_params()`

Get the parameters of this RcodeBlock.

Usage

RcodeBlock$get_params()

Returns

character the parameters of this RcodeBlock.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$get_params()

Method `get_available_params()`

Get available array of parameters available to this RcodeBlock.

Usage

RcodeBlock$get_available_params()

Returns

A character array of parameters.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$get_available_params()

Method `from_list()`

Create the RcodeBlock from a list.

Usage

RcodeBlock$from_list(x)

Arguments

x: (⁠named list⁠) with two fields text and params. Use the get_available_params method to get all possible parameters.

Returns

self, invisibly.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$from_list(list(text = "sth", params = list()))

Method `to_list()`

Convert the RcodeBlock to a list.

Usage

RcodeBlock$to_list()

Returns

⁠named list⁠ with a text and params.

Examples

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$to_list()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

RcodeBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `RcodeBlock$new`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()


## ------------------------------------------------
## Method `RcodeBlock$set_content`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$set_content("a <- 1")


## ------------------------------------------------
## Method `RcodeBlock$set_params`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$set_params(list(echo = TRUE))


## ------------------------------------------------
## Method `RcodeBlock$get_params`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$get_params()


## ------------------------------------------------
## Method `RcodeBlock$get_available_params`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$get_available_params()


## ------------------------------------------------
## Method `RcodeBlock$from_list`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$from_list(list(text = "sth", params = list()))


## ------------------------------------------------
## Method `RcodeBlock$to_list`
## ------------------------------------------------

RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter")
block <- RcodeBlock$new()
block$to_list()

`Renderer`

Description

A class for rendering reports from ContentBlock into various formats using rmarkdown. It supports TextBlock, PictureBlock, RcodeBlock, NewpageBlock, and TableBlock.

Methods

Public methods

Renderer$new()
Renderer$finalize()
Renderer$renderRmd()
Renderer$render()
Renderer$get_output_dir()
Renderer$clone()

Method `new()`

Initialize a Renderer object.

Usage

Renderer$new()

Details

Creates a new instance of Renderer with a temporary directory for storing report files.

Returns

Object of class Renderer, invisibly.

Examples

Renderer <- getFromNamespace("Renderer", "teal.reporter")
Renderer$new()

Method `finalize()`

Finalizes a Renderer object.

Usage

Renderer$finalize()

Method `renderRmd()`

Getting the Rmd text which could be easily rendered later.

Usage

Renderer$renderRmd(
  blocks,
  yaml_header,
  global_knitr = getOption("teal.reporter.global_knitr")
)

Arguments

blocks: (list) of TextBlock, PictureBlock and NewpageBlock objects.
yaml_header: (character) an rmarkdown yaml header.
global_knitr: (list) of knitr parameters (passed to knitr::opts_chunk$set) for customizing the rendering process.

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

Returns

Character vector constituting rmarkdown text (yaml header + body), ready to be rendered.

Method `render()`

Renders the Report to the desired output format by compiling the rmarkdown file.

Usage

Renderer$render(
  blocks,
  yaml_header,
  global_knitr = getOption("teal.reporter.global_knitr"),
  ...
)

Arguments

blocks: (list) of TextBlock, PictureBlock or NewpageBlock objects.
yaml_header: (character) an rmarkdown yaml header.
global_knitr: (list) of knitr parameters (passed to knitr::opts_chunk$set) for customizing the rendering process.
...: rmarkdown::render arguments, input and output_dir should not be updated.

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

Returns

character path to the output.

Method `get_output_dir()`

Get output_dir field.

Usage

Renderer$get_output_dir()

Returns

character a output_dir field path.

Examples

Renderer <- getFromNamespace("Renderer", "teal.reporter")$new()
Renderer$get_output_dir()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

Renderer$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


library(yaml)
library(rtables)
library(ggplot2)

ReportCard <- getFromNamespace("ReportCard", "teal.reporter")
Reporter <- getFromNamespace("Reporter", "teal.reporter")
yaml_quoted <- getFromNamespace("yaml_quoted", "teal.reporter")
md_header <- getFromNamespace("md_header", "teal.reporter")
Renderer <- getFromNamespace("Renderer", "teal.reporter")

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

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

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

yaml_l <- list(
  author = yaml_quoted("NEST"),
  title = yaml_quoted("Report"),
  date = yaml_quoted("07/04/2019"),
  output = list(html_document = list(toc = FALSE))
)

yaml_header <- md_header(as.yaml(yaml_l))

result_path <- Renderer$new()$renderRmd(reporter$get_blocks(), yaml_header)


library(yaml)
library(ggplot2)

ReportCard <- getFromNamespace("ReportCard", "teal.reporter")
Reporter <- getFromNamespace("Reporter", "teal.reporter")
yaml_quoted <- getFromNamespace("yaml_quoted", "teal.reporter")
md_header <- getFromNamespace("md_header", "teal.reporter")
Renderer <- getFromNamespace("Renderer", "teal.reporter")

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

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

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

yaml_l <- list(
  author = yaml_quoted("NEST"),
  title = yaml_quoted("Report"),
  date = yaml_quoted("07/04/2019"),
  output = list(html_document = list(toc = FALSE))
)

yaml_header <- md_header(as.yaml(yaml_l))
result_path <- Renderer$new()$render(reporter$get_blocks(), yaml_header)


## ------------------------------------------------
## Method `Renderer$new`
## ------------------------------------------------

Renderer <- getFromNamespace("Renderer", "teal.reporter")
Renderer$new()


## ------------------------------------------------
## Method `Renderer$get_output_dir`
## ------------------------------------------------

Renderer <- getFromNamespace("Renderer", "teal.reporter")$new()
Renderer$get_output_dir()

`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, header2, header3, 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()

`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")
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")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)

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")
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")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)

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")
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")
lyt <- analyze(split_rows_by(basic_table(), "Day"), "Ozone", afun = mean)
table_res2 <- build_table(lyt, airquality)
card2$append_table(table_res2)

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)

`TableBlock`

Description

Specialized FileBlock for managing table content in reports. It's designed to handle various table formats, converting them into a consistent, document-ready format (e.g., flextable) for inclusion in reports.

Super classes

teal.reporter::ContentBlock -> teal.reporter::FileBlock -> TableBlock

Methods

Public methods

TableBlock$new()
TableBlock$set_content()
TableBlock$clone()

Inherited methods

Method `new()`

Initialize a TableBlock object.

Usage

TableBlock$new(table)

Arguments

table: (data.frame or rtables or TableTree or ElementaryTable or listing_df) a table assigned to this TableBlock

Returns

Object of class TableBlock, invisibly.

Method `set_content()`

Sets content of this TableBlock.

Usage

TableBlock$set_content(content)

Arguments

content: (data.frame or rtables or TableTree or ElementaryTable or listing_df) a table assigned to this TableBlock

Details

Raises error if argument is not a table-like object.

Returns

self, invisibly.

Examples

TableBlock <- getFromNamespace("TableBlock", "teal.reporter")
block <- TableBlock$new()
block$set_content(iris)

Method `clone()`

The objects of this class are cloneable with this method.

Usage

TableBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `TableBlock$set_content`
## ------------------------------------------------

TableBlock <- getFromNamespace("TableBlock", "teal.reporter")
block <- TableBlock$new()
block$set_content(iris)

`TextBlock`

Description

Specialized ContentBlock for embedding styled text within reports. It supports multiple styling options to accommodate various text roles, such as headers or verbatim text, in the report content.

Super class

teal.reporter::ContentBlock -> TextBlock

Methods

Public methods

TextBlock$new()
TextBlock$set_content()
TextBlock$set_style()
TextBlock$get_style()
TextBlock$get_available_styles()
TextBlock$from_list()
TextBlock$to_list()
TextBlock$clone()

Inherited methods

teal.reporter::ContentBlock$get_content()

Method `new()`

Initialize a TextBlock object.

Usage

TextBlock$new(content = character(0), style = private$styles[1])

Arguments

content: (character) a string assigned to this TextBlock
style: (character(1)) one of: "default", "header2", "header3" "verbatim"

Details

Constructs a TextBlock object with no content and the default style.

Returns

Object of class TextBlock, invisibly.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()

Method `set_content()`

Sets content of this TextBlock.

Usage

TextBlock$set_content(content)

Arguments

content: (any) R object

Returns

self, invisibly.

Examples

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$set_content("Base64 encoded picture")

Method `set_style()`

Sets the style of this TextBlock.

Usage

TextBlock$set_style(style)

Arguments

style: (character(1)) one of: "default", "header2", "header3" "verbatim"

Details

The style has bearing on the rendering of this block.

Returns

self, invisibly.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$set_style("header2")

Method `get_style()`

Get the style of this TextBlock.

Usage

TextBlock$get_style()

Returns

character(1) the style of this TextBlock.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$get_style()

Method `get_available_styles()`

Get available an array of styles available to this TextBlock.

Usage

TextBlock$get_available_styles()

Returns

A character array of styles.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$get_available_styles()

Method `from_list()`

Create the TextBlock from a list.

Usage

TextBlock$from_list(x)

Arguments

x: (⁠named list⁠) with two fields text and style. Use the get_available_styles method to get all possible styles.

Returns

self, invisibly.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$from_list(list(text = "sth", style = "default"))

Method `to_list()`

Convert the TextBlock to a list.

Usage

TextBlock$to_list()

Returns

⁠named list⁠ with a text and style.

Examples

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$to_list()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

TextBlock$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `TextBlock$new`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()


## ------------------------------------------------
## Method `TextBlock$set_content`
## ------------------------------------------------

ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
block <- ContentBlock$new()
block$set_content("Base64 encoded picture")


## ------------------------------------------------
## Method `TextBlock$set_style`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$set_style("header2")


## ------------------------------------------------
## Method `TextBlock$get_style`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$get_style()


## ------------------------------------------------
## Method `TextBlock$get_available_styles`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$get_available_styles()


## ------------------------------------------------
## Method `TextBlock$from_list`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$from_list(list(text = "sth", style = "default"))


## ------------------------------------------------
## Method `TextBlock$to_list`
## ------------------------------------------------

TextBlock <- getFromNamespace("TextBlock", "teal.reporter")
block <- TextBlock$new()
block$to_list()

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)

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
)

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
)

Convert `yaml` representation of a boolean strings to logical Values

Description

Converts a single character string representing a yaml boolean value into a logical value in R.

Usage

conv_str_logi(
  input,
  name = "",
  pos_logi = c("TRUE", "true", "True", "yes", "y", "Y", "on"),
  neg_logi = c("FALSE", "false", "False", "no", "n", "N", "off"),
  silent = TRUE
)

Arguments

input

(character(1))

name

(charcter(1))

pos_logi

(character) vector of yaml values which should be treated as TRUE.

neg_logi

(character) vector of yaml values which should be treated as FALSE.

silent

(logical(1)) if to suppress the messages and warnings.

Value

input argument or the appropriate logical value.

Examples

conv_str_logi <- getFromNamespace("conv_str_logi", "teal.reporter")
conv_str_logi("TRUE")
conv_str_logi("True")

conv_str_logi("off")
conv_str_logi("n")

conv_str_logi("sth")

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)
)

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.

Get bootstrap current version

Description

Get bootstrap current version

Usage

get_bs_version()

Note

will work properly mainly inside a tag .renderHook

Extract field from `yaml` text

Description

Parses yaml text, extracting the specified field. Returns list names if it's a list; otherwise, the field itself.

Usage

get_yaml_field(yaml_text, field_name)

Arguments

yaml_text

(rmd_yaml_header or character) vector containing the yaml text.

field_name

(character) the name of the field to extract.

Value

If the field is a list, it returns the names of elements in the list; otherwise, it returns the extracted field.

Create `markdown` header from `yaml` string

Description

This function wraps a yaml-formatted string in Markdown header delimiters.

Usage

md_header(x)

Arguments

x

(character) yaml formatted string.

Examples

library(yaml)
yaml_quoted <- getFromNamespace("yaml_quoted", "teal.reporter")
yaml <- list(
  author = yaml_quoted("NEST"),
  title = yaml_quoted("Report"),
  date = yaml_quoted("07/04/2019"),
  output = list(pdf_document = list(keep_tex = TRUE))
)
md_header <- getFromNamespace("md_header", "teal.reporter")
md_header(as.yaml(yaml))

Panel group widget

Description

Usage

panel_item(title, ..., collapsed = TRUE, input_id = NULL)

Arguments

title

(character) title of panel

...

content of panel

collapsed

(logical, optional) whether to initially collapse panel

input_id

(character, optional) name of the panel item element. If supplied, this will register a shiny input variable that indicates whether the panel item is open or collapsed and is accessed with input$input_id.

Value

shiny.tag.

Print method for the `yaml_header` class

Description

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)

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)

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)

Arguments

id

character(1) this shiny module's id.

Value

shiny::tagList

Render the report

Description

Render the report and zip the created directory.

Usage

report_render_and_compress(
  reporter,
  input_list,
  global_knitr,
  file = tempdir()
)

Arguments

reporter

(Reporter) instance.

input_list

(list) like shiny input converted to a regular named list.

global_knitr

(list) a global knitr parameters, like echo. But if local parameter is set it will have priority.

file

(character(1)) where to copy the returned directory.

Value

file argument, invisibly.

Get the custom list of UI inputs

Description

Get the custom list of UI inputs

Usage

reporter_download_inputs(rmd_yaml_args, rmd_output, showrcode, session)

Arguments

rmd_yaml_args

rmd_output

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")
)

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

rmd_yaml_args

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)

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)

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

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

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

rmd_yaml_args

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)
    }
  )
}

Divide text block into smaller blocks

Description

Split a text block into smaller blocks with a specified number of lines.

Usage

split_text_block(x, n)

Arguments

x

(character) string containing the input block of text

n

(integer) number of lines per block

Details

A single character string containing a text block of multiple lines (separated by ⁠\n⁠) is split into multiple strings with n or less lines each.

Value

List of character strings with up to n lines in each element.

Convert content into a `flextable`

Description

Converts supported table formats into a flextable for enhanced formatting and presentation.

Usage

to_flextable(content)

Arguments

content

Supported formats: data.frame, rtables, TableTree, ElementaryTable, listing_df

Details

Function merges cells with colspan > 1, aligns columns to the center and row names to the left, indents the row names by 10 times indentation.

Value

flextable.

Mark strings for quotation in `yaml` serialization

Description

This function is designed for use with the yaml package to explicitly, It adds an attribute to character strings, indicating that they should be serialized with double quotes.

Usage

yaml_quoted(x)

Arguments

x

(character)

Examples

library(yaml)
yaml_quoted <- getFromNamespace("yaml_quoted", "teal.reporter")
yaml <- list(
  author = yaml_quoted("NEST"),
  title = yaml_quoted("Report"),
  date = yaml_quoted("07/04/2019"),
  output = list(pdf_document = list(keep_tex = TRUE))
)
as.yaml(yaml)

Reporting tools for shiny modules.

Description

Author(s)

See Also

ContentBlock: A building block for report content

Description

Methods

Public methods

Method set_content()

Usage

Arguments

Returns

Examples

Method get_content()

Usage

Returns

Examples

Method from_list()

Usage

Arguments

Returns

Method to_list()

Usage

Returns

Method clone()

Usage

Arguments

Examples

FileBlock

Description

Super class

Methods

Public methods

Method finalize()

Usage

Details

Method from_list()

Usage

Arguments

Returns

Examples

Method to_list()

Usage

Arguments

Returns

Examples

Method clone()

Usage

Arguments

Examples

HTMLBlock

Description

Super class

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method from_list()

Usage

Arguments

Returns

Examples

Method to_list()

Usage

Returns

Examples

Method clone()

Usage

Arguments

Examples

NewpageBlock

Description

Super class

Methods

Public methods

Method new()

Usage

Details

Reporting tools for `shiny` modules.

`ContentBlock`: A building block for report content

Method `set_content()`

Method `get_content()`

Method `from_list()`

Method `to_list()`

Method `clone()`

`FileBlock`

Method `finalize()`

Method `from_list()`

Method `to_list()`

Method `clone()`

`HTMLBlock`

Method `new()`

Method `from_list()`

Method `to_list()`

Method `clone()`

`NewpageBlock`

Method `new()`

Method `clone()`

`PictureBlock`

Method `new()`

Method `set_content()`

Method `set_title()`

Method `get_title()`

Method `set_dim()`

Method `get_dim()`

Method `clone()`

`RcodeBlock`

Method `new()`

Method `set_content()`

Method `set_params()`

Method `get_params()`