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We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
Examples of behavior that contributes to a positive environment for our community include:
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Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the reporter of any incident.
Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
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Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
Community Impact: A serious violation of community standards, including sustained inappropriate behavior.
Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
Consequence: A permanent ban from any sort of public interaction within the community.
This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.
For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.
🙏 Thank you for taking the time to contribute!
Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.
👶 Getting started
📔 Code of Conduct
🗃 License
Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.
A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.
All your contributions will be covered by this project’s license.
We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.
For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.
This repository uses the GitHub Flow model for collaboration. To submit a pull request:
Create a branch
Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.
Make changes
Make sure your code
Create a pull request (PR)
In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.
Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.
<issue_id>_<short_description>
_
420_fix_ui_bug
420
If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.
<issue_id>_<issue_repo>_<short description>
69_awesomeproject_fix_spelling_error
69
awesomeproject
monorepo
staged.dependencies
Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.
staged_dependencies.yaml
Please refer to the staged.dependencies package documentation for more details.
This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.
This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.
tidyverse
lintr
.lintr
Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.
If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the DESCRIPTION file. In particular: if the development version requires (imports) the development version of another package - it is required to put abc (>= 1.2.3.9000).
DESCRIPTION
abc (>= 1.2.3.9000)
We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().
R CMD check
sessionInfo()
If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.
pre-commit
We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.
R hooks for pre-commit
Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.
.pre-commit-config.yaml
As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:
git blame
*Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.
roxygen
renv.lock
The package maintainer also reserves the right to adjust the criteria to recognize contributions.
If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.
If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.
Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.
Instead, please send an email to vulnerability.management[@]roche.com.
Please include as much of the information listed below as you can to help us better understand and resolve the issue:
This information will help us triage your report more quickly.
Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.
Dawid Kaledkowski. Author, maintainer.
F. Hoffmann-La Roche AG. Copyright holder, funder.
Kaledkowski D, Kirar K, Kosinski M, Nasinski M, Pagacz K, Hallal M (2024). teal.reporter: Reporting Tools for 'shiny' Modules. -R package version 0.3.1.9017, +R package version 0.3.1.9018, https://insightsengineering.github.io/teal.reporter/, https://github.com/insightsengineering/teal.reporter.
@Manual{, title = {teal.reporter: Reporting Tools for 'shiny' Modules}, author = {Dawid Kaledkowski and Kartikeya Kirar and Marcin Kosinski and Maciej Nasinski and Konrad Pagacz and Mahmoud Hallal}, year = {2024}, - note = {R package version 0.3.1.9017, + note = {R package version 0.3.1.9018, https://insightsengineering.github.io/teal.reporter/}, url = {https://github.com/insightsengineering/teal.reporter}, }
shiny
CRAN release: 2024-03-15
shinybusy
CRAN release: 2024-02-16
add_card_button_srv
card_fun
label
Rcode
formatR
CRAN release: 2023-09-08
TableBlock
flextables
RcodeBlock
rmarkdown
reporter_previewer_ui
id
AddCardModule
knitr
append_src
TealReportCard
Archiver
Report
append_fs
list
ElementaryTree
append_table
ReportCard
dim
append_plot
trellis
set_content
PictureBlock
to_list
from_list
metadata
content
ContentBlock
R/ContentBlock.R
ContentBlock.Rd
ContentBlock$new()
ContentBlock$set_content()
ContentBlock$get_content()
ContentBlock$from_list()
ContentBlock$to_list()
ContentBlock$clone()
new()
Initialize a ContentBlock object.
Returns a ContentBlock object with no content and the default style.
Object of class ContentBlock, invisibly.
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") +Examples +ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") ContentBlock$new() - - - +
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") ContentBlock$new() -
set_content()
Sets content of this ContentBlock.
ContentBlock$set_content(content)
(character(0) or character(1)) string or file path assigned to this ContentBlock
character(0)
character(1)
self, invisibly.
self
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") +Examples +ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") block <- ContentBlock$new() block$set_content("Base64 encoded picture") - - - +
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") block <- ContentBlock$new() block$set_content("Base64 encoded picture") -
get_content()
Retrieves the content assigned to this block.
character string or file path assigned to this ContentBlock.
character
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") +Examples +ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") block <- ContentBlock$new() block$get_content() - - - +
ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter") block <- ContentBlock$new() block$get_content() -
from_list()
Create the ContentBlock from a list.
ContentBlock$from_list(x)
x
(named list) with two fields text and style. Use the get_available_styles method to get all possible styles.
named list
text
style
get_available_styles
to_list()
Convert the ContentBlock to a list.
named list with a text and style.
clone()
The objects of this class are cloneable with this method.
ContentBlock$clone(deep = FALSE)
deep
Whether to make a deep clone.
## ------------------------------------------------ ## Method `ContentBlock$new` @@ -383,19 +237,17 @@ ExamplesOn this page - -
FileBlock
teal.reporter::ContentBlock -> FileBlock
teal.reporter::ContentBlock
FileBlock$finalize()
FileBlock$from_list()
FileBlock$to_list()
FileBlock$clone()
Inherited methods -teal.reporter::ContentBlock$get_content() +
teal.reporter::ContentBlock$get_content()
Inherited methodsteal.reporter::ContentBlock$get_content() teal.reporter::ContentBlock$initialize() teal.reporter::ContentBlock$set_content() -
teal.reporter::ContentBlock$initialize()
teal.reporter::ContentBlock$set_content()
finalize()
Finalize the FileBlock.
Removes the temporary file created in the constructor.
Create the FileBlock from a list. -The list should contain one named field, "basename".
"basename"
FileBlock$from_list(x, output_dir)
(named list) with one field "basename", a name of the file.
FileBlock <- getFromNamespace("FileBlock", "teal.reporter") +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)) - - - +
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)) -
Convert the FileBlock to a list.
FileBlock$to_list(output_dir)
output_dir
(character) with a path to the directory where a file will be copied.
named list with a basename of the file.
basename
FileBlock <- getFromNamespace("FileBlock", "teal.reporter") +Examples +FileBlock <- getFromNamespace("FileBlock", "teal.reporter") block <- FileBlock$new() block$to_list(tempdir()) - - - +
FileBlock <- getFromNamespace("FileBlock", "teal.reporter") block <- FileBlock$new() block$to_list(tempdir()) -
FileBlock$clone(deep = FALSE)
## ------------------------------------------------ ## Method `FileBlock$from_list` @@ -314,19 +195,17 @@ ExamplesOn this page - -
NewpageBlock
teal.reporter::ContentBlock -> NewpageBlock
NewpageBlock$new()
NewpageBlock$clone()
Inherited methods -teal.reporter::ContentBlock$from_list() +
teal.reporter::ContentBlock$from_list()
Inherited methodsteal.reporter::ContentBlock$from_list() teal.reporter::ContentBlock$get_content() teal.reporter::ContentBlock$set_content() teal.reporter::ContentBlock$to_list() -
teal.reporter::ContentBlock$to_list()
Initialize a NewpageBlock object.
Returns a NewpageBlock object with no content and the default style.
Object of class NewpageBlock, invisibly.
NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") +Examples +NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") block <- NewpageBlock$new() - - - +
NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") block <- NewpageBlock$new() -
NewpageBlock$clone(deep = FALSE)
## ------------------------------------------------ ## Method `NewpageBlock$new` @@ -205,19 +124,17 @@ ExamplesOn this page - -
teal.reporter::ContentBlock -> teal.reporter::FileBlock -> PictureBlock
teal.reporter::FileBlock
PictureBlock$new()
PictureBlock$set_content()
PictureBlock$set_title()
PictureBlock$get_title()
PictureBlock$set_dim()
PictureBlock$get_dim()
PictureBlock$clone()
Inherited methodsteal.reporter::ContentBlock$get_content() teal.reporter::FileBlock$finalize() teal.reporter::FileBlock$from_list() teal.reporter::FileBlock$to_list() -
teal.reporter::FileBlock$finalize()
teal.reporter::FileBlock$from_list()
teal.reporter::FileBlock$to_list()
Initialize a PictureBlock object.
PictureBlock$new(plot)
plot
(ggplot or grid) a picture in this PictureBlock
ggplot
grid
Object of class PictureBlock, invisibly.
Sets the content of this PictureBlock.
PictureBlock$set_content(content)
(ggplot or grob or trellis) a picture in this PictureBlock
grob
Raises error if argument is not a ggplot, grob or trellis plot.
set_title()
Sets the title of this PictureBlock.
PictureBlock$set_title(title)
title
(character(1)) a string assigned to this PictureBlock
Raises error if argument is not character(1).
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") +Examples +PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$set_title("Title") - - - +
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$set_title("Title") -
get_title()
Get the title of this PictureBlock.
The content of this PictureBlock.
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") +Examples +PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$get_title() - - - +
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$get_title() -
set_dim()
Sets the dimensions of this PictureBlock.
PictureBlock$set_dim(dim)
(numeric(2)) figure dimensions (width and height) in pixels.
numeric(2)
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") +Examples +PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$set_dim(c(800, 600)) - - - +
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() block$set_dim(c(800, 600)) -
get_dim()
Get PictureBlock dimensions as a numeric vector.
numeric the array of 2 numeric values representing width and height in pixels.
numeric
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") +Examples +PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() -block$get_dim() - - +block$get_dim()
PictureBlock <- getFromNamespace("PictureBlock", "teal.reporter") block <- PictureBlock$new() -block$get_dim()
PictureBlock$clone(deep = FALSE)
library(ggplot2) library(lattice) @@ -475,19 +299,17 @@ ExamplesOn this page - -
teal.reporter::ContentBlock -> RcodeBlock
RcodeBlock$new()
RcodeBlock$set_params()
RcodeBlock$get_params()
RcodeBlock$get_available_params()
RcodeBlock$from_list()
RcodeBlock$to_list()
RcodeBlock$clone()
Inherited methodsteal.reporter::ContentBlock$get_content() teal.reporter::ContentBlock$set_content() -
Initialize a RcodeBlock object.
RcodeBlock$new(content = character(0), ...)
(character(1) or character(0)) a string assigned to this RcodeBlock
Returns a RcodeBlock object with no content and no parameters.
Object of class RcodeBlock, invisibly.
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() -
set_params()
Sets the parameters of this RcodeBlock.
RcodeBlock$set_params(params)
params
(list) any rmarkdown R chunk parameter and its value.
Configures rmarkdown chunk parameters for the R code block, influencing its rendering and execution behavior.
R
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$set_params(list(echo = TRUE)) - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$set_params(list(echo = TRUE)) -
get_params()
Get the parameters of this RcodeBlock.
character the parameters of this RcodeBlock.
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$get_params() - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$get_params() -
get_available_params()
Get available array of parameters available to this RcodeBlock.
A character array of parameters.
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$get_available_params() - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$get_available_params() -
Create the RcodeBlock from a list.
RcodeBlock$from_list(x)
(named list) with two fields text and params. Use the get_available_params method to get all possible parameters.
get_available_params
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$from_list(list(text = "sth", params = list())) - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$from_list(list(text = "sth", params = list())) -
Convert the RcodeBlock to a list.
named list with a text and params.
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") +Examples +RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$to_list() - - - +
RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") block <- RcodeBlock$new() block$to_list() -
RcodeBlock$clone(deep = FALSE)
## ------------------------------------------------ ## Method `RcodeBlock$new` @@ -508,19 +328,17 @@ ExamplesOn this page - -
Renderer
Renderer$new()
Renderer$finalize()
Renderer$renderRmd()
Renderer$render()
Renderer$get_output_dir()
Renderer$clone()
Initialize a Renderer object.
Creates a new instance of Renderer with a temporary directory for storing report files.
Object of class Renderer, invisibly.
Renderer <- getFromNamespace("Renderer", "teal.reporter") +Examples +Renderer <- getFromNamespace("Renderer", "teal.reporter") Renderer$new() - - - +
Renderer <- getFromNamespace("Renderer", "teal.reporter") Renderer$new() -
Finalizes a Renderer object.
renderRmd()
Getting the Rmd text which could be easily rendered later.
Rmd
Renderer$renderRmd( +
Renderer$renderRmd( blocks, yaml_header, global_knitr = getOption("teal.reporter.global_knitr") -)
blocks
(list) of TextBlock, PictureBlock and NewpageBlock objects.
TextBlock
To access the default values for the global_knitr parameter, -use getOption('teal.reporter.global_knitr'). These defaults include:
global_knitr
getOption('teal.reporter.global_knitr')
echo = TRUE
tidy.opts = list(width.cutoff = 60)
tidy = TRUE if formatR package is installed, FALSE otherwise
tidy = TRUE
FALSE
Character vector constituting rmarkdown text (yaml header + body), ready to be rendered.
yaml
render()
Renders the Report to the desired output format by compiling the rmarkdown file.
Renderer$render( +
Renderer$render( blocks, yaml_header, global_knitr = getOption("teal.reporter.global_knitr"), ... -)
(list) of TextBlock, PictureBlock or NewpageBlock objects.
input
character path to the output.
get_output_dir()
Get output_dir field.
character a output_dir field path.
Renderer <- getFromNamespace("Renderer", "teal.reporter")$new() +Examples +Renderer <- getFromNamespace("Renderer", "teal.reporter")$new() Renderer$get_output_dir() - - - +
Renderer <- getFromNamespace("Renderer", "teal.reporter")$new() Renderer$get_output_dir() -
Renderer$clone(deep = FALSE)
library(yaml) library(rtables) #> Loading required package: formatters @@ -489,7 +342,7 @@ Examples#> renderRmd: function (blocks, yaml_header, global_knitr = getOption("teal.reporter.global_knitr")) #> Private: #> block2md: function (block) -#> output_dir: /tmp/RtmplgXhu5/report_202411271424155990 +#> output_dir: /tmp/Rtmpvcn05j/report_202412110930215968 #> pictureBlock2md: function (block) #> rcodeBlock2md: function (block) #> report_type: NULL @@ -503,24 +356,22 @@ Examples Renderer <- getFromNamespace("Renderer", "teal.reporter")$new() Renderer$get_output_dir() -#> [1] "/tmp/RtmplgXhu5/report_202411271424156007" +#> [1] "/tmp/Rtmpvcn05j/report_202412110930215986"
R6
R/ReportCard.R
ReportCard.Rd
ReportCard$new()
ReportCard$append_table()
ReportCard$append_plot()
ReportCard$append_text()
ReportCard$to_list()
ReportCard$from_list()
ReportCard$clone()
Initialize a ReportCard object.
Object of class ReportCard, invisibly.
card <- ReportCard$new() -
card <- ReportCard$new() +
append_table()
Appends a table to this ReportCard.
ReportCard$append_table(table)
table
A (data.frame or rtables or TableTree or ElementaryTable or listing_df) that can be coerced into a table.
data.frame
rtables
TableTree
ElementaryTable
listing_df
card <- ReportCard$new()$append_table(iris) -
card <- ReportCard$new()$append_table(iris) +
append_plot()
Appends a plot to this ReportCard.
ReportCard$append_plot(plot, dim = NULL)
(ggplot or grob or trellis) plot object.
append_text()
Appends a text paragraph to this ReportCard.
ReportCard$append_text(text, style = TextBlock$new()$get_available_styles()[1])
(character) The text content to add.
card <- ReportCard$new()$append_text("A paragraph of default text") -
card <- ReportCard$new()$append_text("A paragraph of default text") +
append_rcode()
Appends an R code chunk to ReportCard.
ReportCard$append_rcode(text, ...)
(character) The R code to include.
card <- ReportCard$new()$append_rcode("2+2", echo = FALSE) -
card <- ReportCard$new()$append_rcode("2+2", echo = FALSE) +
append_content()
Appends a generic ContentBlock to this ReportCard.
ReportCard$append_content(content)
(ContentBlock) object.
NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") +Examples +NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") card <- ReportCard$new()$append_content(NewpageBlock$new()) - - - +
NewpageBlock <- getFromNamespace("NewpageBlock", "teal.reporter") card <- ReportCard$new()$append_content(NewpageBlock$new()) -
Get all content blocks from this ReportCard.
ReportCard$get_content()
list() list of TableBlock, TextBlock and PictureBlock.
list()
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") +Examples +card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") card$get_content() - - - +
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") card$get_content() -
reset()
Clears all content and metadata from ReportCard.
ReportCard$reset()
get_metadata()
Get the metadata associated with ReportCard.
ReportCard$get_metadata()
named list list of elements.
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") +Examples +card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") card$get_metadata() - - - +
card <- ReportCard$new()$append_text("Some text")$append_metadata("rc", "a <- 2 + 2") card$get_metadata() -
append_metadata()
Appends metadata to this ReportCard.
ReportCard$append_metadata(key, value)
key
(character(1)) string specifying the metadata key.
get_name()
Get the name of the ReportCard.
ReportCard$get_name()
character a card name.
ReportCard$new()$set_name("NAME")$get_name()
set_name()
Set the name of the ReportCard.
ReportCard$set_name(name)
name
(character(1)) a card name.
Convert the ReportCard to a list, including content and metadata.
ReportCard$to_list(output_dir)
(character) with a path to the directory where files will be copied.
(named list) a ReportCard representation.
Reconstructs the ReportCard from a list representation.
ReportCard$from_list(card, output_dir)
card
ReportCard$clone(deep = FALSE)
library(ggplot2) card <- ReportCard$new()$append_plot( @@ -790,7 +474,7 @@ Examples#> set_title: function (title) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file3981aadf2d2.png +#> content: /tmp/Rtmpvcn05j/file39351142e2e.png #> deep_clone: function (name, value) #> dim: 800 600 #> supported_plots: ggplot grob trellis Heatmap @@ -870,7 +554,7 @@ Examples#> set_title: function (title) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file398396e510f.png +#> content: /tmp/Rtmpvcn05j/file39319cbf263.png #> deep_clone: function (name, value) #> dim: 800 600 #> supported_plots: ggplot grob trellis Heatmap @@ -909,7 +593,7 @@ Examples#> #> $blocks$PictureBlock #> $blocks$PictureBlock$basename -#> [1] "file398396e510f.png" +#> [1] "file39319cbf263.png" #> #> #> $blocks$TextBlock @@ -979,7 +663,7 @@ Examples#> set_title: function (title) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file3986734632c.png +#> content: /tmp/Rtmpvcn05j/file3933b9cbc80.png #> deep_clone: function (name, value) #> dim: 800 600 #> supported_plots: ggplot grob trellis Heatmap @@ -1101,19 +785,17 @@ ExamplesOn this page - -
Reporter
R/Reporter.R
Reporter.Rd
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.
Reporter$new()
Reporter$append_cards()
Reporter$get_cards()
Reporter$get_blocks()
Reporter$set_id()
Reporter$get_id()
Reporter$clone()
Initialize a Reporter object.
Object of class Reporter, invisibly.
reporter <- Reporter$new() -
reporter <- Reporter$new() +
append_cards()
Append one or more ReportCard objects to the Reporter.
Reporter$append_cards(cards)
cards
(ReportCard) or a list of such objects
get_cards()
Retrieves all ReportCard objects contained in the Reporter.
A (list) of ReportCard objects.
get_blocks()
Compiles and returns all content blocks from the ReportCard in the Reporter.
Reporter$get_blocks(sep = NewpageBlock$new())
sep
An optional separator to insert between each content block. Default is a NewpageBlock$new()object.
list() list of TableBlock, TextBlock, PictureBlock and NewpageBlock.
Resets the Reporter, removing all ReportCard objects and metadata.
Reporter$reset()
remove_cards()
Removes specific ReportCard objects from the Reporter by their indices.
Reporter$remove_cards(ids = NULL)
ids
(integer(id)) the indexes of cards
integer(id)
swap_cards()
Swaps the positions of two ReportCard objects within the Reporter.
Reporter$swap_cards(start, end)
start
(integer) the index of the first card
integer
get_reactive_add_card()
Gets the current value of the reactive variable for adding cards.
Reporter$get_reactive_add_card()
reactive_add_card current numeric value of the reactive variable.
reactive_add_card
library(shiny) +Examples +library(shiny) -isolate(Reporter$new()$get_reactive_add_card()) - - +isolate(Reporter$new()$get_reactive_add_card())
library(shiny) -isolate(Reporter$new()$get_reactive_add_card())
Get the metadata associated with this Reporter.
Reporter$get_metadata()
named list of metadata to be appended.
reporter <- Reporter$new()$append_metadata(list(sth = "sth")) +Examples +reporter <- Reporter$new()$append_metadata(list(sth = "sth")) reporter$get_metadata() - - - +
reporter <- Reporter$new()$append_metadata(list(sth = "sth")) reporter$get_metadata() -
Appends metadata to this Reporter.
Reporter$append_metadata(meta)
meta
(named list) of metadata to be appended.
from_reporter()
Reinitializes a Reporter instance by copying the report cards and metadata from another Reporter.
Reporter$from_reporter(reporter)
reporter
(Reporter) instance to copy from.
invisibly self
reporter <- Reporter$new() -reporter$from_reporter(reporter)
reporter <- Reporter$new() +reporter$from_reporter(reporter)
Convert a Reporter to a list and transfer any associated files to specified directory.
Reporter$to_list(output_dir)
(character(1)) a path to the directory where files will be copied.
named list representing the Reporter instance, including version information, metadata, and report cards.
reporter <- Reporter$new() +Examples +reporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "testdir") dir.create(tmp_dir) -reporter$to_list(tmp_dir) - - +reporter$to_list(tmp_dir)
reporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "testdir") dir.create(tmp_dir) -reporter$to_list(tmp_dir)
Reinitializes a Reporter from a list representation and associated files in a specified directory.
Reporter$from_list(rlist, output_dir)
rlist
(named list) representing a Reporter instance.
reporter <- Reporter$new() +Examples +reporter <- Reporter$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) - - +reporter$from_list(reporter$to_list(tmp_dir), tmp_dir)
reporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "testdir") unlink(tmp_dir, recursive = TRUE) dir.create(tmp_dir) -reporter$from_list(reporter$to_list(tmp_dir), tmp_dir)
to_jsondir()
Serializes the Reporter to a JSON file and copies any associated files to a specified directory.
JSON
Reporter$to_jsondir(output_dir)
(character(1)) a path to the directory where files will be copied, JSON and statics.
output_dir argument.
reporter <- Reporter$new() +Examples +reporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "jsondir") dir.create(tmp_dir) -reporter$to_jsondir(tmp_dir) - - +reporter$to_jsondir(tmp_dir)
reporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "jsondir") dir.create(tmp_dir) -reporter$to_jsondir(tmp_dir)
from_jsondir()
Reinitializes a Reporter from a JSON file and files in a specified directory.
Reporter$from_jsondir(output_dir)
(character(1)) a path to the directory with files, JSON and statics.
reporter <- Reporter$new() +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$from_jsondir(tmp_dir) - - +reporter$from_jsondir(tmp_dir)
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$from_jsondir(tmp_dir)
set_id()
Set the Reporter id Optionally add id to a Reporter which will be compared when it is rebuilt from a list. -The id is added to the downloaded file name.
Reporter$set_id(id)
(character(1)) a Report id.
get_id()
Get the Reporter id
character(1) the Reporter id.
Reporter$clone(deep = FALSE)
library(ggplot2) library(rtables) @@ -1021,7 +659,7 @@ Examples#> set_title: function (title) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file398a46506d.png +#> content: /tmp/Rtmpvcn05j/file3936d104858.png #> deep_clone: function (name, value) #> dim: 800 600 #> supported_plots: ggplot grob trellis Heatmap @@ -1094,7 +732,7 @@ Examples#> set_content: function (content) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file3984ae010cb.rds +#> content: /tmp/Rtmpvcn05j/file39342ca252f.rds #> deep_clone: function (name, value) #> supported_tables: data.frame rtables TableTree ElementaryTable listing_df #> @@ -1110,7 +748,7 @@ Examples#> set_content: function (content) #> to_list: function (output_dir) #> Private: -#> content: /tmp/RtmplgXhu5/file39844e61db.rds +#> content: /tmp/Rtmpvcn05j/file3935c961792.rds #> deep_clone: function (name, value) #> supported_tables: data.frame rtables TableTree ElementaryTable listing_df #> @@ -1202,7 +840,7 @@ Examplestmp_dir <- file.path(tempdir(), "jsondir") dir.create(tmp_dir) reporter$to_jsondir(tmp_dir) -#> [1] "/tmp/RtmplgXhu5/jsondir" +#> [1] "/tmp/Rtmpvcn05j/jsondir" ## ------------------------------------------------ ## Method `Reporter$from_jsondir` @@ -1211,27 +849,25 @@ Examplesreporter <- Reporter$new() tmp_dir <- file.path(tempdir(), "jsondir") dir.create(tmp_dir) -#> Warning: '/tmp/RtmplgXhu5/jsondir' already exists +#> Warning: '/tmp/Rtmpvcn05j/jsondir' already exists unlink(list.files(tmp_dir, recursive = TRUE)) reporter$to_jsondir(tmp_dir) -#> [1] "/tmp/RtmplgXhu5/jsondir" +#> [1] "/tmp/Rtmpvcn05j/jsondir" reporter$from_jsondir(tmp_dir)
teal.reporter::ContentBlock -> teal.reporter::FileBlock -> TableBlock
TableBlock$new()
TableBlock$set_content()
TableBlock$clone()
Initialize a TableBlock object.
TableBlock$new(table)
(data.frame or rtables or TableTree or ElementaryTable or listing_df) a table assigned to this TableBlock
Object of class TableBlock, invisibly.
Sets content of this TableBlock.
TableBlock$set_content(content)
Raises error if argument is not a table-like object.
TableBlock <- getFromNamespace("TableBlock", "teal.reporter") +Examples +TableBlock <- getFromNamespace("TableBlock", "teal.reporter") block <- TableBlock$new() block$set_content(iris) - - - +
TableBlock <- getFromNamespace("TableBlock", "teal.reporter") block <- TableBlock$new() block$set_content(iris) -
TableBlock$clone(deep = FALSE)
## ------------------------------------------------ ## Method `TableBlock$set_content` @@ -267,19 +163,17 @@ ExamplesOn this page - -
teal.reporter::ContentBlock -> TextBlock
TextBlock$new()
TextBlock$set_style()
TextBlock$get_style()
TextBlock$get_available_styles()
TextBlock$from_list()
TextBlock$to_list()
TextBlock$clone()
Initialize a TextBlock object.
TextBlock$new(content = character(0), style = private$styles[1])
(character) a string assigned to this TextBlock
"header2"
"header3"
"verbatim"
Constructs a TextBlock object with no content and the default style.
Object of class TextBlock, invisibly.
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() -
set_style()
Sets the style of this TextBlock.
TextBlock$set_style(style)
(character(1)) one of: "default", "header2", "header3" "verbatim"
"default"
The style has bearing on the rendering of this block.
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$set_style("header2") - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$set_style("header2") -
get_style()
Get the style of this TextBlock.
character(1) the style of this TextBlock.
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$get_style() - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$get_style() -
get_available_styles()
Get available an array of styles available to this TextBlock.
A character array of styles.
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$get_available_styles() - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$get_available_styles() -
Create the TextBlock from a list.
TextBlock$from_list(x)
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$from_list(list(text = "sth", style = "default")) - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$from_list(list(text = "sth", style = "default")) -
Convert the TextBlock to a list.
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") +Examples +TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$to_list() - - - +
TextBlock <- getFromNamespace("TextBlock", "teal.reporter") block <- TextBlock$new() block$to_list() -
TextBlock$clone(deep = FALSE)
## ------------------------------------------------ ## Method `TextBlock$new` @@ -500,19 +320,17 @@ ExamplesOn this page - -
add_card_button_ui(id) add_card_button_srv(id, reporter, card_fun)
(character(1)) this shiny module's id.
(Reporter) instance.
(function) which returns a ReportCard instance. See Details.
function
Details
NULL.
NULL
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$append_text() - if card_fun does not have the comment parameter, then comment from Add Card UI module will be added at the end of the content of the card.
comment
card$append_text()
Add Card UI
The label parameter enables customization of the card's name and its content through card$append_text()- if card_fun does not have the label parameter, then card name will be set to the name passed in Add Card UI module, but no text will be added to the content of the card.
This module supports using a subclass of ReportCard for added flexibility. +
This module supports using a subclass of ReportCard for added flexibility. A subclass instance should be passed as the default value of the card argument in the card_fun function. See below:
CustomReportCard <- R6::R6Class( +CustomReportCard <- R6::R6Class( classname = "CustomReportCard", inherit = teal.reporter::ReportCard ) custom_function <- function(card = CustomReportCard$new()) { card -} - - +}
CustomReportCard <- R6::R6Class( classname = "CustomReportCard", inherit = teal.reporter::ReportCard ) custom_function <- function(card = CustomReportCard$new()) { card -}
as_yaml_auto( input_list, as_header = TRUE, @@ -110,62 +68,50 @@ Usage
(named list) non nested with slots names and their values compatible with Rmd yaml header.
(logical(1)) optionally wrap with result with the internal md_header(), default TRUE.
logical(1)
md_header()
TRUE
(logical(1)) convert a character values to logical, if they are recognized as quoted yaml logical values , default TRUE.
(logical(1)) multi output slots in the input argument, default FALSE.
output
(logical(1)) suppress messages and warnings, default FALSE.
character with rmd_yaml_header class, result of yaml::as.yaml, optionally wrapped with internal md_header().
rmd_yaml_header
yaml::as.yaml
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.
author
date
subtitle
abstract
keywords
subject
description
category
lang
Only non-nested lists are automatically parsed. Nested lists require direct processing with yaml::as.yaml.
# nested so using yaml::as.yaml directly as_yaml_auto( list(author = "", output = list(pdf_document = list(toc = TRUE))) @@ -293,19 +239,17 @@ ExamplesOn this page - -
conv_str_logi( input, name = "", @@ -104,46 +62,36 @@ Usage
(character(1))
(charcter(1))
charcter(1)
(character) vector of yaml values which should be treated as TRUE.
(character) vector of yaml values which should be treated as FALSE.
(logical(1)) if to suppress the messages and warnings.
input argument or the appropriate logical value.
logical
conv_str_logi <- getFromNamespace("conv_str_logi", "teal.reporter") conv_str_logi("TRUE") #> [1] TRUE @@ -160,19 +108,17 @@ ExamplesOn this page - -
download_report_button_ui(id) download_report_button_srv( @@ -114,75 +72,60 @@ Usage
(list) of knitr parameters (passed to knitr::opts_chunk$set) for customizing the rendering process.
knitr::opts_chunk$set
(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.
pdf_document
html_document
powerpoint_presentation
word_document
UI
(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.
list(author = "NEST", title = "Report", date = Sys.Date(), output = "html_document", toc = FALSE)
"output"
rmd_output
get_bs_version()
will work properly mainly inside a tag .renderHook
.renderHook
get_yaml_field(yaml_text, field_name)
(rmd_yaml_header or character) vector containing the yaml text.
(character) the name of the field to extract.
If the field is a list, it returns the names of elements in the list; otherwise, it returns the extracted field.
add_card_button_ui()
add_card_button_srv()
reporter_previewer_ui()
reporter_previewer_srv()
simple_reporter_ui()
simple_reporter_srv()
download_report_button_ui()
download_report_button_srv()
reset_report_button_ui()
reset_report_button_srv()
report_load_srv()
report_load_ui()
as_yaml_auto()
print(<rmd_yaml_header>)
yaml_header
rmd_output_arguments()
rmd_outputs()
markdown
md_header(x)
(character) yaml formatted string.
library(yaml) yaml_quoted <- getFromNamespace("yaml_quoted", "teal.reporter") yaml <- list( @@ -127,19 +80,17 @@ ExamplesOn this page - -
panel_item(title, ..., collapsed = TRUE, input_id = NULL)
(character) title of panel
content of panel
(logical, optional) whether to initially collapse panel
(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.
input$input_id
shiny.tag.
shiny.tag
# S3 method for class 'rmd_yaml_header' print(x, ...)
(rmd_yaml_header) class object.
optional text.
input <- list(author = "", output = "pdf_document", toc = TRUE, keep_tex = TRUE) out <- as_yaml_auto(input) out @@ -145,19 +96,17 @@ ExamplesOn this page - -
R/LoadReporterModule.R
report_load_srv.Rd
report_load_srv(id, reporter)
character(1) this shiny module's id.
Reporter instance.
shiny::moduleServer
report_load_ui.Rd
report_load_ui(id)
shiny::tagList
report_render_and_compress( reporter, input_list, @@ -103,53 +61,43 @@ Usage
(list) like shiny input converted to a regular named list.
(list) a global knitr parameters, like echo. But if local parameter is set it will have priority.
(character(1)) where to copy the returned directory.
file argument, invisibly.
file
reporter_download_inputs(rmd_yaml_args, rmd_output, showrcode, session)
(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). @@ -112,29 +67,25 @@
reporter_previewer_ui(id) reporter_previewer_srv( @@ -124,36 +82,29 @@ Usage
(character(1)) shiny module instance id.
(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). @@ -161,45 +112,36 @@
(character) set of modules to include with c("download", "load", "reset") possible values and "download" is required. Default c("download", "load", "reset")
c("download", "load", "reset")
"download"
reset_report_button_ui(id, label = NULL) reset_report_button_srv(id, reporter)
(character(1)) label before the icon. By default NULL.
