From dd0c748f2ae301c2d94cae56642e43c3166adbbb Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 8 Nov 2024 14:08:59 +0000 Subject: [PATCH] Update pkgdown documentation 4063d5ae01c668e08a4d42973ed92fbc93428e55 --- main/404.html | 17 +- main/CODE_OF_CONDUCT.html | 110 ++--- main/CONTRIBUTING.html | 138 ++---- main/LICENSE-text.html | 65 +-- main/SECURITY.html | 77 +-- main/articles/data-expectations.html | 17 +- main/articles/index.html | 78 +-- main/articles/teal-goshawk.html | 21 +- main/articles/user-guide.html | 17 +- main/authors.html | 75 +-- main/index.html | 17 +- main/news/index.html | 455 ++++++------------ main/pkgdown.yml | 2 +- main/reference/get_choices.html | 87 +--- main/reference/include_css_files.html | 87 +--- main/reference/index.html | 119 ++--- main/reference/maptrt.html | 89 +--- .../report_card_template_goshawk.html | 116 ++--- main/reference/srv_arbitrary_lines.html | 87 +--- main/reference/teal.goshawk-package.html | 96 +--- main/reference/tm_g_gh_boxplot.html | 189 +++----- main/reference/tm_g_gh_correlationplot.html | 209 +++----- .../tm_g_gh_density_distribution_plot.html | 166 ++----- main/reference/tm_g_gh_lineplot.html | 195 +++----- main/reference/tm_g_gh_scatterplot.html | 169 ++----- main/reference/tm_g_gh_spaghettiplot.html | 206 +++----- main/reference/toggle_slider.html | 93 +--- main/reference/ui_arbitrary_lines.html | 95 +--- main/search.json | 2 +- 29 files changed, 876 insertions(+), 2218 deletions(-) diff --git a/main/404.html b/main/404.html index bbea84d3..66db74f2 100644 --- a/main/404.html +++ b/main/404.html @@ -1,4 +1,5 @@ - + + @@ -21,7 +22,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -80,80 +47,65 @@

Contributor Covenant Code of Conduct

-

Our Pledge -

+

Our Pledge

We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

-

Our Standards -

+

Our Standards

Examples of behavior that contributes to a positive environment for our community include:

-
+
-

Enforcement Responsibilities -

+

Enforcement Responsibilities

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.

-

Scope -

+

Scope

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.

-

Enforcement -

+

Enforcement

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.

-

Enforcement Guidelines -

+

Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

-

1. Correction -

+

1. Correction

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.

-

2. Warning -

+

2. Warning

Community Impact: A violation through a single incident or series of actions.

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.

-

3. Temporary Ban -

+

3. Temporary 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.

-

4. Permanent Ban -

+

4. 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.

-

Attribution -

+

Attribution

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.

@@ -161,19 +113,17 @@

Attribution -

+ - + + + - - diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html index f96fcaa0..bc957b82 100644 --- a/main/CONTRIBUTING.html +++ b/main/CONTRIBUTING.html @@ -1,19 +1,5 @@ - - - - - - -Contribution Guidelines • teal.goshawk - - - - - - - - - + +Contribution Guidelines • teal.goshawk Skip to contents @@ -21,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -82,8 +49,7 @@

Contribution Guidelines

🙏 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.

-

Table of contents -

+

Table of contents

👶 Getting started

📔 Code of Conduct

🗃 License

@@ -94,47 +60,38 @@

Table of contents❓ Questions

-

Getting started -

+

Getting started

Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

-

Code of Conduct -

+

Code of Conduct

A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

-

License -

+

License

All your contributions will be covered by this project’s license.

-

Issues -

+

Issues

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.

-

Pull requests -

+

Pull requests

-

GitHub Flow -

+

GitHub Flow

This repository uses the GitHub Flow model for collaboration. To submit a pull request:

-
    -
  1. +
    1. Create a branch

      Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

    2. Make changes

      Make sure your code

      -
        -
      • passes all checks imposed by GitHub Actions
      • +
        • passes all checks imposed by GitHub Actions
        • is well documented
        • is well tested with unit tests sufficiently covering the changes introduced
        • -
        - +
    3. 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.

      @@ -148,93 +105,76 @@

      GitHub Flow -

      Branch naming convention -

      +

      Branch naming convention

      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.

      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.

monorepo and 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.

Please refer to the staged.dependencies package documentation for more details.

-

Coding guidelines -

+

Coding guidelines

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.

-

Style guide -

+

Style guide

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.

-

Dependency management -

+

Dependency management

Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.

-

Dependency version management -

+

Dependency version management

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).

- +
-

R & package versions -

+

R & package versions

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().

If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

-

-pre-commit -

+

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.

Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

-

Recognition model -

+

Recognition model

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:

-

*Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

The package maintainer also reserves the right to adjust the criteria to recognize contributions.

-

Questions -

+

Questions

If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

- + - + + + - - diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html index 746c77ac..bcee496a 100644 --- a/main/LICENSE-text.html +++ b/main/LICENSE-text.html @@ -1,19 +1,5 @@ - - - - - - -License • teal.goshawk - - - - - - - - - + +License • teal.goshawk Skip to contents @@ -21,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -92,19 +59,17 @@

License

limitations under the License. - - + - + + + - - diff --git a/main/SECURITY.html b/main/SECURITY.html index 556c669a..d3fe6389 100644 --- a/main/SECURITY.html +++ b/main/SECURITY.html @@ -1,19 +1,5 @@ - - - - - - -Security Policy • teal.goshawk - - - - - - - - - + +Security Policy • teal.goshawk Skip to contents @@ -21,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -80,44 +47,38 @@

Security Policy

-

Reporting Security Issues -

+

Reporting Security Issues

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.

-

Data Security Standards (DSS) -

+

Data Security Standards (DSS)

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.

- + - + + + - - diff --git a/main/articles/data-expectations.html b/main/articles/data-expectations.html index 171dae91..2d7e6973 100644 --- a/main/articles/data-expectations.html +++ b/main/articles/data-expectations.html @@ -1,4 +1,5 @@ - + + @@ -21,7 +22,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -80,31 +47,24 @@

Articles

All vignettes

-
-
Data Expectations
+
Data Expectations
-
-
Getting started with teal.goshawk
+
Getting started with teal.goshawk
-
-
User Guide
+
User Guide
-
-
- - - +
+ - + + + - - diff --git a/main/articles/teal-goshawk.html b/main/articles/teal-goshawk.html index 8b4492e7..77c3716e 100644 --- a/main/articles/teal-goshawk.html +++ b/main/articles/teal-goshawk.html @@ -1,4 +1,5 @@ - + + @@ -21,7 +22,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -79,8 +46,7 @@

Authors and Citation

Authors

-
+

Citation

@@ -133,33 +98,31 @@

Citation

Paszty N, Kaledkowski D, Hallal M, Rucki P, Liu W, Tomlinson J, Toth B, Zhao J, Nasinski M (2024). teal.goshawk: Longitudinal Visualization 'teal' Modules. -R package version 0.2.0.9016, +R package version 0.2.0.9017, https://github.com/insightsengineering/teal.goshawk/, https://insightsengineering.github.io/teal.goshawk/.

@Manual{,
   title = {teal.goshawk: Longitudinal Visualization `teal` Modules},
   author = {Nick Paszty and Dawid Kaledkowski and Mahmoud Hallal and Pawel Rucki and Wenyi Liu and Jeffrey Tomlinson and Bali Toth and Junlue Zhao and Maciej Nasinski},
   year = {2024},
-  note = {R package version 0.2.0.9016,
+  note = {R package version 0.2.0.9017,
     https://github.com/insightsengineering/teal.goshawk/},
   url = {https://insightsengineering.github.io/teal.goshawk/},
 }
- + - + + + - - diff --git a/main/index.html b/main/index.html index a4bc5802..3f5c571c 100644 --- a/main/index.html +++ b/main/index.html @@ -1,4 +1,5 @@ - + + @@ -23,7 +24,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -78,393 +45,261 @@

Changelog

-

teal.goshawk 0.2.0.9016 -

+

teal.goshawk 0.2.0.9017

-

teal.goshawk 0.2.0 -

+

teal.goshawk 0.2.0

-

Breaking Changes -

- -
+

Breaking Changes

+
-

Enhancements -

-
+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.15 -

+

teal.goshawk 0.1.15

-

Enhancements -

-
+
-

Breaking changes -

-
+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.14 -

+

teal.goshawk 0.1.14

-

Enhancements -

-
+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.13 -

+

teal.goshawk 0.1.13

-

Miscellaneous -

-
+
-

teal.goshawk 0.1.12 -

+

teal.goshawk 0.1.12

-

Breaking Changes -

- -
+

Breaking Changes

+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.11 -

+

teal.goshawk 0.1.11

-

Enhancements -

- -
+

Enhancements

+
-

Bug Fixes -

- -
+

Bug Fixes

+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.10 -

+

teal.goshawk 0.1.10

-

New Features -

- -
+

New Features

+
-

Breaking Changes -

-
+ +
-

Bug Fixes -

- -
+

Bug Fixes

+
-

Miscellaneous -

-
+
-

teal.goshawk 0.1.9 -

+

teal.goshawk 0.1.9

-

Enhancements -

-
+
-

teal.goshawk 0.1.8 -

+

teal.goshawk 0.1.8

-

Enhancements -

-
+
-

Bug fixes -

- -
+

Bug fixes

+
-

Miscellaneous -

- -
+

Miscellaneous

+
-

teal.goshawk 0.1.7 -

+

teal.goshawk 0.1.7

-

Enhancements -

-
+ +
-

Bug fixes -

-
+ +
-

Miscellaneous -

- -
+

Miscellaneous

+
-

teal.goshawk 0.1.6 -

+

teal.goshawk 0.1.6

-

Enhancements -

-
+ +
-

General -

-
+
-

teal.goshawk 0.1.5 -

-
+
-

teal.goshawk 0.1.4 -

-
+
-

teal.goshawk 0.1.3 -

-
+
-

teal.goshawk 0.1.2 -

-
+
-

teal.goshawk 0.1.1 -

- -
+

teal.goshawk 0.1.1

+ - + - + + + - - diff --git a/main/pkgdown.yml b/main/pkgdown.yml index ef279cff..f1b676d7 100644 --- a/main/pkgdown.yml +++ b/main/pkgdown.yml @@ -5,7 +5,7 @@ articles: data-expectations: data-expectations.html teal-goshawk: teal-goshawk.html user-guide: user-guide.html -last_built: 2024-10-28T15:57Z +last_built: 2024-11-08T14:08Z urls: reference: https://insightsengineering.github.io/teal.goshawk/reference article: https://insightsengineering.github.io/teal.goshawk/articles diff --git a/main/reference/get_choices.html b/main/reference/get_choices.html index 792ca27d..33fbcd66 100644 --- a/main/reference/get_choices.html +++ b/main/reference/get_choices.html @@ -1,29 +1,13 @@ - - - - - - -Get Choices — get_choices • teal.goshawk - - - - - -Get Choices — get_choices • teal.goshawk - - - - - +Otherwise, it returns the input as is."> Skip to contents @@ -31,7 +15,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -97,43 +62,35 @@

Get Choices

-

Usage -

+

Usage

get_choices(choices)
-

Arguments -

+

Arguments

-
-
choices -
+
choices

An object that contains choices.

-
-
+
-

Value -

+

Value

A vector of choices.

- + - + + + - - diff --git a/main/reference/include_css_files.html b/main/reference/include_css_files.html index b470cf5c..6c8dd004 100644 --- a/main/reference/include_css_files.html +++ b/main/reference/include_css_files.html @@ -1,25 +1,9 @@ - - - - - - -Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.goshawk - - - - - -Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.goshawk - - - - - +as needed. Thus, we do not export this method."> Skip to contents @@ -27,7 +11,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -91,43 +56,35 @@

Include CSS files from /inst/css/ package director
-

Usage -

+

Usage

include_css_files(pattern = "*")
-

Arguments -

+

Arguments

-
-
pattern -
+
pattern

(character) pattern of files to be included

-
-
+
-

Value -

+

Value

HTML code that includes CSS files

- + - + + + - - diff --git a/main/reference/index.html b/main/reference/index.html index 4a38644e..2add31ca 100644 --- a/main/reference/index.html +++ b/main/reference/index.html @@ -1,19 +1,5 @@ - - - - - - -Package index • teal.goshawk - - - - - - - - - + +Package index • teal.goshawk Skip to contents @@ -21,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -77,117 +44,93 @@

Package index

-

Modules -

+

Modules

These modules render the UI and call the respective longitudinal visualization function

-
-
+
-
-
+
tm_g_gh_boxplot()
Box Plot
-
-
-
+
tm_g_gh_correlationplot()
Scatter Plot Teal Module For Biomarker Analysis
-
-
-
+
tm_g_gh_density_distribution_plot()
Density Distribution Plot
-
-
-
+
tm_g_gh_lineplot()
Line plot
-
-
-
+
tm_g_gh_spaghettiplot()
Spaghetti Plot
-
-
-
-

Helper -

+
+

Helper

Utility functions

-
-
+
-
-
+
maptrt()
helper for writing arm mapping and ordering code.
-
-
-
-

Deprecated -

+
+

Deprecated

These functions have been deprecated

-
-
+
-
-
+
tm_g_gh_scatterplot() deprecated
Scatter Plot Teal Module For Biomarker Analysis
-
-
+ - + - + + + - - diff --git a/main/reference/maptrt.html b/main/reference/maptrt.html index b04dc176..db6df5ab 100644 --- a/main/reference/maptrt.html +++ b/main/reference/maptrt.html @@ -1,21 +1,5 @@ - - - - - - -helper for writing arm mapping and ordering code. — maptrt • teal.goshawk - - - - - - - - - - - + +helper for writing arm mapping and ordering code. — maptrt • teal.goshawk Skip to contents @@ -23,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -85,31 +50,24 @@

helper for writing arm mapping and ordering code.

-

Usage -

+

Usage

maptrt(df_armvar, code = c("M", "O"))
-

Arguments -

+

Arguments

-
-
df_armvar -
+
df_armvar

the dataframe and column name containing treatment code. e.g. ADSL$ARMCD

-
code -
+
code

controls whether mapping or ordering code is written to console. Valid values: "M" and "O".

-
-
+
-

Details -

+

Details

SPA configure study specific pre-processing for deploying goshawk. writing the code for ARM mapping and ordering is tedious. this function helps to get that started by providing the left hand side of the mapping and ordering syntax. call the function and then copy and paste the resulting code from the console @@ -117,8 +75,7 @@

Details
-

Examples -

+

Examples

ADSL <- rADSL
 
 # get treatment mapping code
@@ -137,19 +94,17 @@ 

Examples -

+
-

+ + + - - diff --git a/main/reference/report_card_template_goshawk.html b/main/reference/report_card_template_goshawk.html index 8163d102..aa06d3fc 100644 --- a/main/reference/report_card_template_goshawk.html +++ b/main/reference/report_card_template_goshawk.html @@ -1,25 +1,9 @@ - - - - - - -Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk • teal.goshawk - - - - - -Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk • teal.goshawk - - - - - +Additionally, it display selected constraint options."> Skip to contents @@ -27,7 +11,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -79,8 +44,7 @@
@@ -92,8 +56,7 @@

Template Function for TealReportCard Creation and Customization

-

Usage -

+

Usage

report_card_template_goshawk(
   title,
   label,
@@ -106,76 +69,59 @@ 

Usage

-

Arguments -

+

Arguments

-
-
title -
+
title

(character(1)) title of the card (unless overwritten by label)

-
label -
+
label

(character(1)) label provided by the user when adding the card

-
with_filter -
+
with_filter

(logical(1)) flag indicating to add filter state

-
filter_panel_api -
+
filter_panel_api

(FilterPanelAPI) object with API that allows the generation of the filter state in the report

-
constraint_list -
-
-

(list) a list containing constraint variables, including:

-
    -
  • constraint_var (character(1)) the constraint variable name.

  • +
    constraint_list
    +

    (list) a list containing constraint variables, including:

    • constraint_var (character(1)) the constraint variable name.

    • constraint_range_min (numeric(1)) the minimum constraint range value.

    • constraint_range_max (numeric(1)) the maximum constraint range value.

    • -
    -
    +
-
constraint_description -
+
constraint_description

(character(1)) description of the constraints.

-
style -
+
style

(character(1)) style of the constraint text block. options: default, verbatim (default is default).

-
-
+
-

Value -

+

Value

(TealReportCard) populated with a title, description, and filter state

- + - + + + - - diff --git a/main/reference/srv_arbitrary_lines.html b/main/reference/srv_arbitrary_lines.html index 178ba563..0079bcb5 100644 --- a/main/reference/srv_arbitrary_lines.html +++ b/main/reference/srv_arbitrary_lines.html @@ -1,23 +1,7 @@ - - - - - - -Server module to arbitrary lines — srv_arbitrary_lines • teal.goshawk - - - - - - - - - - - + +Server module to arbitrary lines — srv_arbitrary_lines • teal.goshawk Skip to contents @@ -25,7 +9,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -88,45 +53,37 @@

Server module to arbitrary lines

-

Usage -

+

Usage

srv_arbitrary_lines(id)
-

Arguments -

+

Arguments

-
-
id -
+
id

An ID string that corresponds with the ID used to call the module's UI function.

-
-
+
-

Value -

+

Value

(reactive) returning a list containing line_arb, line_arb_color, line_arb_label which are validated and could be passed to goshawk plot functions.

- + - + + + - - diff --git a/main/reference/teal.goshawk-package.html b/main/reference/teal.goshawk-package.html index 151b1765..4bb5fae4 100644 --- a/main/reference/teal.goshawk-package.html +++ b/main/reference/teal.goshawk-package.html @@ -1,21 +1,5 @@ - - - - - - -teal.goshawk core packages — teal.goshawk-package • teal.goshawk - - - - - - - - - - - + +teal.goshawk core packages — teal.goshawk-package • teal.goshawk Skip to contents @@ -23,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -86,30 +51,21 @@

teal.goshawk core packages

-

Details -

+

Details

The data used for teal.goshawk have some constraints. It must contain the columns AVISITCD, BASE, BASE2, AVALU, LBSTRESC, LOQFL, CHG2, and PCHG2.

-

Author -

+

Author

Maintainer: Nick Paszty nick.paszty@gene.com

-

Authors:

-
+ - + - + + + - - diff --git a/main/reference/tm_g_gh_boxplot.html b/main/reference/tm_g_gh_boxplot.html index 2f78840d..6e86fc00 100644 --- a/main/reference/tm_g_gh_boxplot.html +++ b/main/reference/tm_g_gh_boxplot.html @@ -1,23 +1,7 @@ - - - - - - -Box Plot — tm_g_gh_boxplot • teal.goshawk - - - - - - - - - - - + +Box Plot — tm_g_gh_boxplot • teal.goshawk Skip to contents @@ -25,7 +9,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -88,8 +53,7 @@

Box Plot

-

Usage -

+

Usage

tm_g_gh_boxplot(
   label,
   dataname,
@@ -121,167 +85,135 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ALB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
param -
+
param

list of biomarkers of interest.

-
yaxis_var -
+
yaxis_var

name of variable containing biomarker results displayed on y-axis e.g. AVAL. When not provided, it defaults to choices_selected(c("AVAL", "CHG"), "AVAL").

-
xaxis_var -
+
xaxis_var

variable to categorize the x-axis. When not provided, it defaults to choices_selected("AVISITCD", "AVISITCD").

-
facet_var -
+
facet_var

variable to facet the plots by. When not provided, it defaults to choices_selected(c("ARM", "ACTARM"), "ARM").

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
color_manual -
+
color_manual

vector of colors applied to treatment values.

-
shape_manual -
+
shape_manual

vector of symbols applied to LOQ values.

-
facet_ncol -
+
facet_ncol

numeric value indicating number of facets per row.

-
loq_legend -
+
loq_legend

loq legend toggle.

-
rotate_xlab -
+
rotate_xlab

45 degree rotation of x-axis values.

-
hline_arb -
+
hline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
hline_arb_color -
+
hline_arb_color

a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

-
hline_arb_label -
+
hline_arb_label

a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

-
hline_vars -
+
hline_vars

a character vector to name the columns that will define additional horizontal lines.

-
hline_vars_colors -
+
hline_vars_colors

a character vector naming the colors for the additional horizontal lines.

-
hline_vars_labels -
+
hline_vars_labels

a character vector naming the labels for the additional horizontal lines that will appear in the legend.

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
font_size -
+
font_size

font size control for title, x-axis label, y-axis label and legend.

-
dot_size -
+
dot_size

plot dot size.

-
alpha -
+
alpha

numeric vector to define transparency of plotted points.

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
-
+
-

Value -

+

Value

an module object

-

Author -

+

Author

Jeff Tomlinson (tomlinsj) jeffrey.tomlinson@roche.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -290,10 +222,10 @@ 

Examples library(stringr) # use non-exported function from goshawk - h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") + .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" @@ -301,7 +233,7 @@

Examples set.seed(1) ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( @@ -322,9 +254,9 @@

Examples ARMCD == "ARM B" ~ 2, ARMCD == "ARM A" ~ 3 ), - ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), + ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), - ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), + ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 50, ANRHI = 75 @@ -341,20 +273,17 @@

Examples )) %>% ungroup() - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] - attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] + attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]] attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit" attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit" # add LLOQ and ULOQ variables - ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL") + ALB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL") ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM") }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames - -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, @@ -386,19 +315,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/tm_g_gh_correlationplot.html b/main/reference/tm_g_gh_correlationplot.html index 01e3caa7..38ae8697 100644 --- a/main/reference/tm_g_gh_correlationplot.html +++ b/main/reference/tm_g_gh_correlationplot.html @@ -1,21 +1,5 @@ - - - - - - -Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot • teal.goshawk - - - - - - - - - - - + +Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot • teal.goshawk Skip to contents @@ -23,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -85,8 +50,7 @@

Scatter Plot Teal Module For Biomarker Analysis

-

Usage -

+

Usage

tm_g_gh_correlationplot(
   label,
   dataname,
@@ -127,206 +91,166 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
xaxis_param -
+
xaxis_param

biomarker selected for x-axis.

-
xaxis_var -
+
xaxis_var

name of variable containing biomarker results displayed on x-axis e.g. BASE.

-
yaxis_param -
+
yaxis_param

biomarker selected for y-axis.

-
yaxis_var -
+
yaxis_var

name of variable containing biomarker results displayed on y-axis e.g. AVAL.

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
color_manual -
+
color_manual

vector of colors applied to treatment values.

-
shape_manual -
+
shape_manual

vector of symbols applied to LOQ values.

-
facet_ncol -
+
facet_ncol

numeric value indicating number of facets per row.

-
visit_facet -
+
visit_facet

visit facet toggle.

-
trt_facet -
+
trt_facet

facet by treatment group trt_group.

-
reg_line -
+
reg_line

include regression line and annotations for slope and coefficient in visualization. Use with facet TRUE.

-
loq_legend -
+
loq_legend

loq legend toggle.

-
rotate_xlab -
+
rotate_xlab

45 degree rotation of x-axis values.

-
hline_arb -
+
hline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
hline_arb_color -
+
hline_arb_color

a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

-
hline_arb_label -
+
hline_arb_label

a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

-
hline_vars -
+
hline_vars

a character vector to name the columns that will define additional horizontal lines.

-
hline_vars_colors -
+
hline_vars_colors

a character vector naming the colors for the additional horizontal lines.

-
hline_vars_labels -
+
hline_vars_labels

a character vector naming the labels for the additional horizontal lines that will appear

-
vline_arb -
+
vline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
vline_arb_color -
+
vline_arb_color

a character vector of at most length of vline_arb. naming the color for the arbitrary horizontal lines.

-
vline_arb_label -
+
vline_arb_label

a character vector of at most length of vline_arb. naming the label for the arbitrary horizontal lines.

-
vline_vars -
+
vline_vars

a character vector to name the columns that will define additional vertical lines.

-
vline_vars_colors -
+
vline_vars_colors

a character vector naming the colors for the additional vertical lines.

-
vline_vars_labels -
+
vline_vars_labels

a character vector naming the labels for the additional vertical lines that will appear

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
font_size -
+
font_size

font size control for title, x-axis label, y-axis label and legend.

-
dot_size -
+
dot_size

plot dot size.

-
reg_text_size -
+
reg_text_size

font size control for regression line annotations.

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
-
+
-

Author -

+

Author

Nick Paszty (npaszty) paszty.nicholas@gene.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -334,22 +258,22 @@ 

Examples library(stringr) # use non-exported function from goshawk - h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") + .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" ) - color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C") + .color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C") # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA" - shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0) + .shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0) set.seed(1) ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate(AVISITCD = case_when( AVISIT == "SCREENING" ~ "SCR", @@ -379,7 +303,7 @@

Examples ifelse(grepl("A", ARMCD), 3, NA) ) )) %>% - mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>% + mutate(ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))])) %>% mutate(ARM = factor(ARM) %>% reorder(TRTORD)) %>% mutate( @@ -407,19 +331,16 @@

Examples paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit" attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit" # add LLOQ and ULOQ variables - ADLB_LOQS <- h_identify_loq_values(ADLB, "LOQFL") + ADLB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL") ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM") }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames - -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, @@ -471,19 +392,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/tm_g_gh_density_distribution_plot.html b/main/reference/tm_g_gh_density_distribution_plot.html index 7ee0794f..5c296044 100644 --- a/main/reference/tm_g_gh_density_distribution_plot.html +++ b/main/reference/tm_g_gh_density_distribution_plot.html @@ -1,23 +1,7 @@ - - - - - - -Density Distribution Plot — tm_g_gh_density_distribution_plot • teal.goshawk - - - - - - - - - - - + +Density Distribution Plot — tm_g_gh_density_distribution_plot • teal.goshawk Skip to contents @@ -25,7 +9,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -88,8 +53,7 @@

Density Distribution Plot

-

Usage -

+

Usage

tm_g_gh_density_distribution_plot(
   label,
   dataname,
@@ -115,133 +79,107 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
param -
+
param

biomarker selected.

-
xaxis_var -
+
xaxis_var

name of variable containing biomarker results displayed on x-axis e.g. BASE.

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
color_manual -
+
color_manual

vector of colors applied to treatment values.

-
color_comb -
+
color_comb

name or hex value for combined treatment color.

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
font_size -
+
font_size

font size control for title, x-axis label, y-axis label and legend.

-
line_size -
+
line_size

plot line thickness.

-
hline_arb -
+
hline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
hline_arb_color -
+
hline_arb_color

a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

-
hline_arb_label -
+
hline_arb_label

a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

-
facet_ncol -
+
facet_ncol

numeric value indicating number of facets per row.

-
comb_line -
+
comb_line

display combined treatment line toggle.

-
rotate_xlab -
+
rotate_xlab

45 degree rotation of x-axis values.

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
-
+
-

Details -

+

Details

None

-

Author -

+

Author

Nick Paszty (npaszty) paszty.nicholas@gene.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -249,14 +187,14 @@ 

Examples library(stringr) # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" ) ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( @@ -277,19 +215,17 @@

Examples ARMCD == "ARM B" ~ 2, ARMCD == "ARM A" ~ 3 ), - ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), + ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), - ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), + ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] - attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] + attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]] }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, @@ -326,19 +262,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/tm_g_gh_lineplot.html b/main/reference/tm_g_gh_lineplot.html index c1382ab1..81f13f8a 100644 --- a/main/reference/tm_g_gh_lineplot.html +++ b/main/reference/tm_g_gh_lineplot.html @@ -1,21 +1,5 @@ - - - - - - -Line plot — tm_g_gh_lineplot • teal.goshawk - - - - - - - - - - - + +Line plot — tm_g_gh_lineplot • teal.goshawk Skip to contents @@ -23,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -85,8 +50,7 @@

Line plot

-

Usage -

+

Usage

tm_g_gh_lineplot(
   label,
   dataname,
@@ -124,196 +88,159 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
param -
+
param

biomarker selected.

-
param_var_label -
+
param_var_label

single name of variable in analysis data that includes parameter labels.

-
xaxis_var -
+
xaxis_var

single name of variable in analysis data that is used as x-axis in the plot for the respective goshawk function.

-
yaxis_var -
+
yaxis_var

single name of variable in analysis data that is used as summary variable in the respective goshawk function.

-
xvar_level -
+
xvar_level

vector that can be used to define the factor level of xvar. Only use it when xvar is character or factor.

-
filter_var -
+
filter_var

data constraint variable.

-
filter_var_choices -
+
filter_var_choices

data constraint variable choices.

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
trt_group_level -
+
trt_group_level

vector that can be used to define factor level of trt_group.

-
shape_choices -
+
shape_choices

Vector or choices_selected object with names of ADSL variables which can be used to change shape

-
stat -
+
stat

string of statistics

-
hline_arb -
+
hline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
hline_arb_color -
+
hline_arb_color

a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

-
hline_arb_label -
+
hline_arb_label

a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

-
color_manual -
+
color_manual

string vector representing customized colors

-
xtick -
+
xtick

numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().

-
xlabel -
+
xlabel

vector with same length of xtick to define the label of x-axis tick values. Default value is waive().

-
rotate_xlab -
+
rotate_xlab

logical(1) value indicating whether to rotate x-axis labels.

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
plot_font_size -
+
plot_font_size

control font size for title, x-axis, y-axis and legend font.

-
dodge -
+
dodge

controls the position dodge of error bar

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
count_threshold -
+
count_threshold

minimum count of observations (as listed in the output table) to plot nodes on the graph

-
table_font_size -
+
table_font_size

controls the font size of values in the table

-
dot_size -
+
dot_size

plot dot size.

-
plot_relative_height_value -
+
plot_relative_height_value

numeric value between 500 and 5000 for controlling the starting value of the relative plot height slider

-
-
+
-

Value -

+

Value

shiny object

-

Author -

+

Author

Wenyi Liu (luiw2) wenyi.liu@roche.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -322,7 +249,7 @@ 

Examples library(nestcolor) # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" @@ -330,7 +257,7 @@

Examples ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( @@ -351,18 +278,16 @@

Examples ARMCD == "ARM B" ~ 2, ARMCD == "ARM A" ~ 3 ), - ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), + ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), - ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), + ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] - attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] + attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]] }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, @@ -390,19 +315,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/tm_g_gh_scatterplot.html b/main/reference/tm_g_gh_scatterplot.html index 2790d551..359ec195 100644 --- a/main/reference/tm_g_gh_scatterplot.html +++ b/main/reference/tm_g_gh_scatterplot.html @@ -1,25 +1,9 @@ - - - - - - -Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot • teal.goshawk - - - - - -Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot • teal.goshawk - - - - - +instead."> Skip to contents @@ -27,7 +11,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -91,8 +56,7 @@

Scatter Plot Teal Module For Biomarker Analysis

-

Usage -

+

Usage

tm_g_gh_scatterplot(
   label,
   dataname,
@@ -120,137 +84,110 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
param -
+
param

biomarker selected.

-
xaxis_var -
+
xaxis_var

name of variable containing biomarker results displayed on x-axis e.g. BASE.

-
yaxis_var -
+
yaxis_var

name of variable containing biomarker results displayed on y-axis e.g. AVAL.

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
color_manual -
+
color_manual

vector of colors applied to treatment values.

-
shape_manual -
+
shape_manual

vector of symbols applied to LOQ values.

-
facet_ncol -
+
facet_ncol

numeric value indicating number of facets per row.

-
trt_facet -
+
trt_facet

facet by treatment group trt_group.

-
reg_line -
+
reg_line

include regression line and annotations for slope and coefficient in visualization. Use with facet TRUE.

-
rotate_xlab -
+
rotate_xlab

45 degree rotation of x-axis values.

-
hline -
+
hline

y-axis value to position of horizontal line.

-
vline -
+
vline

x-axis value to position a vertical line.

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
font_size -
+
font_size

font size control for title, x-axis label, y-axis label and legend.

-
dot_size -
+
dot_size

plot dot size.

-
reg_text_size -
+
reg_text_size

font size control for regression line annotations.

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
-
+
-

Author -

+

Author

Nick Paszty (npaszty) paszty.nicholas@gene.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -258,7 +195,7 @@ 

Examples library(stringr) # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" @@ -266,7 +203,7 @@

Examples ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( @@ -287,18 +224,16 @@

Examples ARMCD == "ARM B" ~ 2, ARMCD == "ARM A" ~ 3 ), - ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), + ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), - ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), + ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] - attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] + attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]] }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( @@ -340,19 +275,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/tm_g_gh_spaghettiplot.html b/main/reference/tm_g_gh_spaghettiplot.html index d0c63539..359beb3a 100644 --- a/main/reference/tm_g_gh_spaghettiplot.html +++ b/main/reference/tm_g_gh_spaghettiplot.html @@ -1,23 +1,7 @@ - - - - - - -Spaghetti Plot — tm_g_gh_spaghettiplot • teal.goshawk - - - - - - - - - - - + +Spaghetti Plot — tm_g_gh_spaghettiplot • teal.goshawk Skip to contents @@ -25,7 +9,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -88,8 +53,7 @@

Spaghetti Plot

-

Usage -

+

Usage

tm_g_gh_spaghettiplot(
   label,
   dataname,
@@ -127,202 +91,164 @@ 

Usage

-

Arguments -

+

Arguments

-
-
label -
+
label

menu item label of the module in the teal app.

-
dataname -
+
dataname

analysis data passed to the data argument of init. E.g. ADaM structured laboratory data frame ADLB.

-
param_var -
+
param_var

name of variable containing biomarker codes e.g. PARAMCD.

-
param -
+
param

biomarker selected.

-
param_var_label -
+
param_var_label

single name of variable in analysis data that includes parameter labels.

-
idvar -
+
idvar

name of unique subject id variable.

-
xaxis_var -
+
xaxis_var

single name of variable in analysis data that is used as x-axis in the plot for the respective goshawk function.

-
yaxis_var -
+
yaxis_var

single name of variable in analysis data that is used as summary variable in the respective goshawk function.

-
xaxis_var_level -
+
xaxis_var_level

vector that can be used to define the factor level of xaxis_var. Only use it when xaxis_var is character or factor.

-
filter_var -
+
filter_var

data constraint variable.

-
trt_group -
+
trt_group

choices_selected object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.

-
trt_group_level -
+
trt_group_level

vector that can be used to define factor level of trt_group.

-
group_stats -
+
group_stats

control group mean or median overlay.

-
man_color -
+
man_color

string vector representing customized colors

-
color_comb -
+
color_comb

name or hex value for combined treatment color.

-
xtick -
+
xtick

numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().

-
xlabel -
+
xlabel

vector with same length of xtick to define the label of x-axis tick values. Default value is waive().

-
rotate_xlab -
+
rotate_xlab

logical(1) value indicating whether to rotate x-axis labels

-
facet_ncol -
+
facet_ncol

numeric value indicating number of facets per row.

-
free_x -
+
free_x

logical(1) should scales be "fixed" (FALSE) of "free" (TRUE) for x-axis in facet_wrap scales parameter.

-
plot_height -
+
plot_height

controls plot height.

-
plot_width -
+
plot_width

optional, controls plot width.

-
font_size -
+
font_size

control font size for title, x-axis, y-axis and legend font.

-
dot_size -
+
dot_size

plot dot size.

-
hline_arb -
+
hline_arb

numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.

-
hline_arb_color -
+
hline_arb_color

a character vector of at most length of hline_arb. naming the color for the arbitrary horizontal lines.

-
hline_arb_label -
+
hline_arb_label

a character vector of at most length of hline_arb. naming the label for the arbitrary horizontal lines.

-
hline_vars -
+
hline_vars

a character vector to name the columns that will define additional horizontal lines.

-
hline_vars_colors -
+
hline_vars_colors

a character vector naming the colors for the additional horizontal lines.

-
hline_vars_labels -
+
hline_vars_labels

a character vector naming the labels for the additional horizontal lines that will appear in the legend.

-
pre_output -
+
pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

-
post_output -
+
post_output

(shiny.tag) optional, with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

-
-
+
-

Value -

+

Value

shiny object

-

Author -

+

Author

Wenyi Liu (luiw2) wenyi.liu@roche.com

Balazs Toth (tothb2) toth.balazs@gene.com

-

Examples -

+

Examples

# Example using ADaM structure analysis dataset.
 data <- teal_data()
 data <- within(data, {
@@ -330,10 +256,10 @@ 

Examples library(stringr) # use non-exported function from goshawk - h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") + .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk") # original ARM value = dose value - arm_mapping <- list( + .arm_mapping <- list( "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination" @@ -341,7 +267,7 @@

Examples set.seed(1) ADSL <- rADSL ADLB <- rADLB - var_labels <- lapply(ADLB, function(x) attributes(x)$label) + .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( @@ -362,9 +288,9 @@

Examples ARMCD == "ARM B" ~ 2, ARMCD == "ARM A" ~ 3 ), - ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), + ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), - ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), + ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 30, ANRHI = 75 @@ -378,19 +304,17 @@

Examples paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() - attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]] - attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]] + attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]] + attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]] attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit" attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit" # add LLOQ and ULOQ variables - ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL") + ALB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL") ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM") }) -datanames <- c("ADSL", "ADLB") -datanames(data) <- datanames -join_keys(data) <- default_cdisc_join_keys[datanames] +join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, @@ -431,19 +355,17 @@

Examples -

+
- + + + - - diff --git a/main/reference/toggle_slider.html b/main/reference/toggle_slider.html index 1bbf60fb..513d57ff 100644 --- a/main/reference/toggle_slider.html +++ b/main/reference/toggle_slider.html @@ -1,25 +1,9 @@ - - - - - - -UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider • teal.goshawk - - - - - -UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider • teal.goshawk - - - - - +The toggle button will show two numeric input field for selecting the from and to range."> Skip to contents @@ -27,7 +11,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -91,8 +56,7 @@

UI with a toggleable dichotomous slider to change between slider and numeric
-

Usage -

+

Usage

toggle_slider_ui(id, label)
 
 toggle_slider_server(id, data_state, ...)
@@ -101,47 +65,38 @@ 

Usage

-

Arguments -

+

Arguments

-
-
id -
+
id

character module id

-
label -
+
label

label label for input field, e.g. slider or numeric inputs

-
... -
+
...

additional parameters to pass to sliderInput

-
-
+
-

Value -

+

Value

NULL.

- + - + + + - - diff --git a/main/reference/ui_arbitrary_lines.html b/main/reference/ui_arbitrary_lines.html index 9c72b992..a16df4a2 100644 --- a/main/reference/ui_arbitrary_lines.html +++ b/main/reference/ui_arbitrary_lines.html @@ -1,21 +1,5 @@ - - - - - - -UI module to arbitrary lines — ui_arbitrary_lines • teal.goshawk - - - - - - - - - - - + +UI module to arbitrary lines — ui_arbitrary_lines • teal.goshawk Skip to contents @@ -23,7 +7,7 @@ teal.goshawk - 0.2.0.9016 + 0.2.0.9017
part of NESTpharmaverse
+ @@ -85,8 +50,7 @@

UI module to arbitrary lines

-

Usage -

+

Usage

ui_arbitrary_lines(
   id,
   line_arb,
@@ -97,63 +61,52 @@ 

Usage

-

Arguments -

+

Arguments

-
-
id -
+
id

(character(1))
defining namespace of the shiny module.

-
line_arb -
+
line_arb

(numeric)
default values for the textInput defining values of arbitrary lines

-
line_arb_label -
+
line_arb_label

(character)
default values for the textInput defining labels of arbitrary lines

-
line_arb_color -
+
line_arb_color

(character)
default values for the textInput defining colors of arbitrary lines

-
title -
+
title

(character(1))
title of the arbitrary lines input. The default is "Arbitrary Horizontal Lines".

-
-
+
-

Value -

+

Value

(shiny.tag) an input to define values, colors and labels for arbitrary straight lines.

- + - + + + - - diff --git a/main/search.json b/main/search.json index 022a7921..e747f9fe 100644 --- a/main/search.json +++ b/main/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Data Expectations","text":"teal.goshawk expects provided ADSL accompanying ADLB clinical trials data set ADaM format. information ADaM please ADaM standards. package provides ready--use teal modules can embed teal application. modules generate highly customizable plots outputs often used exploratory data analysis, e.g.: box plots - tm_g_gh_boxplot() correlation scatter plots - tm_g_gh_correlationplot() tm_g_gh_scatterplot() density distribution plots - tm_g_gh_density_distribution_plot() line plots - tm_g_gh_lineplot() spaghetti plots - tm_g_spaghettiplot() See package functions / modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"adsl","dir":"Articles","previous_headings":"Data Expectations","what":"ADSL","title":"Data Expectations","text":"subject level data set one record per subject includes variables intended used plot splitting e.g. ABCWK24 represents two level outcome variable values \"Y\" \"N\" Week 24.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"adlb","dir":"Articles","previous_headings":"Data Expectations","what":"ADLB","title":"Data Expectations","text":"Basic Data Structure (BDS) data set meaning multiple records per subject per assay (PARAM) across unique time points. Additional variables intended used plot splitting joined ADLB. See ADSL example ABCWK24 need joined ADLB","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"other-basic-data-structures","dir":"Articles","previous_headings":"Data Expectations","what":"Other Basic Data Structures","title":"Data Expectations","text":"BDS data sets provisioned teal.goshawk like ADQS contains multiple records per subject per question (PARAM) across unique time points. However cases ADLB likely workarounds needed. example concept assay units, stored AVALU, really relevant BDS like ADQS contains questionnaire data. Given teal.goshawk expects AVALU variable uses values plot title y-axis label, AVALU need added ADQS appropriate value: Perhaps \"Q\". value provided \"()\" portion title y-axis label empty.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"required-variables","dir":"Articles","previous_headings":"","what":"Required Variables","title":"Data Expectations","text":"Several variables required realize full functionality teal.goshawk.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"trtord","dir":"Articles","previous_headings":"Required Variables","what":"TRTORD","title":"Data Expectations","text":"Definition: variable orders treatment values legend Rationale: Allows congruent ordering compared outputs generated study team Alternative: Variable required","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"avisitcd","dir":"Articles","previous_headings":"Required Variables","what":"AVISITCD","title":"Data Expectations","text":"Definition: variable contains abbreviated values AVISIT values Rationale: Many AVISIT values long contain arguably superfluous information cases. Using long values x-axis tick labels can really chew real estate area available plot. Using thoughtful abbreviations conveys chronology substantive loss information maximizes area available plot. Alternative: cases creating abbreviations helpful simply set AVISITCD <- AVISIT","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"avisitcdn","dir":"Articles","previous_headings":"Required Variables","what":"AVISITCDN","title":"Data Expectations","text":"Definition: variable contains numeric portion AVISITCD values Rationale: Often AVISITN contains values particularly helpful reflect proportional chronology visits. AVISITCD created helpful create numeric values AVISITCD values can seen intuitively reflecting visit chronology. example: 0, 2, 4, 12, 24, 56, 84 etc. weeks 0, 14, 28, 84, 168, 392, 588 etc. days. Using , longitudinal visualization x-axis nicely reflect proportional distances visits. Alternative: cases creating intuitive numeric chronology helpful simply set AVISITCDN <- AVISITN","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"avalu","dir":"Articles","previous_headings":"Required Variables","what":"AVALU","title":"Data Expectations","text":"Definition: Analysis Value Unit Rationale: Used plot title y-axis labels. Please see \"BDS data sets\" comments Alternative: Variable required.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"lbstresc","dir":"Articles","previous_headings":"Required Variables","what":"LBSTRESC","title":"Data Expectations","text":"Definition: SDTM Character Result/Finding Std Format Rationale: character type variable, variable contains values include limits quantitation (LOQ). might look like \"2.1<\" \">20.7\". case AVAL often missing. important able still capture values following derivation used needed LOQFL variable set \"Y\". signifies AVAL value record derived. - values limit quantitation, AVAL set numeric portion LBSTRESC divided 2. - values limit quantitation, AVAL set numeric portion LBSTRESC. Alternative: Variable required","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"loqfl","dir":"Articles","previous_headings":"Required Variables","what":"LOQFL","title":"Data Expectations","text":"Definition: ADaM standard variable represents Limit Quantitation Flag Rationale: Set \"Y\" LBSTRESC value used populate AVAL LBSTRESC value either limit quantitation assay limit quantitation assay. Derivations AVAL LOQFL look like following mutate() statement. - AVAL = if_else(grepl(\"<|>\", LBSTRESC), .numeric(gsub(\"[^0-9, .]+\", \"\", LBSTRESC)), AVAL) - LOQFL = if_else(grepl(\"<|>\", LBSTRESC), \"Y\", \"N\") Alternative: limit quantitation concept relevant please set LOQFL <- \"N\"","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"base2","dir":"Articles","previous_headings":"Required Variables","what":"BASE2","title":"Data Expectations","text":"Definition: ADaM standard variable represents assay value Screening Rationale: change Screening visit analyses needed variable contains assay value Screening Alternative: Screening visit analyses relevant please set BASE2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"chg2","dir":"Articles","previous_headings":"Required Variables","what":"CHG2","title":"Data Expectations","text":"Definition: ADaM standard variable represents change Screening assay value Rationale: change Screening visit analyses needed variable contains assay value change Screening subsequent visit Alternative: Screening visit analyses relevant please set CHG2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"pchg2","dir":"Articles","previous_headings":"Required Variables","what":"PCHG2","title":"Data Expectations","text":"Definition: ADaM standard variable represents percent change Screening assay value Rationale: percent change Screening visit analyses needed variable contains assay value percent change Screening subsequent visit Alternative: Screening visit analyses relevant please set PCHG2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"additional-variables","dir":"Articles","previous_headings":"","what":"Additional Variables","title":"Data Expectations","text":"additional data manipulations performed create variables useful context longitudinal visualizations","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/data-expectations.html","id":"avall2-basel2-base2l2","dir":"Articles","previous_headings":"Additional Variables","what":"AVALL2, BASEL2, BASE2L2","title":"Data Expectations","text":"Description: Log 2 AVAL, BASE BASE2 respectively Rationale: transformation addresses data variance improve interpretability appearance plots.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/teal-goshawk.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting started with teal.goshawk","text":"teal.goshawk package implementing number teal modules helpful exploring clinical trials data, specifically targeted data following ADaM standards. teal.goshawk modules can used data ADaM standard clinical data features package likely applicable. concepts presented require knowledge core features teal, specifically launch teal application pass data . Therefore, highly recommended refer README file introductory vignette teal package.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/teal-goshawk.html","id":"main-features","dir":"Articles","previous_headings":"","what":"Main features","title":"Getting started with teal.goshawk","text":"package provides ready--use teal modules can embed teal application. modules generate highly customizable plots outputs often used exploratory data analysis, e.g.: box plots - tm_g_gh_boxplot() correlation scatter plots - tm_g_gh_correlationplot() tm_g_gh_scatterplot() density distribution plots - tm_g_gh_density_distribution_plot() line plots - tm_g_gh_lineplot() spaghetti plots - tm_g_spaghettiplot() See package functions / modules.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/teal-goshawk.html","id":"a-simple-application","dir":"Articles","previous_headings":"","what":"A simple application","title":"Getting started with teal.goshawk","text":"teal.goshawk module needs embedded inside shiny / teal application interact . need load teal teal.goshawk already depends . nestcolor optional package can loaded apply standardized NEST color palette module plots. simple application including box plot module look like : Refer Get Started section teal.modules.clinical package provides additional detail teal concepts applied another simple app example. Please see additional information Articles data expectations, requirements pre/post-processing rationale","code":"library(teal.goshawk) library(nestcolor) data <- teal_data() data <- within(data, { ADSL <- goshawk::rADSL %>% mutate(TRTORD = case_when( TRT01P == \"A: Drug X\" ~ 1, TRT01P == \"C: Combination\" ~ 2, TRT01P == \"B: Placebo\" ~ 3, TRUE ~ as.numeric(NA) ) ) ADLB <- goshawk::rADLB %>% mutate(AVISITCD = AVISIT, TRTORD = case_when( TRT01P == \"A: Drug X\" ~ 1, TRT01P == \"C: Combination\" ~ 2, TRT01P == \"B: Placebo\" ~ 3, TRUE ~ as.numeric(NA) ) ) }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data)<- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- teal::init( data = data, modules = list( tm_g_gh_boxplot( label = \"Longitudinal Analysis\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = teal.transform::choices_selected( choices = c(\"ALT\", \"CRP\", \"IGA\"), selected = c(\"ALT\") ), trt_group = teal.transform::choices_selected( choices = c(\"TRT01P\", \"TRT01A\"), selected = c(\"TRT01P\") ), facet_var = teal.transform::choices_selected( choices = c(\"TRT01P\", \"TRT01A\"), selected = c(\"TRT01P\") ), rotate_xlab = TRUE ) ) ) if (interactive()) shiny::shinyApp(app$ui, app$server)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"paramcd","dir":"Articles","previous_headings":"User Guide","what":"PARAMCD","title":"User Guide","text":"“Parameter Code” (PARAMCD) variable used select biomarker/lab interest. biomarker/lab selection pull menu items concatenation PARAMCD PARAM ease identification.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"pull-down-menus","dir":"Articles","previous_headings":"User Guide","what":"Pull down menus","title":"User Guide","text":"containing many items include search functionality ease finding menu items.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"avisit","dir":"Articles","previous_headings":"User Guide","what":"AVISIT","title":"User Guide","text":"“Analysis Visit” (AVISIT) variable used display visit abbreviated analysis visit value (AVISITCD). See Data Expectations article detail AVISITCD variable.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"the-data-constraint-filter","dir":"Articles","previous_headings":"User Guide","what":"The Data Constraint Filter","title":"User Guide","text":"Selecting Screening constraint remove subjects satisfy filter range based screening value given assay. Selecting Baseline constraint remove subjects satisfy filter range based baseline value given assay. Example: Consider subject #58 baseline value 5 assay x range assay x across subjects 1 10. baseline constraint selected value changed range 7 10 subjects meet condition removed visualizations. Since subject #58 baseline value 5 assay x one subjects removed.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"data-point-brushing","dir":"Articles","previous_headings":"User Guide","what":"Data Point Brushing","title":"User Guide","text":"Selecting specific data points reveal Subject ID data available Box, Correlation Spaghetti Plot visualizations.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"log2---points-to-consider","dir":"Articles","previous_headings":"User Guide","what":"Log2 - Points to Consider","title":"User Guide","text":"biomarker/lab values already log2 transformed represent change value. excluded log2 transformation applied biomarkers/labs large. Biomarkers/labs value 0 log2 transformed taking log2 minimum non-zero value biomarker/lab, divided 2.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"right-hand-data-filter-panel","dir":"Articles","previous_headings":"User Guide","what":"Right Hand Data Filter Panel","title":"User Guide","text":"filters hierarchical used filter analysis variables. filter analysis variables please use filtering controls available left hand panel. Use right hand data panel filters filter categorical variables: AVISIT exclude/include specific visits visualizations. LOQFL exclude/include LOQ flagged values. SEX exclude/include specific gender. etc.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/articles/user-guide.html","id":"visualization-specifics","dir":"Articles","previous_headings":"User Guide","what":"Visualization Specifics","title":"User Guide","text":"Box Plot: Selecting STUDYID X-Axis variable produce visualization subjects combined identify study x-axis. Correlation Plot data constraint can placed Screening Baseline records associated analysis variable biomarker/lab selected x-axis . Limit Quantification (LOQFL) flag set either biomarker/lab values identified LOQ. brushing table column header reflects LOQFL_COMB. “Regression Line” option used conjunction “Treatment Faceting” option. Otherwise per treatment regression formula coefficient annotations overlay. Line Plot: error displayed related plot height ’s best first alter relative plot height left panel using slider. additional plot height control, use icons upper right corner visualization.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nick Paszty. Author, maintainer. Dawid Kaledkowski. Author. Mahmoud Hallal. Author. Pawel Rucki. Author. Wenyi Liu. Author. Jeffrey Tomlinson. Author. Bali Toth. Author. Junlue Zhao. Author. Maciej Nasinski. Author. Maximilian Mordig. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paszty N, Kaledkowski D, Hallal M, Rucki P, Liu W, Tomlinson J, Toth B, Zhao J, Nasinski M (2024). teal.goshawk: Longitudinal Visualization 'teal' Modules. R package version 0.2.0.9016, https://github.com/insightsengineering/teal.goshawk/, https://insightsengineering.github.io/teal.goshawk/main/.","code":"@Manual{, title = {teal.goshawk: Longitudinal Visualization `teal` Modules}, author = {Nick Paszty and Dawid Kaledkowski and Mahmoud Hallal and Pawel Rucki and Wenyi Liu and Jeffrey Tomlinson and Bali Toth and Junlue Zhao and Maciej Nasinski}, year = {2024}, note = {R package version 0.2.0.9016, https://github.com/insightsengineering/teal.goshawk/}, url = {https://insightsengineering.github.io/teal.goshawk/main/}, }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/index.html","id":"tealgoshawk","dir":"","previous_headings":"","what":"Longitudinal Visualization `teal` Modules","title":"Longitudinal Visualization `teal` Modules","text":"teal.goshawk package provides teal modules longitudinal visualization functions goshawk R package. enables teal app developers easily create applications explore longitudinal clinical trial data.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/index.html","id":"modules","dir":"","previous_headings":"","what":"Modules","title":"Longitudinal Visualization `teal` Modules","text":"tm_g_gh_boxplot tm_g_gh_correlationplot tm_g_gh_density_distribution_plot tm_g_gh_lineplot tm_g_gh_spaghettiplot","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Longitudinal Visualization `teal` Modules","text":"","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.goshawk@*release\") # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.goshawk\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/get_choices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Choices — get_choices","title":"Get Choices — get_choices","text":"function returns choices based class input. input class delayed_data, returns subset input. subset NULL input contains var_label var_choices, throws error prompting resolve delayed inputs. Otherwise, returns input .","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/get_choices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Choices — get_choices","text":"","code":"get_choices(choices)"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/get_choices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Choices — get_choices","text":"choices object contains choices.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/get_choices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Choices — get_choices","text":"vector choices.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/maptrt.html","id":null,"dir":"Reference","previous_headings":"","what":"helper for writing arm mapping and ordering code. — maptrt","title":"helper for writing arm mapping and ordering code. — maptrt","text":"Provides lines code left hand side arm mapping. user must provide right hand side","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/maptrt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"helper for writing arm mapping and ordering code. — maptrt","text":"","code":"maptrt(df_armvar, code = c(\"M\", \"O\"))"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/maptrt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"helper for writing arm mapping and ordering code. — maptrt","text":"df_armvar dataframe column name containing treatment code. e.g. ADSL$ARMCD code controls whether mapping ordering code written console. Valid values: \"M\" \"O\".","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/maptrt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"helper for writing arm mapping and ordering code. — maptrt","text":"SPA configure study specific pre-processing deploying goshawk. writing code ARM mapping ordering tedious. function helps get started providing left hand side mapping ordering syntax. call function copy paste resulting code console app.R file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/maptrt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"helper for writing arm mapping and ordering code. — maptrt","text":"","code":"ADSL <- rADSL # get treatment mapping code maptrt(df_armvar = ADSL$ARMCD, code = \"M\") #> #> \"ARM A\" = \"\", #> \"ARM C\" = \"\", #> \"ARM B\" = \"\", # get treatment ordering code maptrt(df_armvar = ADSL$ARMCD, code = \"O\") #> #> ARMCD == \"ARM A\" ~ , #> ARMCD == \"ARM C\" ~ , #> ARMCD == \"ARM B\" ~ ,"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/report_card_template_goshawk.html","id":null,"dir":"Reference","previous_headings":"","what":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"function generates report card title, optional description, option append filter state list. Additionally, display selected constraint options.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/report_card_template_goshawk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"","code":"report_card_template_goshawk( title, label, with_filter, filter_panel_api, constraint_list, constraint_description = NULL, style = \"default\" )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/report_card_template_goshawk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"title (character(1)) title card (unless overwritten label) label (character(1)) label provided user adding card with_filter (logical(1)) flag indicating add filter state filter_panel_api (FilterPanelAPI) object API allows generation filter state report constraint_list (list) list containing constraint variables, including: constraint_var (character(1)) constraint variable name. constraint_range_min (numeric(1)) minimum constraint range value. constraint_range_max (numeric(1)) maximum constraint range value. constraint_description (character(1)) description constraints. style (character(1)) style constraint text block. options: default, verbatim (default default).","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/report_card_template_goshawk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"(TealReportCard) populated title, description, filter state","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/srv_arbitrary_lines.html","id":null,"dir":"Reference","previous_headings":"","what":"Server module to arbitrary lines — srv_arbitrary_lines","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"Server validate transform comma separated values vectors values passed goshawk functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/srv_arbitrary_lines.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"","code":"srv_arbitrary_lines(id)"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/srv_arbitrary_lines.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"id ID string corresponds ID used call module's UI function.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/srv_arbitrary_lines.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"(reactive) returning list containing line_arb, line_arb_color, line_arb_label validated passed goshawk plot functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/teal.goshawk-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.goshawk core packages — teal.goshawk-package","title":"teal.goshawk core packages — teal.goshawk-package","text":"teal.goshawk package renders UI calls respective biomarker visualization functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/teal.goshawk-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal.goshawk core packages — teal.goshawk-package","text":"data used teal.goshawk constraints. must contain columns AVISITCD, BASE, BASE2, AVALU, LBSTRESC, LOQFL, CHG2, PCHG2.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/teal.goshawk-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.goshawk core packages — teal.goshawk-package","text":"Maintainer: Nick Paszty nick.paszty@gene.com Authors: Dawid Kaledkowski dawid.kaledkowski@roche.com Mahmoud Hallal mahmoud.hallal@roche.com Pawel Rucki pawel.rucki@roche.com Wenyi Liu liu.wenyi@roche.com Jeffrey Tomlinson tomlinson.jeffrey@roche.com Bali Toth toth.balazs@gene.com Junlue Zhao Maciej Nasinski contributors: Maximilian Mordig [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Box Plot — tm_g_gh_boxplot","title":"Box Plot — tm_g_gh_boxplot","text":"teal module renders UI calls functions create box plot accompanying summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Box Plot — tm_g_gh_boxplot","text":"","code":"tm_g_gh_boxplot( label, dataname, param_var, param, yaxis_var = teal.transform::choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"), xaxis_var = teal.transform::choices_selected(\"AVISITCD\", \"AVISITCD\"), facet_var = teal.transform::choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = NULL, loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, plot_height = c(600, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(2, 1, 12), alpha = c(0.8, 0, 1), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Box Plot — tm_g_gh_boxplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ALB. param_var name variable containing biomarker codes e.g. PARAMCD. param list biomarkers interest. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. provided, defaults choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"). xaxis_var variable categorize x-axis. provided, defaults choices_selected(\"AVISITCD\", \"AVISITCD\"). facet_var variable facet plots . provided, defaults choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"). trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. loq_legend loq legend toggle. rotate_xlab 45 degree rotation x-axis values. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear legend. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. alpha numeric vector define transparency plotted points. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Box Plot — tm_g_gh_boxplot","text":"module object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Box Plot — tm_g_gh_boxplot","text":"Jeff Tomlinson (tomlinsj) jeffrey.tomlinson@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Box Plot — tm_g_gh_boxplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(nestcolor) library(stringr) # use non-exported function from goshawk h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) set.seed(1) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 50, ANRHI = 75 ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- var_labels[[\"ACTARM\"]] attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" # add LLOQ and ULOQ variables ALB_LOQS <- h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ALB_LOQS, by = \"PARAM\") }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_boxplot( label = \"Box Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\"), \"AVAL\"), xaxis_var = choices_selected(c(\"ACTARM\", \"ARM\", \"AVISITCD\", \"STUDYID\"), \"ARM\"), facet_var = choices_selected(c(\"ACTARM\", \"ARM\", \"AVISITCD\", \"SEX\"), \"AVISITCD\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = c(60, 55), hline_arb_color = c(\"grey\", \"red\"), hline_arb_label = c(\"default_hori_A\", \"default_hori_B\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"pink\", \"brown\", \"purple\", \"black\"), ) ) ) #> Initializing tm_g_gh_boxplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_correlationplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"Scatter Plot Teal Module Biomarker Analysis","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_correlationplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"","code":"tm_g_gh_correlationplot( label, dataname, param_var = \"PARAMCD\", xaxis_param = \"ALT\", xaxis_var = \"BASE\", yaxis_param = \"CRP\", yaxis_var = \"AVAL\", trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = 2, visit_facet = TRUE, trt_facet = FALSE, reg_line = FALSE, loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, vline_arb = numeric(0), vline_arb_color = \"red\", vline_arb_label = \"Vertical line\", vline_vars = character(0), vline_vars_colors = \"green\", vline_vars_labels = vline_vars, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_correlationplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. xaxis_param biomarker selected x-axis. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. yaxis_param biomarker selected y-axis. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. visit_facet visit facet toggle. trt_facet facet treatment group trt_group. reg_line include regression line annotations slope coefficient visualization. Use facet TRUE. loq_legend loq legend toggle. rotate_xlab 45 degree rotation x-axis values. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear vline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. vline_arb_color character vector length vline_arb. naming color arbitrary horizontal lines. vline_arb_label character vector length vline_arb. naming label arbitrary horizontal lines. vline_vars character vector name columns define additional vertical lines. vline_vars_colors character vector naming colors additional vertical lines. vline_vars_labels character vector naming labels additional vertical lines appear plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. reg_text_size font size control regression line annotations. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_correlationplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_correlationplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # use non-exported function from goshawk h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) color_manual <- c(\"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\") # assign LOQ flag symbols: circles for \"N\" and triangles for \"Y\", squares for \"NA\" shape_manual <- c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0) set.seed(1) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate(AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste( \"W\", trimws( substr( AVISIT, start = 6, stop = str_locate(AVISIT, \"DAY\") - 1 ) ) ), TRUE ~ NA_character_ )) %>% mutate(AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ NA_real_ )) %>% # use ARMCD values to order treatment in visualization legend mutate(TRTORD = ifelse(grepl(\"C\", ARMCD), 1, ifelse(grepl(\"B\", ARMCD), 2, ifelse(grepl(\"A\", ARMCD), 3, NA) ) )) %>% mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>% mutate(ARM = factor(ARM) %>% reorder(TRTORD)) %>% mutate( ANRHI = case_when( PARAMCD == \"ALT\" ~ 60, PARAMCD == \"CRP\" ~ 70, PARAMCD == \"IGA\" ~ 80, TRUE ~ NA_real_ ), ANRLO = case_when( PARAMCD == \"ALT\" ~ 20, PARAMCD == \"CRP\" ~ 30, PARAMCD == \"IGA\" ~ 40, TRUE ~ NA_real_ ) ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" # add LLOQ and ULOQ variables ADLB_LOQS <- h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ADLB_LOQS, by = \"PARAM\") }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_correlationplot( label = \"Correlation Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", xaxis_param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), yaxis_param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"CRP\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"BASE\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"Drug X 100mg\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination 100mg\" = \"#E74C3C\" ), shape_manual = c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0), plot_height = c(500, 200, 2000), facet_ncol = 2, visit_facet = TRUE, reg_line = FALSE, loq_legend = TRUE, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), hline_arb = c(40, 50), hline_arb_label = \"arb hori label\", hline_arb_color = c(\"red\", \"blue\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"green\", \"blue\", \"purple\", \"cyan\"), hline_vars_labels = c(\"ANRHI Label\", \"ANRLO Label\", \"ULOQN Label\", \"LLOQN Label\"), vline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), vline_vars_colors = c(\"yellow\", \"orange\", \"brown\", \"gold\"), vline_vars_labels = c(\"ANRHI Label\", \"ANRLO Label\", \"ULOQN Label\", \"LLOQN Label\"), vline_arb = c(50, 70), vline_arb_label = \"arb vert A\", vline_arb_color = c(\"green\", \"orange\") ) ) ) #> Initializing tm_g_gh_correlationplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Density Distribution Plot — tm_g_gh_density_distribution_plot","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"teal module renders UI calls functions create density distribution plot accompanying summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"","code":"tm_g_gh_density_distribution_plot( label, dataname, param_var, param, xaxis_var, trt_group, color_manual = NULL, color_comb = NULL, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), line_size = c(1, 0.25, 3), hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", facet_ncol = 2L, comb_line = TRUE, rotate_xlab = FALSE, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. color_comb name hex value combined treatment color. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. line_size plot line thickness. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. facet_ncol numeric value indicating number facets per row. comb_line display combined treatment line toggle. rotate_xlab 45 degree rotation x-axis values. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"None","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_density_distribution_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- var_labels[[\"ACTARM\"]] }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_density_distribution_plot( label = \"Density Distribution Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\" ), color_comb = \"#39ff14\", comb_line = TRUE, plot_height = c(500, 200, 2000), font_size = c(12, 8, 20), line_size = c(1, .25, 3), hline_arb = c(.02, .05), hline_arb_color = c(\"red\", \"black\"), hline_arb_label = c(\"Horizontal Line A\", \"Horizontal Line B\") ) ) ) #> Initializing tm_g_gh_density_distribution_plot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot — tm_g_gh_lineplot","title":"Line plot — tm_g_gh_lineplot","text":"teal module renders UI calls function creates line plot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot — tm_g_gh_lineplot","text":"","code":"tm_g_gh_lineplot( label, dataname, param_var, param, param_var_label = \"PARAM\", xaxis_var, yaxis_var, xvar_level = NULL, filter_var = yaxis_var, filter_var_choices = filter_var, trt_group, trt_group_level = NULL, shape_choices = NULL, stat = \"mean\", hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", color_manual = c(getOption(\"ggplot2.discrete.colour\"), c(\"#ff0000\", \"#008000\", \"#4ca3dd\", \"#8a2be2\"))[1:4], xtick = ggplot2::waiver(), xlabel = xtick, rotate_xlab = FALSE, plot_height = c(600, 200, 4000), plot_width = NULL, plot_font_size = c(12, 8, 20), dodge = c(0.4, 0, 1), pre_output = NULL, post_output = NULL, count_threshold = 0, table_font_size = c(12, 4, 20), dot_size = c(2, 1, 12), plot_relative_height_value = 1000 )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot — tm_g_gh_lineplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. param_var_label single name variable analysis data includes parameter labels. xaxis_var single name variable analysis data used x-axis plot respective goshawk function. yaxis_var single name variable analysis data used summary variable respective goshawk function. xvar_level vector can used define factor level xvar. use xvar character factor. filter_var data constraint variable. filter_var_choices data constraint variable choices. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. trt_group_level vector can used define factor level trt_group. shape_choices Vector choices_selected object names ADSL variables can used change shape stat string statistics hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. color_manual string vector representing customized colors xtick numeric vector define tick values x-axis x variable numeric. Default value waive(). xlabel vector length xtick define label x-axis tick values. Default value waive(). rotate_xlab logical(1) value indicating whether rotate x-axis labels. plot_height controls plot height. plot_width optional, controls plot width. plot_font_size control font size title, x-axis, y-axis legend font. dodge controls position dodge error bar pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. count_threshold minimum count observations (listed output table) plot nodes graph table_font_size controls font size values table dot_size plot dot size. plot_relative_height_value numeric value 500 5000 controlling starting value relative plot height slider","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot — tm_g_gh_lineplot","text":"shiny object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Line plot — tm_g_gh_lineplot","text":"Wenyi Liu (luiw2) wenyi.liu@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot — tm_g_gh_lineplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) library(nestcolor) # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- var_labels[[\"ACTARM\"]] }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_lineplot( label = \"Line Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), shape_choices = c(\"SEX\", \"RACE\"), xaxis_var = choices_selected(\"AVISITCD\", \"AVISITCD\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), hline_arb = c(20.5, 19.5), hline_arb_color = c(\"red\", \"green\"), hline_arb_label = c(\"A\", \"B\") ) ) ) #> Initializing tm_g_gh_lineplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"tm_g_gh_scatterplot deprecated. Please use tm_g_gh_correlationplot instead.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"","code":"tm_g_gh_scatterplot( label, dataname, param_var, param, xaxis_var, yaxis_var, trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = 2, trt_facet = FALSE, reg_line = FALSE, rotate_xlab = FALSE, hline = NULL, vline = NULL, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. trt_facet facet treatment group trt_group. reg_line include regression line annotations slope coefficient visualization. Use facet TRUE. rotate_xlab 45 degree rotation x-axis values. hline y-axis value position horizontal line. vline x-axis value position vertical line. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. reg_text_size font size control regression line annotations. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_scatterplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- var_labels[[\"ACTARM\"]] }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_scatterplot( label = \"Scatter Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"BASE\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\" ), shape_manual = c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0), plot_height = c(500, 200, 2000), facet_ncol = 2, trt_facet = FALSE, reg_line = FALSE, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10) ) ) ) #> Warning: `tm_g_gh_scatterplot()` was deprecated in teal.goshawk 0.1.15. #> ℹ You should use teal.goshawk::tm_g_gh_correlationplot instead of #> teal.goshawk::tm_g_gh_scatterplot #> Initializing tm_g_gh_scatterplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Spaghetti Plot — tm_g_gh_spaghettiplot","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"teal module renders UI calls function creates spaghetti plot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"","code":"tm_g_gh_spaghettiplot( label, dataname, param_var, param, param_var_label = \"PARAM\", idvar, xaxis_var, yaxis_var, xaxis_var_level = NULL, filter_var = yaxis_var, trt_group, trt_group_level = NULL, group_stats = \"NONE\", man_color = NULL, color_comb = NULL, xtick = ggplot2::waiver(), xlabel = xtick, rotate_xlab = FALSE, facet_ncol = 2, free_x = FALSE, plot_height = c(600, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(2, 1, 12), hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. param_var_label single name variable analysis data includes parameter labels. idvar name unique subject id variable. xaxis_var single name variable analysis data used x-axis plot respective goshawk function. yaxis_var single name variable analysis data used summary variable respective goshawk function. xaxis_var_level vector can used define factor level xaxis_var. use xaxis_var character factor. filter_var data constraint variable. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. trt_group_level vector can used define factor level trt_group. group_stats control group mean median overlay. man_color string vector representing customized colors color_comb name hex value combined treatment color. xtick numeric vector define tick values x-axis x variable numeric. Default value waive(). xlabel vector length xtick define label x-axis tick values. Default value waive(). rotate_xlab logical(1) value indicating whether rotate x-axis labels facet_ncol numeric value indicating number facets per row. free_x logical(1) scales \"fixed\" (FALSE) \"free\" (TRUE) x-axis facet_wrap scales parameter. plot_height controls plot height. plot_width optional, controls plot width. font_size control font size title, x-axis, y-axis legend font. dot_size plot dot size. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear legend. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"shiny object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"Wenyi Liu (luiw2) wenyi.liu@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/tm_g_gh_spaghettiplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # use non-exported function from goshawk h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) set.seed(1) ADSL <- rADSL ADLB <- rADLB var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 30, ANRHI = 75 ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- var_labels[[\"ACTARM\"]] attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" # add LLOQ and ULOQ variables ALB_LOQS <- h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ALB_LOQS, by = \"PARAM\") }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( tm_g_gh_spaghettiplot( label = \"Spaghetti Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), idvar = \"USUBJID\", xaxis_var = choices_selected(c(\"Analysis Visit Code\" = \"AVISITCD\"), \"AVISITCD\"), yaxis_var = choices_selected(c(\"AVAL\", \"CHG\", \"PCHG\"), \"AVAL\"), filter_var = choices_selected( c(\"None\" = \"NONE\", \"Screening\" = \"BASE2\", \"Baseline\" = \"BASE\"), \"NONE\" ), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_comb = \"#39ff14\", man_color = c( \"Combination\" = \"#000000\", \"Placebo\" = \"#fce300\", \"150mg QD\" = \"#5a2f5f\" ), hline_arb = c(60, 50), hline_arb_color = c(\"grey\", \"red\"), hline_arb_label = c(\"default A\", \"default B\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"pink\", \"brown\", \"purple\", \"black\"), ) ) ) #> Initializing tm_g_gh_spaghettiplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/toggle_slider.html","id":null,"dir":"Reference","previous_headings":"","what":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"useful slider shown, sometimes hard configure sliders, one can toggle one two numeric input fields set slider instead. toggle button show two numeric input field selecting range.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/toggle_slider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"","code":"toggle_slider_ui(id, label) toggle_slider_server(id, data_state, ...) get_data_range_states(varname, paramname, ANL, trt_group = NULL, step = NULL)"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/toggle_slider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"id character module id label label label input field, e.g. slider numeric inputs ... additional parameters pass sliderInput","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/toggle_slider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/ui_arbitrary_lines.html","id":null,"dir":"Reference","previous_headings":"","what":"UI module to arbitrary lines — ui_arbitrary_lines","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"UI module input either horizontal vertical lines plot via comma separated values","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/ui_arbitrary_lines.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"","code":"ui_arbitrary_lines( id, line_arb, line_arb_label, line_arb_color, title = \"Arbitrary Horizontal Lines:\" )"},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/ui_arbitrary_lines.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"id (character(1)) defining namespace shiny module. line_arb (numeric) default values textInput defining values arbitrary lines line_arb_label (character) default values textInput defining labels arbitrary lines line_arb_color (character) default values textInput defining colors arbitrary lines title (character(1)) title arbitrary lines input. default \"Arbitrary Horizontal Lines\".","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/reference/ui_arbitrary_lines.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"(shiny.tag) input define values, colors labels arbitrary straight lines.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"breaking-changes-0-2-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.2.0","text":"Adapted modules use teal_data objects.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-2-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.2.0","text":"Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Removed Show Warnings modals modules. Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-2-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.2.0","text":"Specified minimal version package dependencies. Fix tm_g_gh_lineplot bug causing --bounds error stops plot working. Enhance tm_g_gh_correlationplot module fix related bugs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.15","text":"Updated encodings input checks use shinyvalidate::InputValidator instead shiny::validate better UI experience. Added tooltip value input ui_arbitrary_lines explain supply multiple values.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"breaking-changes-0-1-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.goshawk 0.1.15","text":"Constraints range calculated filtered data instead unfiltered. Replaced chunks simpler qenv class. Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.15","text":"Deprecated tm_g_gh_scatterplot. Use tm_g_gh_correlationplot instead. Removed scda package dependency examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.14","text":"Added teal.reporter reporting package modules. Added optional argument plot_relative_height_value tm_g_gh_lineplot control initial value relative plot height slider. Implemented nestcolor slight refactoring tm_g_gh_lineplot added nestcolor examples custom color manuals.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.14","text":"Fixed minor type coercion warning srv_arbitrary_lines. Updated modules use datasets suffix _FILTERED package works breaking changes teal.slice.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.13","text":"Added template pkgdown site. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"breaking-changes-0-1-12","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.1.12","text":"Converted hline parameter tm_g_gh_lineplot three parameters: hline_arb, hline_arb_color hline_arb_label.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.12","text":"Added basic logging modules. Rewrote modules use moduleServer updated calls teal.devel modules also written use moduleServer. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Adjusted package imports take account changes teal framework.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-11","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.11","text":"Added UI input component add additional arbitrary horizontal lines tm_g_gh_spaghettiplot, tm_g_gh_boxplot, tm_g_gh_density_distribution_plot well two additional UI input components add additional horizontal additional vertical line tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"bug-fixes-0-1-11","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.goshawk 0.1.11","text":"Fixed error tm_g_gh_boxplot facet variable selected.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-11","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.11","text":"Updated R version requirement R >= 3.6. Removed dependency test.nest package. Removed dependency utils.nest package replaced functions equivalents checkmate package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"new-features-0-1-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.goshawk 0.1.10","text":"Lab normal range LOQs horizontal line feature tm_g_gh_spaghettiplot, tm_g_gh_boxplot tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"breaking-changes-0-1-10","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.1.10","text":"hline replaced hline_arb, hline_arb_color hline_arb_label modules. vline replaced vline_arb_var, vline_arb_color vline_arb_label tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"bug-fixes-0-1-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.goshawk 0.1.10","text":"Fixed bug tm_g_gh_boxplot module always used AVISITCD variable Visit Column table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.10","text":"Updated LICENCE README new package references. Updated examples documentation using scda synthetic data instead random.cdisc.data. Added error_on_lint: TRUE .lintr. Replaced tidyr’s gather spread pivot_wider pivot_longer package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-9","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.9","text":"Updated tm_g_gh_correlationplot tm_g_gh_scatterplot encodings checkbox facet treatment variable instead drop menu. Updated starting line type solid instead dashed tm_g_gh_lineplot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.8","text":"Updated plot remove x-axis label x-axis numeric data corresponding y-axis variable. Added slider control relative size plot tables. Replaced function brushedPoints clean_brushedPoints tm_g_gh_boxplot, tm_g_gh_correlationplot, tm_g_gh_scatterplot tm_g_gh_spaghettiplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"bug-fixes-0-1-8","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.goshawk 0.1.8","text":"Fixed infinite reactive loop inside toggle_slider_server.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.8","text":"Renamed toggle.R file toggleable.R file consistent accepted correct spelling word.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.7","text":"Added table display summary statistics.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"bug-fixes-0-1-7","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.goshawk 0.1.7","text":"Fixed displaying number messages, warnings errors Debug Info button. Fixed treatment variable values symbols (e.g. ‘:’). Allow treatment variables different arm levels.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"miscellaneous-0-1-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.7","text":"Reduced minimum number records required dataset either 1 2 modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"enhancements-0-1-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.6","text":"Changed slider title “Transparency” “Alpha”. Added facet_var argument UI drop . Rug plot option added. Argument changes: font_size –> plot_font_size. Line symbol type can now configured. especially useful line splitting used. Can set minimum records threshold rendering data point plot. Table font size can now controlled. Added facet_var argument UI drop . Changed slider title “Transparency” “Alpha”.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"general-0-1-6","dir":"Changelog","previous_headings":"","what":"General","title":"teal.goshawk 0.1.6","text":"Moved code argument cdisc_dataset (cdisc_data) examples. Implemented new plot_with_settings functionality modules support plot resizing, zooming, downloading functionality. Added drop selector treatment ARM.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"tealgoshawk-015","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.5","title":"teal.goshawk 0.1.5","text":"templ_ui_params_vars now uses optionalSelectInput teal. shape_choices argument tm_g_gh_lineplot can either character vector choices_selected.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"tealgoshawk-014","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.4","title":"teal.goshawk 0.1.4","text":"bug fix correlation plot module related axis ranges reflect changes data filter panel re-factoring modification correlation module pass data data driven LLOQ ULOQ footnote","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"tealgoshawk-013","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.3","title":"teal.goshawk 0.1.3","text":"Added .data PARAMCD new functions related sliders reactivity. Fixing doc small fixes. Added toggleable slider modules. Added data driven data constraints UI rendering.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"tealgoshawk-012","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.2","title":"teal.goshawk 0.1.2","text":"Box: Toggle LoQ legend /. Correlation: Toggle LoQ legend /, toggle visit facetting /. Density: Toggle combined treatment line /. Modified line-plot vertical axis range match parameter value CI range.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/main/news/index.html","id":"tealgoshawk-011","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.1","title":"teal.goshawk 0.1.1","text":"First release.","code":""}] +[{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Data Expectations","text":"teal.goshawk expects provided ADSL accompanying ADLB clinical trials data set ADaM format. information ADaM please ADaM standards. package provides ready--use teal modules can embed teal application. modules generate highly customizable plots outputs often used exploratory data analysis, e.g.: box plots - tm_g_gh_boxplot() correlation scatter plots - tm_g_gh_correlationplot() tm_g_gh_scatterplot() density distribution plots - tm_g_gh_density_distribution_plot() line plots - tm_g_gh_lineplot() spaghetti plots - tm_g_spaghettiplot() See package functions / modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"adsl","dir":"Articles","previous_headings":"Data Expectations","what":"ADSL","title":"Data Expectations","text":"subject level data set one record per subject includes variables intended used plot splitting e.g. ABCWK24 represents two level outcome variable values \"Y\" \"N\" Week 24.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"adlb","dir":"Articles","previous_headings":"Data Expectations","what":"ADLB","title":"Data Expectations","text":"Basic Data Structure (BDS) data set meaning multiple records per subject per assay (PARAM) across unique time points. Additional variables intended used plot splitting joined ADLB. See ADSL example ABCWK24 need joined ADLB","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"other-basic-data-structures","dir":"Articles","previous_headings":"Data Expectations","what":"Other Basic Data Structures","title":"Data Expectations","text":"BDS data sets provisioned teal.goshawk like ADQS contains multiple records per subject per question (PARAM) across unique time points. However cases ADLB likely workarounds needed. example concept assay units, stored AVALU, really relevant BDS like ADQS contains questionnaire data. Given teal.goshawk expects AVALU variable uses values plot title y-axis label, AVALU need added ADQS appropriate value: Perhaps \"Q\". value provided \"()\" portion title y-axis label empty.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"required-variables","dir":"Articles","previous_headings":"","what":"Required Variables","title":"Data Expectations","text":"Several variables required realize full functionality teal.goshawk.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"trtord","dir":"Articles","previous_headings":"Required Variables","what":"TRTORD","title":"Data Expectations","text":"Definition: variable orders treatment values legend Rationale: Allows congruent ordering compared outputs generated study team Alternative: Variable required","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"avisitcd","dir":"Articles","previous_headings":"Required Variables","what":"AVISITCD","title":"Data Expectations","text":"Definition: variable contains abbreviated values AVISIT values Rationale: Many AVISIT values long contain arguably superfluous information cases. Using long values x-axis tick labels can really chew real estate area available plot. Using thoughtful abbreviations conveys chronology substantive loss information maximizes area available plot. Alternative: cases creating abbreviations helpful simply set AVISITCD <- AVISIT","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"avisitcdn","dir":"Articles","previous_headings":"Required Variables","what":"AVISITCDN","title":"Data Expectations","text":"Definition: variable contains numeric portion AVISITCD values Rationale: Often AVISITN contains values particularly helpful reflect proportional chronology visits. AVISITCD created helpful create numeric values AVISITCD values can seen intuitively reflecting visit chronology. example: 0, 2, 4, 12, 24, 56, 84 etc. weeks 0, 14, 28, 84, 168, 392, 588 etc. days. Using , longitudinal visualization x-axis nicely reflect proportional distances visits. Alternative: cases creating intuitive numeric chronology helpful simply set AVISITCDN <- AVISITN","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"avalu","dir":"Articles","previous_headings":"Required Variables","what":"AVALU","title":"Data Expectations","text":"Definition: Analysis Value Unit Rationale: Used plot title y-axis labels. Please see \"BDS data sets\" comments Alternative: Variable required.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"lbstresc","dir":"Articles","previous_headings":"Required Variables","what":"LBSTRESC","title":"Data Expectations","text":"Definition: SDTM Character Result/Finding Std Format Rationale: character type variable, variable contains values include limits quantitation (LOQ). might look like \"2.1<\" \">20.7\". case AVAL often missing. important able still capture values following derivation used needed LOQFL variable set \"Y\". signifies AVAL value record derived. - values limit quantitation, AVAL set numeric portion LBSTRESC divided 2. - values limit quantitation, AVAL set numeric portion LBSTRESC. Alternative: Variable required","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"loqfl","dir":"Articles","previous_headings":"Required Variables","what":"LOQFL","title":"Data Expectations","text":"Definition: ADaM standard variable represents Limit Quantitation Flag Rationale: Set \"Y\" LBSTRESC value used populate AVAL LBSTRESC value either limit quantitation assay limit quantitation assay. Derivations AVAL LOQFL look like following mutate() statement. - AVAL = if_else(grepl(\"<|>\", LBSTRESC), .numeric(gsub(\"[^0-9, .]+\", \"\", LBSTRESC)), AVAL) - LOQFL = if_else(grepl(\"<|>\", LBSTRESC), \"Y\", \"N\") Alternative: limit quantitation concept relevant please set LOQFL <- \"N\"","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"base2","dir":"Articles","previous_headings":"Required Variables","what":"BASE2","title":"Data Expectations","text":"Definition: ADaM standard variable represents assay value Screening Rationale: change Screening visit analyses needed variable contains assay value Screening Alternative: Screening visit analyses relevant please set BASE2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"chg2","dir":"Articles","previous_headings":"Required Variables","what":"CHG2","title":"Data Expectations","text":"Definition: ADaM standard variable represents change Screening assay value Rationale: change Screening visit analyses needed variable contains assay value change Screening subsequent visit Alternative: Screening visit analyses relevant please set CHG2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"pchg2","dir":"Articles","previous_headings":"Required Variables","what":"PCHG2","title":"Data Expectations","text":"Definition: ADaM standard variable represents percent change Screening assay value Rationale: percent change Screening visit analyses needed variable contains assay value percent change Screening subsequent visit Alternative: Screening visit analyses relevant please set PCHG2 <- NA","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"additional-variables","dir":"Articles","previous_headings":"","what":"Additional Variables","title":"Data Expectations","text":"additional data manipulations performed create variables useful context longitudinal visualizations","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/data-expectations.html","id":"avall2-basel2-base2l2","dir":"Articles","previous_headings":"Additional Variables","what":"AVALL2, BASEL2, BASE2L2","title":"Data Expectations","text":"Description: Log 2 AVAL, BASE BASE2 respectively Rationale: transformation addresses data variance improve interpretability appearance plots.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/teal-goshawk.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting started with teal.goshawk","text":"teal.goshawk package implementing number teal modules helpful exploring clinical trials data, specifically targeted data following ADaM standards. teal.goshawk modules can used data ADaM standard clinical data features package likely applicable. concepts presented require knowledge core features teal, specifically launch teal application pass data . Therefore, highly recommended refer README file introductory vignette teal package.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/teal-goshawk.html","id":"main-features","dir":"Articles","previous_headings":"","what":"Main features","title":"Getting started with teal.goshawk","text":"package provides ready--use teal modules can embed teal application. modules generate highly customizable plots outputs often used exploratory data analysis, e.g.: box plots - tm_g_gh_boxplot() correlation scatter plots - tm_g_gh_correlationplot() tm_g_gh_scatterplot() density distribution plots - tm_g_gh_density_distribution_plot() line plots - tm_g_gh_lineplot() spaghetti plots - tm_g_spaghettiplot() See package functions / modules.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/teal-goshawk.html","id":"a-simple-application","dir":"Articles","previous_headings":"","what":"A simple application","title":"Getting started with teal.goshawk","text":"teal.goshawk module needs embedded inside shiny / teal application interact . need load teal teal.goshawk already depends . nestcolor optional package can loaded apply standardized NEST color palette module plots. simple application including box plot module look like : Refer Get Started section teal.modules.clinical package provides additional detail teal concepts applied another simple app example. Please see additional information Articles data expectations, requirements pre/post-processing rationale","code":"library(teal.goshawk) library(nestcolor) data <- teal_data() data <- within(data, { ADSL <- goshawk::rADSL %>% mutate(TRTORD = case_when( TRT01P == \"A: Drug X\" ~ 1, TRT01P == \"C: Combination\" ~ 2, TRT01P == \"B: Placebo\" ~ 3, TRUE ~ as.numeric(NA) ) ) ADLB <- goshawk::rADLB %>% mutate(AVISITCD = AVISIT, TRTORD = case_when( TRT01P == \"A: Drug X\" ~ 1, TRT01P == \"C: Combination\" ~ 2, TRT01P == \"B: Placebo\" ~ 3, TRUE ~ as.numeric(NA) ) ) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- teal::init( data = data, modules = list( tm_g_gh_boxplot( label = \"Longitudinal Analysis\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = teal.transform::choices_selected( choices = c(\"ALT\", \"CRP\", \"IGA\"), selected = c(\"ALT\") ), trt_group = teal.transform::choices_selected( choices = c(\"TRT01P\", \"TRT01A\"), selected = c(\"TRT01P\") ), facet_var = teal.transform::choices_selected( choices = c(\"TRT01P\", \"TRT01A\"), selected = c(\"TRT01P\") ), rotate_xlab = TRUE ) ) ) if (interactive()) shiny::shinyApp(app$ui, app$server)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"paramcd","dir":"Articles","previous_headings":"User Guide","what":"PARAMCD","title":"User Guide","text":"“Parameter Code” (PARAMCD) variable used select biomarker/lab interest. biomarker/lab selection pull menu items concatenation PARAMCD PARAM ease identification.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"pull-down-menus","dir":"Articles","previous_headings":"User Guide","what":"Pull down menus","title":"User Guide","text":"containing many items include search functionality ease finding menu items.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"avisit","dir":"Articles","previous_headings":"User Guide","what":"AVISIT","title":"User Guide","text":"“Analysis Visit” (AVISIT) variable used display visit abbreviated analysis visit value (AVISITCD). See Data Expectations article detail AVISITCD variable.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"the-data-constraint-filter","dir":"Articles","previous_headings":"User Guide","what":"The Data Constraint Filter","title":"User Guide","text":"Selecting Screening constraint remove subjects satisfy filter range based screening value given assay. Selecting Baseline constraint remove subjects satisfy filter range based baseline value given assay. Example: Consider subject #58 baseline value 5 assay x range assay x across subjects 1 10. baseline constraint selected value changed range 7 10 subjects meet condition removed visualizations. Since subject #58 baseline value 5 assay x one subjects removed.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"data-point-brushing","dir":"Articles","previous_headings":"User Guide","what":"Data Point Brushing","title":"User Guide","text":"Selecting specific data points reveal Subject ID data available Box, Correlation Spaghetti Plot visualizations.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"log2---points-to-consider","dir":"Articles","previous_headings":"User Guide","what":"Log2 - Points to Consider","title":"User Guide","text":"biomarker/lab values already log2 transformed represent change value. excluded log2 transformation applied biomarkers/labs large. Biomarkers/labs value 0 log2 transformed taking log2 minimum non-zero value biomarker/lab, divided 2.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"right-hand-data-filter-panel","dir":"Articles","previous_headings":"User Guide","what":"Right Hand Data Filter Panel","title":"User Guide","text":"filters hierarchical used filter analysis variables. filter analysis variables please use filtering controls available left hand panel. Use right hand data panel filters filter categorical variables: AVISIT exclude/include specific visits visualizations. LOQFL exclude/include LOQ flagged values. SEX exclude/include specific gender. etc.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/articles/user-guide.html","id":"visualization-specifics","dir":"Articles","previous_headings":"User Guide","what":"Visualization Specifics","title":"User Guide","text":"Box Plot: Selecting STUDYID X-Axis variable produce visualization subjects combined identify study x-axis. Correlation Plot data constraint can placed Screening Baseline records associated analysis variable biomarker/lab selected x-axis . Limit Quantification (LOQFL) flag set either biomarker/lab values identified LOQ. brushing table column header reflects LOQFL_COMB. “Regression Line” option used conjunction “Treatment Faceting” option. Otherwise per treatment regression formula coefficient annotations overlay. Line Plot: error displayed related plot height ’s best first alter relative plot height left panel using slider. additional plot height control, use icons upper right corner visualization.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nick Paszty. Author, maintainer. Dawid Kaledkowski. Author. Mahmoud Hallal. Author. Pawel Rucki. Author. Wenyi Liu. Author. Jeffrey Tomlinson. Author. Bali Toth. Author. Junlue Zhao. Author. Maciej Nasinski. Author. Maximilian Mordig. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paszty N, Kaledkowski D, Hallal M, Rucki P, Liu W, Tomlinson J, Toth B, Zhao J, Nasinski M (2024). teal.goshawk: Longitudinal Visualization 'teal' Modules. R package version 0.2.0.9017, https://github.com/insightsengineering/teal.goshawk/, https://insightsengineering.github.io/teal.goshawk/.","code":"@Manual{, title = {teal.goshawk: Longitudinal Visualization `teal` Modules}, author = {Nick Paszty and Dawid Kaledkowski and Mahmoud Hallal and Pawel Rucki and Wenyi Liu and Jeffrey Tomlinson and Bali Toth and Junlue Zhao and Maciej Nasinski}, year = {2024}, note = {R package version 0.2.0.9017, https://github.com/insightsengineering/teal.goshawk/}, url = {https://insightsengineering.github.io/teal.goshawk/}, }"},{"path":"https://insightsengineering.github.io/teal.goshawk/index.html","id":"tealgoshawk","dir":"","previous_headings":"","what":"Longitudinal Visualization `teal` Modules","title":"Longitudinal Visualization `teal` Modules","text":"teal.goshawk package provides teal modules longitudinal visualization functions goshawk R package. enables teal app developers easily create applications explore longitudinal clinical trial data.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/index.html","id":"modules","dir":"","previous_headings":"","what":"Modules","title":"Longitudinal Visualization `teal` Modules","text":"tm_g_gh_boxplot tm_g_gh_correlationplot tm_g_gh_density_distribution_plot tm_g_gh_lineplot tm_g_gh_spaghettiplot","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Longitudinal Visualization `teal` Modules","text":"","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.goshawk@*release\") # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.goshawk\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/get_choices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Choices — get_choices","title":"Get Choices — get_choices","text":"function returns choices based class input. input class delayed_data, returns subset input. subset NULL input contains var_label var_choices, throws error prompting resolve delayed inputs. Otherwise, returns input .","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/get_choices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Choices — get_choices","text":"","code":"get_choices(choices)"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/get_choices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Choices — get_choices","text":"choices object contains choices.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/get_choices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Choices — get_choices","text":"vector choices.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/maptrt.html","id":null,"dir":"Reference","previous_headings":"","what":"helper for writing arm mapping and ordering code. — maptrt","title":"helper for writing arm mapping and ordering code. — maptrt","text":"Provides lines code left hand side arm mapping. user must provide right hand side","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/maptrt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"helper for writing arm mapping and ordering code. — maptrt","text":"","code":"maptrt(df_armvar, code = c(\"M\", \"O\"))"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/maptrt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"helper for writing arm mapping and ordering code. — maptrt","text":"df_armvar dataframe column name containing treatment code. e.g. ADSL$ARMCD code controls whether mapping ordering code written console. Valid values: \"M\" \"O\".","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/maptrt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"helper for writing arm mapping and ordering code. — maptrt","text":"SPA configure study specific pre-processing deploying goshawk. writing code ARM mapping ordering tedious. function helps get started providing left hand side mapping ordering syntax. call function copy paste resulting code console app.R file.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/maptrt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"helper for writing arm mapping and ordering code. — maptrt","text":"","code":"ADSL <- rADSL # get treatment mapping code maptrt(df_armvar = ADSL$ARMCD, code = \"M\") #> #> \"ARM A\" = \"\", #> \"ARM C\" = \"\", #> \"ARM B\" = \"\", # get treatment ordering code maptrt(df_armvar = ADSL$ARMCD, code = \"O\") #> #> ARMCD == \"ARM A\" ~ , #> ARMCD == \"ARM C\" ~ , #> ARMCD == \"ARM B\" ~ ,"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/report_card_template_goshawk.html","id":null,"dir":"Reference","previous_headings":"","what":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"function generates report card title, optional description, option append filter state list. Additionally, display selected constraint options.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/report_card_template_goshawk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"","code":"report_card_template_goshawk( title, label, with_filter, filter_panel_api, constraint_list, constraint_description = NULL, style = \"default\" )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/report_card_template_goshawk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"title (character(1)) title card (unless overwritten label) label (character(1)) label provided user adding card with_filter (logical(1)) flag indicating add filter state filter_panel_api (FilterPanelAPI) object API allows generation filter state report constraint_list (list) list containing constraint variables, including: constraint_var (character(1)) constraint variable name. constraint_range_min (numeric(1)) minimum constraint range value. constraint_range_max (numeric(1)) maximum constraint range value. constraint_description (character(1)) description constraints. style (character(1)) style constraint text block. options: default, verbatim (default default).","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/report_card_template_goshawk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template Function for TealReportCard Creation and Customization in teal.goshawk — report_card_template_goshawk","text":"(TealReportCard) populated title, description, filter state","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/srv_arbitrary_lines.html","id":null,"dir":"Reference","previous_headings":"","what":"Server module to arbitrary lines — srv_arbitrary_lines","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"Server validate transform comma separated values vectors values passed goshawk functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/srv_arbitrary_lines.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"","code":"srv_arbitrary_lines(id)"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/srv_arbitrary_lines.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"id ID string corresponds ID used call module's UI function.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/srv_arbitrary_lines.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Server module to arbitrary lines — srv_arbitrary_lines","text":"(reactive) returning list containing line_arb, line_arb_color, line_arb_label validated passed goshawk plot functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/teal.goshawk-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.goshawk core packages — teal.goshawk-package","title":"teal.goshawk core packages — teal.goshawk-package","text":"teal.goshawk package renders UI calls respective biomarker visualization functions.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/teal.goshawk-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal.goshawk core packages — teal.goshawk-package","text":"data used teal.goshawk constraints. must contain columns AVISITCD, BASE, BASE2, AVALU, LBSTRESC, LOQFL, CHG2, PCHG2.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/teal.goshawk-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.goshawk core packages — teal.goshawk-package","text":"Maintainer: Nick Paszty nick.paszty@gene.com Authors: Dawid Kaledkowski dawid.kaledkowski@roche.com Mahmoud Hallal mahmoud.hallal@roche.com Pawel Rucki pawel.rucki@roche.com Wenyi Liu liu.wenyi@roche.com Jeffrey Tomlinson tomlinson.jeffrey@roche.com Bali Toth toth.balazs@gene.com Junlue Zhao Maciej Nasinski contributors: Maximilian Mordig [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Box Plot — tm_g_gh_boxplot","title":"Box Plot — tm_g_gh_boxplot","text":"teal module renders UI calls functions create box plot accompanying summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Box Plot — tm_g_gh_boxplot","text":"","code":"tm_g_gh_boxplot( label, dataname, param_var, param, yaxis_var = teal.transform::choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"), xaxis_var = teal.transform::choices_selected(\"AVISITCD\", \"AVISITCD\"), facet_var = teal.transform::choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = NULL, loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, plot_height = c(600, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(2, 1, 12), alpha = c(0.8, 0, 1), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Box Plot — tm_g_gh_boxplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ALB. param_var name variable containing biomarker codes e.g. PARAMCD. param list biomarkers interest. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. provided, defaults choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"). xaxis_var variable categorize x-axis. provided, defaults choices_selected(\"AVISITCD\", \"AVISITCD\"). facet_var variable facet plots . provided, defaults choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"). trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. loq_legend loq legend toggle. rotate_xlab 45 degree rotation x-axis values. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear legend. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. alpha numeric vector define transparency plotted points. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Box Plot — tm_g_gh_boxplot","text":"module object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Box Plot — tm_g_gh_boxplot","text":"Jeff Tomlinson (tomlinsj) jeffrey.tomlinson@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Box Plot — tm_g_gh_boxplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(nestcolor) library(stringr) # use non-exported function from goshawk .h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) set.seed(1) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 50, ANRHI = 75 ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- .var_labels[[\"ACTARM\"]] attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" # add LLOQ and ULOQ variables ALB_LOQS <- .h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ALB_LOQS, by = \"PARAM\") }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_boxplot( label = \"Box Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\"), \"AVAL\"), xaxis_var = choices_selected(c(\"ACTARM\", \"ARM\", \"AVISITCD\", \"STUDYID\"), \"ARM\"), facet_var = choices_selected(c(\"ACTARM\", \"ARM\", \"AVISITCD\", \"SEX\"), \"AVISITCD\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = c(60, 55), hline_arb_color = c(\"grey\", \"red\"), hline_arb_label = c(\"default_hori_A\", \"default_hori_B\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"pink\", \"brown\", \"purple\", \"black\"), ) ) ) #> Initializing tm_g_gh_boxplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_correlationplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"Scatter Plot Teal Module Biomarker Analysis","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_correlationplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"","code":"tm_g_gh_correlationplot( label, dataname, param_var = \"PARAMCD\", xaxis_param = \"ALT\", xaxis_var = \"BASE\", yaxis_param = \"CRP\", yaxis_var = \"AVAL\", trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = 2, visit_facet = TRUE, trt_facet = FALSE, reg_line = FALSE, loq_legend = TRUE, rotate_xlab = FALSE, hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, vline_arb = numeric(0), vline_arb_color = \"red\", vline_arb_label = \"Vertical line\", vline_vars = character(0), vline_vars_colors = \"green\", vline_vars_labels = vline_vars, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_correlationplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. xaxis_param biomarker selected x-axis. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. yaxis_param biomarker selected y-axis. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. visit_facet visit facet toggle. trt_facet facet treatment group trt_group. reg_line include regression line annotations slope coefficient visualization. Use facet TRUE. loq_legend loq legend toggle. rotate_xlab 45 degree rotation x-axis values. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear vline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. vline_arb_color character vector length vline_arb. naming color arbitrary horizontal lines. vline_arb_label character vector length vline_arb. naming label arbitrary horizontal lines. vline_vars character vector name columns define additional vertical lines. vline_vars_colors character vector naming colors additional vertical lines. vline_vars_labels character vector naming labels additional vertical lines appear plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. reg_text_size font size control regression line annotations. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_correlationplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_correlationplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_correlationplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # use non-exported function from goshawk .h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) .color_manual <- c(\"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\") # assign LOQ flag symbols: circles for \"N\" and triangles for \"Y\", squares for \"NA\" .shape_manual <- c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0) set.seed(1) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate(AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste( \"W\", trimws( substr( AVISIT, start = 6, stop = str_locate(AVISIT, \"DAY\") - 1 ) ) ), TRUE ~ NA_character_ )) %>% mutate(AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ NA_real_ )) %>% # use ARMCD values to order treatment in visualization legend mutate(TRTORD = ifelse(grepl(\"C\", ARMCD), 1, ifelse(grepl(\"B\", ARMCD), 2, ifelse(grepl(\"A\", ARMCD), 3, NA) ) )) %>% mutate(ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))])) %>% mutate(ARM = factor(ARM) %>% reorder(TRTORD)) %>% mutate( ANRHI = case_when( PARAMCD == \"ALT\" ~ 60, PARAMCD == \"CRP\" ~ 70, PARAMCD == \"IGA\" ~ 80, TRUE ~ NA_real_ ), ANRLO = case_when( PARAMCD == \"ALT\" ~ 20, PARAMCD == \"CRP\" ~ 30, PARAMCD == \"IGA\" ~ 40, TRUE ~ NA_real_ ) ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse( USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" # add LLOQ and ULOQ variables ADLB_LOQS <- .h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ADLB_LOQS, by = \"PARAM\") }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_correlationplot( label = \"Correlation Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", xaxis_param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), yaxis_param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"CRP\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"BASE\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"Drug X 100mg\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination 100mg\" = \"#E74C3C\" ), shape_manual = c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0), plot_height = c(500, 200, 2000), facet_ncol = 2, visit_facet = TRUE, reg_line = FALSE, loq_legend = TRUE, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), hline_arb = c(40, 50), hline_arb_label = \"arb hori label\", hline_arb_color = c(\"red\", \"blue\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"green\", \"blue\", \"purple\", \"cyan\"), hline_vars_labels = c(\"ANRHI Label\", \"ANRLO Label\", \"ULOQN Label\", \"LLOQN Label\"), vline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), vline_vars_colors = c(\"yellow\", \"orange\", \"brown\", \"gold\"), vline_vars_labels = c(\"ANRHI Label\", \"ANRLO Label\", \"ULOQN Label\", \"LLOQN Label\"), vline_arb = c(50, 70), vline_arb_label = \"arb vert A\", vline_arb_color = c(\"green\", \"orange\") ) ) ) #> Initializing tm_g_gh_correlationplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Density Distribution Plot — tm_g_gh_density_distribution_plot","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"teal module renders UI calls functions create density distribution plot accompanying summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"","code":"tm_g_gh_density_distribution_plot( label, dataname, param_var, param, xaxis_var, trt_group, color_manual = NULL, color_comb = NULL, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), line_size = c(1, 0.25, 3), hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", facet_ncol = 2L, comb_line = TRUE, rotate_xlab = FALSE, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. color_comb name hex value combined treatment color. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. line_size plot line thickness. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. facet_ncol numeric value indicating number facets per row. comb_line display combined treatment line toggle. rotate_xlab 45 degree rotation x-axis values. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"None","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_density_distribution_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density Distribution Plot — tm_g_gh_density_distribution_plot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- .var_labels[[\"ACTARM\"]] }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_density_distribution_plot( label = \"Density Distribution Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\" ), color_comb = \"#39ff14\", comb_line = TRUE, plot_height = c(500, 200, 2000), font_size = c(12, 8, 20), line_size = c(1, .25, 3), hline_arb = c(.02, .05), hline_arb_color = c(\"red\", \"black\"), hline_arb_label = c(\"Horizontal Line A\", \"Horizontal Line B\") ) ) ) #> Initializing tm_g_gh_density_distribution_plot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot — tm_g_gh_lineplot","title":"Line plot — tm_g_gh_lineplot","text":"teal module renders UI calls function creates line plot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot — tm_g_gh_lineplot","text":"","code":"tm_g_gh_lineplot( label, dataname, param_var, param, param_var_label = \"PARAM\", xaxis_var, yaxis_var, xvar_level = NULL, filter_var = yaxis_var, filter_var_choices = filter_var, trt_group, trt_group_level = NULL, shape_choices = NULL, stat = \"mean\", hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", color_manual = c(getOption(\"ggplot2.discrete.colour\"), c(\"#ff0000\", \"#008000\", \"#4ca3dd\", \"#8a2be2\"))[1:4], xtick = ggplot2::waiver(), xlabel = xtick, rotate_xlab = FALSE, plot_height = c(600, 200, 4000), plot_width = NULL, plot_font_size = c(12, 8, 20), dodge = c(0.4, 0, 1), pre_output = NULL, post_output = NULL, count_threshold = 0, table_font_size = c(12, 4, 20), dot_size = c(2, 1, 12), plot_relative_height_value = 1000 )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot — tm_g_gh_lineplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. param_var_label single name variable analysis data includes parameter labels. xaxis_var single name variable analysis data used x-axis plot respective goshawk function. yaxis_var single name variable analysis data used summary variable respective goshawk function. xvar_level vector can used define factor level xvar. use xvar character factor. filter_var data constraint variable. filter_var_choices data constraint variable choices. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. trt_group_level vector can used define factor level trt_group. shape_choices Vector choices_selected object names ADSL variables can used change shape stat string statistics hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. color_manual string vector representing customized colors xtick numeric vector define tick values x-axis x variable numeric. Default value waive(). xlabel vector length xtick define label x-axis tick values. Default value waive(). rotate_xlab logical(1) value indicating whether rotate x-axis labels. plot_height controls plot height. plot_width optional, controls plot width. plot_font_size control font size title, x-axis, y-axis legend font. dodge controls position dodge error bar pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. count_threshold minimum count observations (listed output table) plot nodes graph table_font_size controls font size values table dot_size plot dot size. plot_relative_height_value numeric value 500 5000 controlling starting value relative plot height slider","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot — tm_g_gh_lineplot","text":"shiny object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Line plot — tm_g_gh_lineplot","text":"Wenyi Liu (luiw2) wenyi.liu@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot — tm_g_gh_lineplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) library(nestcolor) # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- .var_labels[[\"ACTARM\"]] }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_lineplot( label = \"Line Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), shape_choices = c(\"SEX\", \"RACE\"), xaxis_var = choices_selected(\"AVISITCD\", \"AVISITCD\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), hline_arb = c(20.5, 19.5), hline_arb_color = c(\"red\", \"green\"), hline_arb_label = c(\"A\", \"B\") ) ) ) #> Initializing tm_g_gh_lineplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"tm_g_gh_scatterplot deprecated. Please use tm_g_gh_correlationplot instead.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"","code":"tm_g_gh_scatterplot( label, dataname, param_var, param, xaxis_var, yaxis_var, trt_group, color_manual = NULL, shape_manual = NULL, facet_ncol = 2, trt_facet = FALSE, reg_line = FALSE, rotate_xlab = FALSE, hline = NULL, vline = NULL, plot_height = c(500, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. xaxis_var name variable containing biomarker results displayed x-axis e.g. BASE. yaxis_var name variable containing biomarker results displayed y-axis e.g. AVAL. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. color_manual vector colors applied treatment values. shape_manual vector symbols applied LOQ values. facet_ncol numeric value indicating number facets per row. trt_facet facet treatment group trt_group. reg_line include regression line annotations slope coefficient visualization. Use facet TRUE. rotate_xlab 45 degree rotation x-axis values. hline y-axis value position horizontal line. vline x-axis value position vertical line. plot_height controls plot height. plot_width optional, controls plot width. font_size font size control title, x-axis label, y-axis label legend. dot_size plot dot size. reg_text_size font size control regression line annotations. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_scatterplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"Nick Paszty (npaszty) paszty.nicholas@gene.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatter Plot Teal Module For Biomarker Analysis — tm_g_gh_scatterplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD) ) attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- .var_labels[[\"ACTARM\"]] }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_scatterplot( label = \"Scatter Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), xaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"BASE\"), yaxis_var = choices_selected(c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\"), \"AVAL\"), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_manual = c( \"150mg QD\" = \"#000000\", \"Placebo\" = \"#3498DB\", \"Combination\" = \"#E74C3C\" ), shape_manual = c(\"N\" = 1, \"Y\" = 2, \"NA\" = 0), plot_height = c(500, 200, 2000), facet_ncol = 2, trt_facet = FALSE, reg_line = FALSE, font_size = c(12, 8, 20), dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10) ) ) ) #> Warning: `tm_g_gh_scatterplot()` was deprecated in teal.goshawk 0.1.15. #> ℹ You should use teal.goshawk::tm_g_gh_correlationplot instead of #> teal.goshawk::tm_g_gh_scatterplot #> Initializing tm_g_gh_scatterplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Spaghetti Plot — tm_g_gh_spaghettiplot","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"teal module renders UI calls function creates spaghetti plot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"","code":"tm_g_gh_spaghettiplot( label, dataname, param_var, param, param_var_label = \"PARAM\", idvar, xaxis_var, yaxis_var, xaxis_var_level = NULL, filter_var = yaxis_var, trt_group, trt_group_level = NULL, group_stats = \"NONE\", man_color = NULL, color_comb = NULL, xtick = ggplot2::waiver(), xlabel = xtick, rotate_xlab = FALSE, facet_ncol = 2, free_x = FALSE, plot_height = c(600, 200, 2000), plot_width = NULL, font_size = c(12, 8, 20), dot_size = c(2, 1, 12), hline_arb = numeric(0), hline_arb_color = \"red\", hline_arb_label = \"Horizontal line\", hline_vars = character(0), hline_vars_colors = \"green\", hline_vars_labels = hline_vars, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"label menu item label module teal app. dataname analysis data passed data argument init. E.g. ADaM structured laboratory data frame ADLB. param_var name variable containing biomarker codes e.g. PARAMCD. param biomarker selected. param_var_label single name variable analysis data includes parameter labels. idvar name unique subject id variable. xaxis_var single name variable analysis data used x-axis plot respective goshawk function. yaxis_var single name variable analysis data used summary variable respective goshawk function. xaxis_var_level vector can used define factor level xaxis_var. use xaxis_var character factor. filter_var data constraint variable. trt_group choices_selected object available choices pre-selected option variable names representing treatment group e.g. ARM. trt_group_level vector can used define factor level trt_group. group_stats control group mean median overlay. man_color string vector representing customized colors color_comb name hex value combined treatment color. xtick numeric vector define tick values x-axis x variable numeric. Default value waive(). xlabel vector length xtick define label x-axis tick values. Default value waive(). rotate_xlab logical(1) value indicating whether rotate x-axis labels facet_ncol numeric value indicating number facets per row. free_x logical(1) scales \"fixed\" (FALSE) \"free\" (TRUE) x-axis facet_wrap scales parameter. plot_height controls plot height. plot_width optional, controls plot width. font_size control font size title, x-axis, y-axis legend font. dot_size plot dot size. hline_arb numeric vector 2 values identifying intercepts arbitrary horizontal lines. hline_arb_color character vector length hline_arb. naming color arbitrary horizontal lines. hline_arb_label character vector length hline_arb. naming label arbitrary horizontal lines. hline_vars character vector name columns define additional horizontal lines. hline_vars_colors character vector naming colors additional horizontal lines. hline_vars_labels character vector naming labels additional horizontal lines appear legend. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"shiny object","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"Wenyi Liu (luiw2) wenyi.liu@roche.com Balazs Toth (tothb2) toth.balazs@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/tm_g_gh_spaghettiplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spaghetti Plot — tm_g_gh_spaghettiplot","text":"","code":"# Example using ADaM structure analysis dataset. data <- teal_data() data <- within(data, { library(dplyr) library(stringr) # use non-exported function from goshawk .h_identify_loq_values <- getFromNamespace(\"h_identify_loq_values\", \"goshawk\") # original ARM value = dose value .arm_mapping <- list( \"A: Drug X\" = \"150mg QD\", \"B: Placebo\" = \"Placebo\", \"C: Combination\" = \"Combination\" ) set.seed(1) ADSL <- rADSL ADLB <- rADLB .var_labels <- lapply(ADLB, function(x) attributes(x)$label) ADLB <- ADLB %>% mutate( AVISITCD = case_when( AVISIT == \"SCREENING\" ~ \"SCR\", AVISIT == \"BASELINE\" ~ \"BL\", grepl(\"WEEK\", AVISIT) ~ paste(\"W\", str_extract(AVISIT, \"(?<=(WEEK ))[0-9]+\")), TRUE ~ as.character(NA) ), AVISITCDN = case_when( AVISITCD == \"SCR\" ~ -2, AVISITCD == \"BL\" ~ 0, grepl(\"W\", AVISITCD) ~ as.numeric(gsub(\"[^0-9]*\", \"\", AVISITCD)), TRUE ~ as.numeric(NA) ), AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN), TRTORD = case_when( ARMCD == \"ARM C\" ~ 1, ARMCD == \"ARM B\" ~ 2, ARMCD == \"ARM A\" ~ 3 ), ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]), ARM = factor(ARM) %>% reorder(TRTORD), ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]), ACTARM = factor(ACTARM) %>% reorder(TRTORD), ANRLO = 30, ANRHI = 75 ) %>% rowwise() %>% group_by(PARAMCD) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\"<\", round(runif(1, min = 25, max = 30))), LBSTRESC )) %>% mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE), paste(\">\", round(runif(1, min = 70, max = 75))), LBSTRESC )) %>% ungroup() attr(ADLB[[\"ARM\"]], \"label\") <- .var_labels[[\"ARM\"]] attr(ADLB[[\"ACTARM\"]], \"label\") <- .var_labels[[\"ACTARM\"]] attr(ADLB[[\"ANRLO\"]], \"label\") <- \"Analysis Normal Range Lower Limit\" attr(ADLB[[\"ANRHI\"]], \"label\") <- \"Analysis Normal Range Upper Limit\" # add LLOQ and ULOQ variables ALB_LOQS <- .h_identify_loq_values(ADLB, \"LOQFL\") ADLB <- left_join(ADLB, ALB_LOQS, by = \"PARAM\") }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_gh_spaghettiplot( label = \"Spaghetti Plot\", dataname = \"ADLB\", param_var = \"PARAMCD\", param = choices_selected(c(\"ALT\", \"CRP\", \"IGA\"), \"ALT\"), idvar = \"USUBJID\", xaxis_var = choices_selected(c(\"Analysis Visit Code\" = \"AVISITCD\"), \"AVISITCD\"), yaxis_var = choices_selected(c(\"AVAL\", \"CHG\", \"PCHG\"), \"AVAL\"), filter_var = choices_selected( c(\"None\" = \"NONE\", \"Screening\" = \"BASE2\", \"Baseline\" = \"BASE\"), \"NONE\" ), trt_group = choices_selected(c(\"ARM\", \"ACTARM\"), \"ARM\"), color_comb = \"#39ff14\", man_color = c( \"Combination\" = \"#000000\", \"Placebo\" = \"#fce300\", \"150mg QD\" = \"#5a2f5f\" ), hline_arb = c(60, 50), hline_arb_color = c(\"grey\", \"red\"), hline_arb_label = c(\"default A\", \"default B\"), hline_vars = c(\"ANRHI\", \"ANRLO\", \"ULOQN\", \"LLOQN\"), hline_vars_colors = c(\"pink\", \"brown\", \"purple\", \"black\"), ) ) ) #> Initializing tm_g_gh_spaghettiplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/toggle_slider.html","id":null,"dir":"Reference","previous_headings":"","what":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"useful slider shown, sometimes hard configure sliders, one can toggle one two numeric input fields set slider instead. toggle button show two numeric input field selecting range.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/toggle_slider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"","code":"toggle_slider_ui(id, label) toggle_slider_server(id, data_state, ...) get_data_range_states(varname, paramname, ANL, trt_group = NULL, step = NULL)"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/toggle_slider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"id character module id label label label input field, e.g. slider numeric inputs ... additional parameters pass sliderInput","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/toggle_slider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI with a toggleable dichotomous slider to change between slider and numeric input fields — toggle_slider","text":"NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/ui_arbitrary_lines.html","id":null,"dir":"Reference","previous_headings":"","what":"UI module to arbitrary lines — ui_arbitrary_lines","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"UI module input either horizontal vertical lines plot via comma separated values","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/ui_arbitrary_lines.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"","code":"ui_arbitrary_lines( id, line_arb, line_arb_label, line_arb_color, title = \"Arbitrary Horizontal Lines:\" )"},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/ui_arbitrary_lines.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"id (character(1)) defining namespace shiny module. line_arb (numeric) default values textInput defining values arbitrary lines line_arb_label (character) default values textInput defining labels arbitrary lines line_arb_color (character) default values textInput defining colors arbitrary lines title (character(1)) title arbitrary lines input. default \"Arbitrary Horizontal Lines\".","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/reference/ui_arbitrary_lines.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI module to arbitrary lines — ui_arbitrary_lines","text":"(shiny.tag) input define values, colors labels arbitrary straight lines.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"breaking-changes-0-2-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.2.0","text":"Adapted modules use teal_data objects.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-2-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.2.0","text":"Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Removed Show Warnings modals modules. Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-2-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.2.0","text":"Specified minimal version package dependencies. Fix tm_g_gh_lineplot bug causing --bounds error stops plot working. Enhance tm_g_gh_correlationplot module fix related bugs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.15","text":"Updated encodings input checks use shinyvalidate::InputValidator instead shiny::validate better UI experience. Added tooltip value input ui_arbitrary_lines explain supply multiple values.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"breaking-changes-0-1-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.goshawk 0.1.15","text":"Constraints range calculated filtered data instead unfiltered. Replaced chunks simpler qenv class. Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.15","text":"Deprecated tm_g_gh_scatterplot. Use tm_g_gh_correlationplot instead. Removed scda package dependency examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.14","text":"Added teal.reporter reporting package modules. Added optional argument plot_relative_height_value tm_g_gh_lineplot control initial value relative plot height slider. Implemented nestcolor slight refactoring tm_g_gh_lineplot added nestcolor examples custom color manuals.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.14","text":"Fixed minor type coercion warning srv_arbitrary_lines. Updated modules use datasets suffix _FILTERED package works breaking changes teal.slice.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.13","text":"Added template pkgdown site. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"breaking-changes-0-1-12","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.1.12","text":"Converted hline parameter tm_g_gh_lineplot three parameters: hline_arb, hline_arb_color hline_arb_label.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.12","text":"Added basic logging modules. Rewrote modules use moduleServer updated calls teal.devel modules also written use moduleServer. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Adjusted package imports take account changes teal framework.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-11","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.11","text":"Added UI input component add additional arbitrary horizontal lines tm_g_gh_spaghettiplot, tm_g_gh_boxplot, tm_g_gh_density_distribution_plot well two additional UI input components add additional horizontal additional vertical line tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"bug-fixes-0-1-11","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.goshawk 0.1.11","text":"Fixed error tm_g_gh_boxplot facet variable selected.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-11","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.11","text":"Updated R version requirement R >= 3.6. Removed dependency test.nest package. Removed dependency utils.nest package replaced functions equivalents checkmate package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"new-features-0-1-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.goshawk 0.1.10","text":"Lab normal range LOQs horizontal line feature tm_g_gh_spaghettiplot, tm_g_gh_boxplot tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"breaking-changes-0-1-10","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.goshawk 0.1.10","text":"hline replaced hline_arb, hline_arb_color hline_arb_label modules. vline replaced vline_arb_var, vline_arb_color vline_arb_label tm_g_gh_correlationplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"bug-fixes-0-1-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.goshawk 0.1.10","text":"Fixed bug tm_g_gh_boxplot module always used AVISITCD variable Visit Column table.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.10","text":"Updated LICENCE README new package references. Updated examples documentation using scda synthetic data instead random.cdisc.data. Added error_on_lint: TRUE .lintr. Replaced tidyr’s gather spread pivot_wider pivot_longer package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-9","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.9","text":"Updated tm_g_gh_correlationplot tm_g_gh_scatterplot encodings checkbox facet treatment variable instead drop menu. Updated starting line type solid instead dashed tm_g_gh_lineplot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.8","text":"Updated plot remove x-axis label x-axis numeric data corresponding y-axis variable. Added slider control relative size plot tables. Replaced function brushedPoints clean_brushedPoints tm_g_gh_boxplot, tm_g_gh_correlationplot, tm_g_gh_scatterplot tm_g_gh_spaghettiplot.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"bug-fixes-0-1-8","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.goshawk 0.1.8","text":"Fixed infinite reactive loop inside toggle_slider_server.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.8","text":"Renamed toggle.R file toggleable.R file consistent accepted correct spelling word.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.7","text":"Added table display summary statistics.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"bug-fixes-0-1-7","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.goshawk 0.1.7","text":"Fixed displaying number messages, warnings errors Debug Info button. Fixed treatment variable values symbols (e.g. ‘:’). Allow treatment variables different arm levels.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"miscellaneous-0-1-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.goshawk 0.1.7","text":"Reduced minimum number records required dataset either 1 2 modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"enhancements-0-1-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.goshawk 0.1.6","text":"Changed slider title “Transparency” “Alpha”. Added facet_var argument UI drop . Rug plot option added. Argument changes: font_size –> plot_font_size. Line symbol type can now configured. especially useful line splitting used. Can set minimum records threshold rendering data point plot. Table font size can now controlled. Added facet_var argument UI drop . Changed slider title “Transparency” “Alpha”.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"general-0-1-6","dir":"Changelog","previous_headings":"","what":"General","title":"teal.goshawk 0.1.6","text":"Moved code argument cdisc_dataset (cdisc_data) examples. Implemented new plot_with_settings functionality modules support plot resizing, zooming, downloading functionality. Added drop selector treatment ARM.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"tealgoshawk-015","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.5","title":"teal.goshawk 0.1.5","text":"templ_ui_params_vars now uses optionalSelectInput teal. shape_choices argument tm_g_gh_lineplot can either character vector choices_selected.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"tealgoshawk-014","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.4","title":"teal.goshawk 0.1.4","text":"bug fix correlation plot module related axis ranges reflect changes data filter panel re-factoring modification correlation module pass data data driven LLOQ ULOQ footnote","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"tealgoshawk-013","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.3","title":"teal.goshawk 0.1.3","text":"Added .data PARAMCD new functions related sliders reactivity. Fixing doc small fixes. Added toggleable slider modules. Added data driven data constraints UI rendering.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"tealgoshawk-012","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.2","title":"teal.goshawk 0.1.2","text":"Box: Toggle LoQ legend /. Correlation: Toggle LoQ legend /, toggle visit facetting /. Density: Toggle combined treatment line /. Modified line-plot vertical axis range match parameter value CI range.","code":""},{"path":"https://insightsengineering.github.io/teal.goshawk/news/index.html","id":"tealgoshawk-011","dir":"Changelog","previous_headings":"","what":"teal.goshawk 0.1.1","title":"teal.goshawk 0.1.1","text":"First release.","code":""}]