From 91553a1a4007e2dc0da3e4cf70ea1ca1a60afaa5 Mon Sep 17 00:00:00 2001 From: vedhav Date: Thu, 12 Dec 2024 00:40:31 +0000 Subject: [PATCH] [actions skip] Built site for teal.osprey@9cef89efa22488daf77b9390dc1c04b0a5f52014 --- main/404.html | 14 +- main/CODE_OF_CONDUCT.html | 101 +++-- main/CONTRIBUTING.html | 129 ++++-- main/LICENSE-text.html | 56 ++- main/SECURITY.html | 68 ++- main/authors.html | 62 ++- main/index.html | 14 +- main/news/index.html | 410 ++++++++++++------ main/reference/argument_convention.html | 96 ++-- .../as_numeric_from_comma_sep_str.html | 75 +++- main/reference/get_choices.html | 78 +++- main/reference/include_css_files.html | 78 +++- main/reference/index.html | 135 ++++-- main/reference/label_aevar.html | 78 +++- main/reference/name_ci.html | 75 +++- main/reference/plot_decorate_output.html | 71 ++- main/reference/quick_filter.html | 87 +++- main/reference/shared_params.html | 78 +++- main/reference/srv_g_decorate.html | 87 +++- main/reference/teal.osprey-package.html | 91 +++- main/reference/tm_g_ae_oview.html | 99 +++-- main/reference/tm_g_ae_sub.html | 102 +++-- main/reference/tm_g_butterfly.html | 129 ++++-- main/reference/tm_g_events_term_id.html | 102 +++-- main/reference/tm_g_heat_bygrade.html | 120 +++-- main/reference/tm_g_patient_profile.html | 142 ++++-- main/reference/tm_g_spiderplot.html | 132 ++++-- main/reference/tm_g_swimlane.html | 132 ++++-- main/reference/tm_g_waterfall.html | 144 ++++-- main/reference/ui_g_decorate.html | 84 +++- main/search.json | 2 +- 31 files changed, 2251 insertions(+), 820 deletions(-) diff --git a/main/404.html b/main/404.html index 49fa878d..15788f65 100644 --- a/main/404.html +++ b/main/404.html @@ -1,5 +1,4 @@ - - + @@ -41,7 +40,16 @@
  • Non-CRAN unit test report
    • - +
  • + +
    + main +latest-tag +v0.1.16 +v0.1.15 +
    +
    • + + @@ -41,65 +71,80 @@

    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.

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    Our Standards

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    Our Standards +

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

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    • Demonstrating empathy and kindness toward other people
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        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
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      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
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      Examples of unacceptable behavior include:

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      • The use of sexualized language or imagery, and sexual attention or advances of any kind
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      Examples of unacceptable behavior include:

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      • The use of sexualized language or imagery, and sexual attention or advances of any kind
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      • Public or private harassment
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      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
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    Enforcement Responsibilities

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    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.

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    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:

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    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

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    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

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    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.

    @@ -107,17 +152,19 @@

    Attribution

    + + - + + - + + diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html index 9c3065f1..34b3d02d 100644 --- a/main/CONTRIBUTING.html +++ b/main/CONTRIBUTING.html @@ -1,5 +1,19 @@ - -Contribution Guidelines • teal.osprey + + + + + + +Contribution Guidelines • teal.osprey + + + + + + + + + Skip to contents @@ -15,18 +29,34 @@ + + @@ -43,7 +73,8 @@

    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

    @@ -54,38 +85,47 @@

    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.

        @@ -99,76 +139,93 @@

        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).

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    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 0b26ce75..98e765fc 100644 --- a/main/LICENSE-text.html +++ b/main/LICENSE-text.html @@ -1,5 +1,19 @@ - -License • teal.osprey + + + + + + +License • teal.osprey + + + + + + + + + Skip to contents @@ -15,18 +29,34 @@ + + @@ -53,17 +83,19 @@

    License

    limitations under the License. - + + - + + - + + diff --git a/main/SECURITY.html b/main/SECURITY.html index 65f183ec..7f9e079e 100644 --- a/main/SECURITY.html +++ b/main/SECURITY.html @@ -1,5 +1,19 @@ - -Security Policy • teal.osprey + + + + + + +Security Policy • teal.osprey + + + + + + + + + Skip to contents @@ -15,18 +29,34 @@ + + @@ -41,38 +71,44 @@

    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:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    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/authors.html b/main/authors.html index c272517c..3aedb27e 100644 --- a/main/authors.html +++ b/main/authors.html @@ -1,5 +1,19 @@ - -Authors and Citation • teal.osprey + + + + + + +Authors and Citation • teal.osprey + + + + + + + + + Skip to contents @@ -15,18 +29,34 @@ + + @@ -40,7 +70,8 @@

    Authors and Citation

    Authors

    -
    + +

    Citation

    @@ -98,17 +130,19 @@

    Citation

    + + - + + - + + diff --git a/main/index.html b/main/index.html index be224039..e8736279 100644 --- a/main/index.html +++ b/main/index.html @@ -1,5 +1,4 @@ - - + @@ -43,7 +42,16 @@
  • Non-CRAN unit test report
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  • + +
    + main +latest-tag +v0.1.16 +v0.1.15 +
    +
    • + + @@ -39,239 +69,359 @@

    Changelog

    -

    teal.osprey 0.1.16.9031

    -
    -

    Enhancements

    -
    • Added teal.logger functionality for logging changes in shiny inputs in all modules.
      • -
    +

    Breaking Changes +

    + +
    +
    +

    Enhancements +

    + +
    -

    Miscellaneous

    -
    +

    Miscellaneous +

    + +
    -

    teal.osprey 0.1.16

    - +
    -

    teal.osprey 0.1.15

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    teal.osprey 0.1.15 +

    -

    Breaking changes

    -
    +

    Breaking changes +

    + +
    -

    Enhancements

    -
    + +
    -

    Miscellaneous

    -
    + +
    -

    teal.osprey 0.1.14

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    teal.osprey 0.1.14 +

    -

    Enhancements

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    • Removed unneeded chunk evaluations in tm_g_patient_profile module.
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    Enhancements +

    + +
    -

    Miscellaneous

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    + +
    -

    teal.osprey 0.1.13

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    teal.osprey 0.1.13 +

    -

    Enhancements

    -
    • Added basic logging to the modules.
      • +

      Enhancements +

      +
        +
      • Added basic logging to the modules.
      • The label of the select input widget to choose the paramcd is no longer hard coded to ADTR in tm_g_spiderplot.
        • -
    + +
    -

    Miscellaneous

    -
    + +
    -

    teal.osprey 0.1.12

    +

    teal.osprey 0.1.12 +

    -

    Breaking changes

    -
    • Refactored tm_g_ae_oview to remove the flag variables generated by the module by default and to replace parameter add_flag with flag_var_anl.
      • -
    +

    Breaking changes +

    + +
    -

    Enhancements

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    + +
    -

    Bug fixes

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    Bug fixes +

    + +
    -

    Miscellaneous

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    + +
    -

    teal.osprey 0.1.11

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    + +
    -

    teal.osprey 0.1.10

    +

    teal.osprey 0.1.10 +

    -

    Enhancements

    -
    • Added a Shiny feature to tm_g_swimlane that will prevent needless re-render of the output when the user has not completely provided inputs to the vertical lines widget.
      • -
    +

    Enhancements +

    + +
    -

    Miscellaneous

    -
    + +
    -

    Bug fixes

    -
    +

    Bug fixes +

    + +
    -

    teal.osprey 0.1.9

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    teal.osprey 0.1.9 +

    -

    New features

    -
    • Added new teal module tm_g_heat_bygrade for a heatmap by grade plot.
      • +

      New features +

      +
        +
      • Added new teal module tm_g_heat_bygrade for a heatmap by grade plot.
      • Added new teal module tm_g_ae_sub for an AE by subgroups plot.
        • -
    + +
    -

    Bug fixes

    -
    + +
    -

    Miscellaneous

    -
    +

    Miscellaneous +

    + +
    -

    teal.osprey 0.1.8

    -
    + +
    -

    teal.osprey 0.1.7

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    teal.osprey 0.1.7 +

    -

    Enhancements

    -
    • Added additional validation for horizontal and vertical reference lines in tm_g_spider_plot.
      • -
    +

    Enhancements +

    + +
    -

    Bug Fixes

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    + +
    -

    Miscellaneous

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    + +
    -

    teal.osprey 0.1.6

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    + +
    -

    teal.osprey 0.1.5

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    + +
    -

    teal.osprey 0.1.4

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    teal.osprey 0.1.4 +

    + +
    -

    teal.osprey 0.1.3

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    +

    teal.osprey 0.1.3 +

    + +
    -

    teal.osprey 0.1.2

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    + +
    -

    teal.osprey 0.1.1

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    + + + +
    -

    teal.osprey 0.1.0

    -
    + + + + + + - + + - + + diff --git a/main/reference/argument_convention.html b/main/reference/argument_convention.html index a0184179..5b027376 100644 --- a/main/reference/argument_convention.html +++ b/main/reference/argument_convention.html @@ -1,7 +1,23 @@ - -Standard Arguments — argument_convention • teal.osprey + + + + + + +Standard Arguments — argument_convention • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -48,56 +80,68 @@

    Standard Arguments

    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    arm_var
    +
    arm_var +

    (choices_selected)
    object with all available choices and the pre-selected option for variable names that can be used as arm_var. See teal.transform::choices_selected() for details. Column arm_var in the dataname has to be a factor.

    -
    paramcd
    +
    paramcd +

    (character(1) or choices_selected)
    variable value designating the studied parameter. See teal.transform::choices_selected() for details.

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Details

    +

    Details +

    Although this function just returns NULL it has two uses, for the teal module users it provides a documentation of arguments that are commonly and consistently used in the framework. For the developer it adds a @@ -106,17 +150,19 @@

    Details

    + + - + + - + + diff --git a/main/reference/as_numeric_from_comma_sep_str.html b/main/reference/as_numeric_from_comma_sep_str.html index 4ccdde82..8979f50b 100644 --- a/main/reference/as_numeric_from_comma_sep_str.html +++ b/main/reference/as_numeric_from_comma_sep_str.html @@ -1,13 +1,29 @@ - -takes input_string, splits by "," and returns a numeric vector with NAs where the split-strings are not numeric. e.g. as_numeric_from_comma_separated_string("4 ,hello,5,, 3") is c(4, NA, 5, NA, 3). If input argument is NULL or just whitespace then NULL is returned — as_numeric_from_comma_sep_str • teal.osprey + +If input argument is NULL or just whitespace then NULL is returned'> + + + + Skip to contents @@ -23,18 +39,34 @@ + + @@ -56,31 +88,38 @@

    takes input_string, splits by "," and returns a numeric vector with NAs wher
    -

    Usage

    +

    Usage +

    as_numeric_from_comma_sep_str(input_string)
    -

    Arguments

    +

    Arguments +

    -
    input_string
    +
    +
    input_string +

    string to be split into numeric vector

    -
    + + + + - + + - + + diff --git a/main/reference/get_choices.html b/main/reference/get_choices.html index e90872a1..5a3228af 100644 --- a/main/reference/get_choices.html +++ b/main/reference/get_choices.html @@ -1,13 +1,29 @@ - -Get Choices — get_choices • teal.osprey + + + + + +Get Choices — get_choices • teal.osprey + + + + + + + +Otherwise, it returns the input as is."> + + + + Skip to contents @@ -23,18 +39,34 @@ + + @@ -56,35 +88,43 @@

    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 b2e25be3..a45a3ecb 100644 --- a/main/reference/include_css_files.html +++ b/main/reference/include_css_files.html @@ -1,9 +1,25 @@ - -Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.osprey + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.osprey + + + + + + + +as needed. Thus, we do not export this method."> + + + + Skip to contents @@ -19,18 +35,34 @@ + + @@ -50,35 +82,43 @@

    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 3194c70e..3f34f026 100644 --- a/main/reference/index.html +++ b/main/reference/index.html @@ -1,5 +1,19 @@ - -Package index • teal.osprey + + + + + + +Package index • teal.osprey + + + + + + + + + Skip to contents @@ -15,18 +29,34 @@ + + @@ -38,124 +68,161 @@

    Package index

    -

    Graph Modules

    +

    Graph Modules +

    Teal graph modules including safety and early efficacy graphs

    -
    +
    +
    -
    +
    +
    tm_g_ae_oview() stable
    Teal module for the AE overview
    -
    +
    +
    +
    tm_g_ae_sub() stable
    teal module for the AE by subgroups
    -
    +
    +
    +
    tm_g_butterfly() stable
    Butterfly plot Teal Module
    -
    +
    +
    +
    tm_g_events_term_id() stable
    Events by Term Plot Teal Module
    -
    +
    +
    +
    tm_g_heat_bygrade() stable
    Teal module for the heatmap by grade
    -
    +
    +
    +
    tm_g_patient_profile() stable
    Patient Profile plot teal module
    -
    +
    +
    +
    tm_g_spiderplot() stable
    Spider plot Teal Module
    -
    +
    +
    +
    tm_g_swimlane() stable
    Teal Module for Swimlane Plot
    -
    +
    +
    +
    tm_g_waterfall() stable
    Teal Module for Waterfall Plot
    -
    -

    Utility

    + +
    +
    +

    Utility +

    Utilities fuctions used in the package

    -
    +
    +
    -
    +
    +
    label_aevar() stable
    -
    Automatically switch variable labels for standard AE variables in AE osprey functions [Stable]
    -
    +
    Automatically switch variable labels for standard AE variables in AE osprey functions [Stable] +
    +
    +
    +
    plot_decorate_output() stable
    Helper function to plot decorated output UI
    -
    +
    +
    +
    quick_filter() stable
    -
    Utility function for quick filter [Stable]
    -
    +
    Utility function for quick filter [Stable] +
    +
    +
    +
    srv_g_decorate() stable
    Helper server function to decorate plot output
    -
    +
    +
    +
    ui_g_decorate() stable
    Helper UI function to decorate plot output UI
    -
    + + + + - + + - + + diff --git a/main/reference/label_aevar.html b/main/reference/label_aevar.html index 17cc30b9..766271a2 100644 --- a/main/reference/label_aevar.html +++ b/main/reference/label_aevar.html @@ -1,7 +1,23 @@ - -Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar • teal.osprey + + + + + + +Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -36,7 +68,8 @@
    -

    Automatically switch variable labels for standard AE variables in AE osprey functions [Stable]

    +

    Automatically switch variable labels for standard AE variables in AE osprey functions [Stable] +

    Source: R/utils.R
    label_aevar.Rd
    @@ -47,31 +80,38 @@

    Automatically switch variable labels for standard AE variables

    -

    Usage

    +

    Usage +

    label_aevar(x)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    variable key

    -
    + + + + - + + - + + diff --git a/main/reference/name_ci.html b/main/reference/name_ci.html index f6c60649..167c77f0 100644 --- a/main/reference/name_ci.html +++ b/main/reference/name_ci.html @@ -1,7 +1,23 @@ - -retrieve name of ci method — name_ci • teal.osprey + + + + + + +retrieve name of ci method — name_ci • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,33 +79,40 @@

    retrieve name of ci method

    -

    Usage

    +

    Usage +

    name_ci(x = ci_choices)
 
 name_ci(x = ci_choices)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    ci method to retrieve its name

    -
    + + + + - + + - + + diff --git a/main/reference/plot_decorate_output.html b/main/reference/plot_decorate_output.html index 1a7b7ab9..92c90e7e 100644 --- a/main/reference/plot_decorate_output.html +++ b/main/reference/plot_decorate_output.html @@ -1,5 +1,21 @@ - -Helper function to plot decorated output UI — plot_decorate_output • teal.osprey + + + + + + +Helper function to plot decorated output UI — plot_decorate_output • teal.osprey + + + + + + + + + + + Skip to contents @@ -15,18 +31,34 @@ + + @@ -44,31 +76,38 @@

    Helper function to plot decorated output UI

    -

    Usage

    +

    Usage +

    plot_decorate_output(id)
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (character) id of this element

    -
    + + + + - + + - + + diff --git a/main/reference/quick_filter.html b/main/reference/quick_filter.html index 804f80dc..64bd6aa4 100644 --- a/main/reference/quick_filter.html +++ b/main/reference/quick_filter.html @@ -1,7 +1,23 @@ - -Utility function for quick filter — quick_filter • teal.osprey + + + + + + +Utility function for quick filter — quick_filter • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -36,7 +68,8 @@
    -

    Utility function for quick filter [Stable]

    +

    Utility function for quick filter [Stable] +

    Source: R/utils.R
    quick_filter.Rd
    @@ -47,43 +80,53 @@

    Utility function for quick filter -

    Usage

    +

    Usage +

    quick_filter(filter_opt, ANL)
    -

    Arguments

    +

    Arguments +

    -
    filter_opt
    +
    +
    filter_opt +

    vector of string names of flag variable to filter (keep Y rows only)

    -
    ANL
    +
    ANL +

    input dataset

    -
    + +
    -

    Value

    +

    Value +

    a filtered dataframe

    -

    Author

    +

    Author +

    Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

    + + - + + - + + diff --git a/main/reference/shared_params.html b/main/reference/shared_params.html index 2cc6710a..2cc17190 100644 --- a/main/reference/shared_params.html +++ b/main/reference/shared_params.html @@ -1,7 +1,23 @@ - -Shared Parameters — shared_params • teal.osprey + + + + + + +Shared Parameters — shared_params • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -48,36 +80,44 @@

    Shared Parameters

    -

    Arguments

    +

    Arguments +

    -
    plot_height
    +
    +
    plot_height +

    (numeric) optional vector of length three with c(value, min, max). Specifies the height of the main plot.

    -
    plot_width
    +
    plot_width +

    (numeric) optional vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

    -
    label
    +
    label +

    (character) module label in the teal app. Please note that this module is developed based on ADaM data structure and ADaM variables.

    -
    + + - + + - + + - + + diff --git a/main/reference/srv_g_decorate.html b/main/reference/srv_g_decorate.html index 85a0dfa5..2e993a3c 100644 --- a/main/reference/srv_g_decorate.html +++ b/main/reference/srv_g_decorate.html @@ -1,7 +1,23 @@ - -Helper server function to decorate plot output — srv_g_decorate • teal.osprey + + + + + + +Helper server function to decorate plot output — srv_g_decorate • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Helper server function to decorate plot output

    -

    Usage

    +

    Usage +

    srv_g_decorate(
   id,
   plot_id = "out",
@@ -58,44 +91,54 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (character) id of the module

    -
    plot_id
    +
    plot_id +

    (character) id for plot output

    -
    plt
    +
    plt +

    (reactive) a reactive object of graph object

    -
    plot_height
    +
    plot_height +

    (numeric) optional vector of length three with c(value, min, max). Specifies the height of the main plot.

    -
    plot_width
    +
    plot_width +

    (numeric) optional vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

    -
    + +
    + + - + + - + + diff --git a/main/reference/teal.osprey-package.html b/main/reference/teal.osprey-package.html index 9f269044..28c62b4a 100644 --- a/main/reference/teal.osprey-package.html +++ b/main/reference/teal.osprey-package.html @@ -1,9 +1,25 @@ - -teal.osprey: teal modules for 'osprey' — teal.osprey-package • teal.osprey + + + + + +teal.osprey: teal modules for 'osprey' — teal.osprey-package • teal.osprey + + + + + + + +This enables teal app developers to easily create applications making use of the osprey analysis functions."> + + + + Skip to contents @@ -19,18 +35,34 @@ + + @@ -38,7 +70,8 @@
    -

    teal.osprey: teal modules for 'osprey'

    +

    +teal.osprey: teal modules for 'osprey'

    Source: R/teal.osprey.R
    teal.osprey-package.Rd
    @@ -51,37 +84,51 @@

    teal.osprey: teal modules for 'osprey'

    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Nina Qi qit3@gene.com

    -

    Authors:

    + +
    + + - + + - + + diff --git a/main/reference/tm_g_ae_oview.html b/main/reference/tm_g_ae_oview.html index ea4de869..9515baef 100644 --- a/main/reference/tm_g_ae_oview.html +++ b/main/reference/tm_g_ae_oview.html @@ -1,7 +1,23 @@ - -Teal module for the AE overview — tm_g_ae_oview • teal.osprey + + + + + + +Teal module for the AE overview — tm_g_ae_oview • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Teal module for the AE overview

    -

    Usage

    +

    Usage +

    tm_g_ae_oview(
   label,
   dataname,
@@ -60,57 +93,69 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    arm_var
    +
    arm_var +

    (choices_selected)
    object with all available choices and the pre-selected option for variable names that can be used as arm_var. See teal.transform::choices_selected() for details. Column arm_var in the dataname has to be a factor.

    -
    flag_var_anl
    +
    flag_var_anl +

    (teal.transform::choices_selected) choices_selected object with variables used to count adverse event sub-groups (e.g. Serious events, Related events, etc.)

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Examples

    +

    Examples +

    data <- teal_data() |>
   within({
     ADSL <- rADSL
@@ -171,17 +216,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_ae_sub.html b/main/reference/tm_g_ae_sub.html index 1427833a..a9f3436c 100644 --- a/main/reference/tm_g_ae_sub.html +++ b/main/reference/tm_g_ae_sub.html @@ -1,7 +1,23 @@ - -teal module for the AE by subgroups — tm_g_ae_sub • teal.osprey + + + + + + +teal module for the AE by subgroups — tm_g_ae_sub • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    teal module for the AE by subgroups

    -

    Usage

    +

    Usage +

    tm_g_ae_sub(
   label,
   dataname,
@@ -60,60 +93,73 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    arm_var
    +
    arm_var +

    (choices_selected)
    object with all available choices and the pre-selected option for variable names that can be used as arm_var. See teal.transform::choices_selected() for details. Column arm_var in the dataname has to be a factor.

    -
    group_var
    +
    group_var +

    (choices_selected) subgroups variables. See teal.transform::choices_selected() for details.

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Author

    +

    Author +

    Liming Li (Lil128) liming.li@roche.com

    Molly He (hey59) hey59@gene.com

    -

    Examples

    +

    Examples +

    # Example using stream (ADaM) dataset
 data <- teal_data() |>
   within({
@@ -150,17 +196,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_butterfly.html b/main/reference/tm_g_butterfly.html index 4b9e99e1..366370cd 100644 --- a/main/reference/tm_g_butterfly.html +++ b/main/reference/tm_g_butterfly.html @@ -1,7 +1,23 @@ - -Butterfly plot Teal Module — tm_g_butterfly • teal.osprey + + + + + + +Butterfly plot Teal Module — tm_g_butterfly • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Butterfly plot Teal Module

    -

    Usage

    +

    Usage +

    tm_g_butterfly(
   label,
   dataname,
@@ -69,86 +102,106 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    filter_var
    +
    filter_var +

    (choices_selected) variable name of data filter, please see details regarding expected values, default isNULL.choices vector with filter_var choices, default is NULL

    -
    right_var
    +
    right_var +

    (choices_selected) dichotomization variable for right side

    -
    left_var
    +
    left_var +

    (choices_selected) dichotomization variable for left side

    -
    category_var
    +
    category_var +

    (choices_selected) category (y axis) variable

    -
    color_by_var
    +
    color_by_var +

    (choices_selected) variable defines color blocks within each bar

    -
    count_by_var
    +
    count_by_var +

    (choices_selected) variable defines how x axis is calculated

    -
    facet_var
    +
    facet_var +

    (choices_selected) variable for row facets

    -
    sort_by_var
    +
    sort_by_var +

    (choices_selected) argument for order of class and term elements in table, default here is "count"

    -
    legend_on
    +
    legend_on +

    (boolean) value for whether legend is displayed

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum 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.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Details

    +

    Details +

    filter_var option is designed to work in conjunction with filtering function provided by teal (encoding panel on the right hand side of the shiny app). It can be used as quick access to predefined @@ -161,13 +214,15 @@

    Details

    -

    Author

    +

    Author +

    Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

    Chendi Liao (liaoc10) chendi.liao@roche.com

    -

    Examples

    +

    Examples +

    # Example using stream (ADaM) dataset
 data <- teal_data() |>
   within({
@@ -235,17 +290,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_events_term_id.html b/main/reference/tm_g_events_term_id.html index 7f9b213e..74db2c5a 100644 --- a/main/reference/tm_g_events_term_id.html +++ b/main/reference/tm_g_events_term_id.html @@ -1,7 +1,23 @@ - -Events by Term Plot Teal Module — tm_g_events_term_id • teal.osprey + + + + + + +Events by Term Plot Teal Module — tm_g_events_term_id • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Events by Term Plot Teal Module

    -

    Usage

    +

    Usage +

    tm_g_events_term_id(
   label,
   dataname,
@@ -60,61 +93,74 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    term_var
    +
    term_var +

    teal.transform::choices_selected object with all available choices and pre-selected option names that can be used to specify the term for events

    -
    arm_var
    +
    arm_var +

    (choices_selected)
    object with all available choices and the pre-selected option for variable names that can be used as arm_var. See teal.transform::choices_selected() for details. Column arm_var in the dataname has to be a factor.

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Author

    +

    Author +

    Liming Li (lil128) liming.li@roche.com

    Molly He (hey59) hey59@gene.com

    -

    Examples

    +

    Examples +

    data <- teal_data() |>
   within({
     ADSL <- rADSL
@@ -153,17 +199,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_heat_bygrade.html b/main/reference/tm_g_heat_bygrade.html index 10c74c79..558aa1a8 100644 --- a/main/reference/tm_g_heat_bygrade.html +++ b/main/reference/tm_g_heat_bygrade.html @@ -1,7 +1,23 @@ - -Teal module for the heatmap by grade — tm_g_heat_bygrade • teal.osprey + + + + + + +Teal module for the heatmap by grade — tm_g_heat_bygrade • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Teal module for the heatmap by grade

    -

    Usage

    +

    Usage +

    tm_g_heat_bygrade(
   label,
   sl_dataname,
@@ -67,89 +100,108 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    sl_dataname
    +
    sl_dataname +

    (character) subject level dataset name, needs to be available in the list passed to the data argument of teal::init()

    -
    ex_dataname
    +
    ex_dataname +

    (character) exposures dataset name, needs to be available in the list passed to the data argument of teal::init()

    -
    ae_dataname
    +
    ae_dataname +

    (character) adverse events dataset name, needs to be available in the list passed to the data argument of teal::init()

    -
    cm_dataname
    +
    cm_dataname +

    (character) concomitant medications dataset name, needs to be available in the list passed to the data argument of teal::init()
    specify to NA if no concomitant medications data is available

    -
    id_var
    +
    id_var +

    (choices_seleced) unique subject ID variable

    -
    visit_var
    +
    visit_var +

    (choices_seleced) analysis visit variable

    -
    ongo_var
    +
    ongo_var +

    (choices_seleced) study ongoing status variable. This variable is a derived logical variable. Usually it can be derived from EOSSTT.

    -
    anno_var
    +
    anno_var +

    (choices_seleced) annotation variable

    -
    heat_var
    +
    heat_var +

    (choices_seleced) heatmap variable

    -
    conmed_var
    +
    conmed_var +

    (choices_seleced) concomitant medications variable, specify to NA if no concomitant medications data is available

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Examples

    +

    Examples +

    data <- teal_data() |>
   within({
     library(dplyr)
@@ -237,17 +289,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_patient_profile.html b/main/reference/tm_g_patient_profile.html index e907edc3..4a7f1421 100644 --- a/main/reference/tm_g_patient_profile.html +++ b/main/reference/tm_g_patient_profile.html @@ -1,7 +1,23 @@ - -Patient Profile plot teal module — tm_g_patient_profile • teal.osprey + + + + + + +Patient Profile plot teal module — tm_g_patient_profile • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Patient Profile plot teal module

    -

    Usage

    +

    Usage +

    tm_g_patient_profile(
   label = "Patient Profile Plot",
   patient_id,
@@ -74,25 +107,31 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    patient_id
    +
    patient_id +

    (choices_seleced) unique subject ID variable

    -
    sl_dataname
    +
    sl_dataname +

    (character) subject level dataset name, needs to be available in the list passed to the data argument of teal::init()

    -
    ex_dataname, ae_dataname, rs_dataname, cm_dataname, lb_dataname
    +
    ex_dataname, ae_dataname, rs_dataname, cm_dataname, lb_dataname +

    (character(1)) names of exposure, adverse events, response, concomitant medications, and labs datasets, respectively; must be available in the list passed to the data @@ -100,27 +139,32 @@

    Argumentssl_start_date +
    sl_start_date +

    choices_selected study start date variable, usually set to treatment start date or randomization date

    -
    ex_var
    +
    ex_var +

    choices_selected exposure variable to plot as each line
    leave unspecified or set to NULL if exposure data is not available

    -
    ae_var
    +
    ae_var +

    choices_selected adverse event variable to plot as each line
    leave unspecified or set to NULL if adverse events data is not available

    -
    ae_line_col_var
    +
    ae_line_col_var +

    choices_selected variable for coloring AE lines
    leave unspecified or set to NULL if adverse events data is not available

    -
    ae_line_col_opt
    +
    ae_line_col_opt +

    aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible @@ -128,63 +172,78 @@

    Argumentsrs_var +
    rs_var +

    choices_selected response variable to plot as each line
    leave unspecified or set to NULL if response data is not available

    -
    cm_var
    +
    cm_var +

    choices_selected concomitant medication variable to plot as each line
    leave unspecified or set to NULL if concomitant medications data is not available

    -
    lb_var
    +
    lb_var +

    choices_selected lab variable to plot as each line
    leave unspecified or set to NULL if labs data is not available

    -
    x_limit
    +
    x_limit +

    a single character string with two numbers separated by a comma indicating the x-axis limit, default is "-28, 365"

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum 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.

    -

    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Details

    +

    Details +

    As the patient profile module plots different domains in one plot, the study day (x-axis) is derived for consistency based the start date of user's choice in the app (for example, -ADSL.RANDDT or ADSL.TRTSDT):

    • In ADAE, ADEX, and ADCM, it would be study day based on ASTDT and/or +ADSL.RANDDT or ADSL.TRTSDT):

      +
        +

      • In ADAE, ADEX, and ADCM, it would be study day based on ASTDT and/or AENDT in reference to the start date

      • In ADRS and ADLB, it would be study day based on ADT in reference to the start date

        • -
    + +
    -

    Author

    +

    Author +

    Xuefeng Hou (houx14) houx14@gene.com

    Tina Cho (chot) tina.cho@roche.com

    Molly He (hey59) hey59@gene.com

    @@ -192,7 +251,8 @@

    Author<

    -

    Examples

    +

    Examples +

    data <- teal_data() |>
   within({
     ADSL <- rADSL
@@ -268,17 +328,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_spiderplot.html b/main/reference/tm_g_spiderplot.html index b2bafae9..2cb9eb83 100644 --- a/main/reference/tm_g_spiderplot.html +++ b/main/reference/tm_g_spiderplot.html @@ -1,7 +1,23 @@ - -Spider plot Teal Module — tm_g_spiderplot • teal.osprey + + + + + + +Spider plot Teal Module — tm_g_spiderplot • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Spider plot Teal Module

    -

    Usage

    +

    Usage +

    tm_g_spiderplot(
   label,
   dataname,
@@ -70,98 +103,121 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    (character(1))
    analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().

    -
    paramcd
    +
    paramcd +

    (character(1) or choices_selected)
    variable value designating the studied parameter. See teal.transform::choices_selected() for details.

    -
    x_var
    +
    x_var +

    x-axis variables

    -
    y_var
    +
    y_var +

    y-axis variables

    -
    marker_var
    +
    marker_var +

    variable dictates marker symbol

    -
    line_colorby_var
    +
    line_colorby_var +

    variable dictates line color

    -
    xfacet_var
    +
    xfacet_var +

    variable for x facets

    -
    yfacet_var
    +
    yfacet_var +

    variable for y facets

    -
    vref_line
    +
    vref_line +

    vertical reference lines

    -
    href_line
    +
    href_line +

    horizontal reference lines

    -
    anno_txt_var
    +
    anno_txt_var +

    annotation text

    -
    legend_on
    +
    legend_on +

    boolean value for whether legend is displayed

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum 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.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Author

    +

    Author +

    Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

    Chendi Liao (liaoc10) chendi.liao@roche.com

    -

    Examples

    +

    Examples +

    # Example using stream (ADaM) dataset
 data <- teal_data() |>
   within({
@@ -219,17 +275,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_swimlane.html b/main/reference/tm_g_swimlane.html index 6ed3e7a1..c6196207 100644 --- a/main/reference/tm_g_swimlane.html +++ b/main/reference/tm_g_swimlane.html @@ -1,7 +1,23 @@ - -Teal Module for Swimlane Plot — tm_g_swimlane • teal.osprey + + + + + + +Teal Module for Swimlane Plot — tm_g_swimlane • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Teal Module for Swimlane Plot

    -

    Usage

    +

    Usage +

    tm_g_swimlane(
   label,
   dataname,
@@ -70,101 +103,124 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname
    +
    dataname +

    analysis data used for plotting, needs to be available in the list passed to the data argument of teal::init(). If no markers are to be plotted in the module, "ADSL" should be the input. If markers are to be plotted, data name for the marker data should be the input

    -
    bar_var
    +
    bar_var +

    teal.transform::choices_selected subject-level numeric variable from dataset to plot as the bar length

    -
    bar_color_var
    +
    bar_color_var +

    teal.transform::choices_selected color by variable (subject-level)

    -
    sort_var
    +
    sort_var +

    choices_selected sort by variable (subject-level)

    -
    marker_pos_var
    +
    marker_pos_var +

    teal.transform::choices_selected variable for marker position from marker data (Note: make sure that marker position has the same relative start day as bar length variable bar_var

    -
    marker_shape_var
    +
    marker_shape_var +

    teal.transform::choices_selected marker shape variable from marker data

    -
    marker_shape_opt
    +
    marker_shape_opt +

    aesthetic values to map shape values (named vector to map shape values to each name). If not NULL, please make sure this contains all possible values for marker_shape_var values, otherwise shape will be assigned by ggplot default

    -
    marker_color_var
    +
    marker_color_var +

    marker color variable from marker data

    -
    marker_color_opt
    +
    marker_color_opt +

    aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for marker_color_var values, otherwise color will be assigned by ggplot default

    -
    anno_txt_var
    +
    anno_txt_var +

    character vector with subject-level variable names that are selected as annotation

    -
    vref_line
    +
    vref_line +

    vertical reference lines

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum 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.

    -
    x_label
    +
    x_label +

    the label of the x axis

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Author

    +

    Author +

    Ting Qi (qit3) qit3@gene.com

    -

    Examples

    +

    Examples +

    # Example using stream (ADaM) dataset
 data <- teal_data() |>
   within({
@@ -239,17 +295,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_waterfall.html b/main/reference/tm_g_waterfall.html index f75e5ccc..8e2bb658 100644 --- a/main/reference/tm_g_waterfall.html +++ b/main/reference/tm_g_waterfall.html @@ -1,7 +1,23 @@ - -Teal Module for Waterfall Plot — tm_g_waterfall • teal.osprey + + + + + + +Teal Module for Waterfall Plot — tm_g_waterfall • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Teal Module for Waterfall Plot

    -

    Usage

    +

    Usage +

    tm_g_waterfall(
   label,
   dataname_tr = "ADTR",
@@ -74,125 +107,152 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (character(1))
    menu item label of the module in the teal app.

    -
    dataname_tr
    +
    dataname_tr +

    tumor burden analysis data used in teal module to plot as bar height, needs to be available in the list passed to the data argument of teal::init()

    -
    dataname_rs
    +
    dataname_rs +

    response analysis data used in teal module to label response parameters, needs to be available in the list passed to the data argument of teal::init()

    -
    bar_paramcd
    +
    bar_paramcd +

    choices_selected parameter in tumor burden data that will be plotted as bar height

    -
    bar_var
    +
    bar_var +

    choices_selected numeric variable from dataset to plot the bar height, e.g., PCHG

    -
    bar_color_var
    +
    bar_color_var +

    choices_selected color by variable (subject level), None corresponds to NULL

    -
    bar_color_opt
    +
    bar_color_opt +

    aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for bar_color_var values, otherwise color will be assigned by ggplot default, please note that NULL needs to be specified in this case

    -
    sort_var
    +
    sort_var +

    choices_selected sort by variable (subject level), None corresponds to NULL

    -
    add_label_var_sl
    +
    add_label_var_sl +

    choices_selected add label to bars (subject level), None corresponds to NULL

    -
    add_label_paramcd_rs
    +
    add_label_paramcd_rs +

    choices_selected add label to bars (response dataset), None corresponds to NULL. At least one of add_label_var_sl and add_label_paramcd_rs needs to be NULL

    -
    anno_txt_var_sl
    +
    anno_txt_var_sl +

    choices_selected subject level variables to be displayed in the annotation table, default is NULL

    -
    anno_txt_paramcd_rs
    +
    anno_txt_paramcd_rs +

    choices_selected analysis dataset variables to be displayed in the annotation table, default is NULL

    -
    facet_var
    +
    facet_var +

    choices_selected facet by variable (subject level), None corresponds to NULL

    -
    ytick_at
    +
    ytick_at +

    bar height axis interval, default is 20

    -
    href_line
    +
    href_line +

    numeric vector to plot horizontal reference lines, default is NULL

    -
    gap_point_val
    +
    gap_point_val +

    singular numeric value for adding bar break when some bars are significantly higher than others, default is NULL

    -
    show_value
    +
    show_value +

    boolean of whether value of bar height is shown, default is TRUE

    -
    plot_height
    +
    plot_height +

    (numeric(3))
    vector to indicate default value, minimum and maximum values.

    -
    plot_width
    +
    plot_width +

    (numeric(3))
    vector to indicate default value, minimum and maximum 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.

    -
    + +
    -

    Value

    +

    Value +

    the teal::module() object.

    -

    Author

    +

    Author +

    Ting Qi (qit3) qit3@gene.com

    houx14 houx14@gene.com

    -

    Examples

    +

    Examples +

    data <- teal_data() |>
   within({
     ADSL <- rADSL
@@ -233,17 +293,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/ui_g_decorate.html b/main/reference/ui_g_decorate.html index 23a5266f..5d06afab 100644 --- a/main/reference/ui_g_decorate.html +++ b/main/reference/ui_g_decorate.html @@ -1,7 +1,23 @@ - -Helper UI function to decorate plot output UI — ui_g_decorate • teal.osprey + + + + + + +Helper UI function to decorate plot output UI — ui_g_decorate • teal.osprey + + + + + + + + + + + Skip to contents @@ -17,18 +33,34 @@ + + @@ -47,7 +79,8 @@

    Helper UI function to decorate plot output UI

    -

    Usage

    +

    Usage +

    ui_g_decorate(
   id,
   titles = "Titles",
@@ -57,42 +90,51 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (character) id of this module. set to NULL if you want to make it identical to the module who called it.

    -
    titles
    +
    titles +

    (character) default titles

    -
    footnotes
    +
    footnotes +

    (character) default footnotes

    -
    fontsize
    +
    fontsize +

    (numeric(1) or numeric(3))
    Defines initial possible range of font-size. fontsize is set for teal.widgets::optionalSliderInputValMinMax() which controls font-size in the output plot.

    -
    + +
    + + - + + - + + diff --git a/main/search.json b/main/search.json index 98f270c8..9b211438 100644 --- a/main/search.json +++ b/main/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nina Qi. Author, maintainer. Dawid Kaledkowski. Author. Chendi Liao. Author. Liming Li. Author. Konrad Pagacz. Author. Molly . Contributor. Carolyn Zhang. Contributor. Tina Cho. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Qi N, Kaledkowski D, Liao C, Li L, Pagacz K (2024). teal.osprey: 'teal' Modules TLG Functions Osprey. R package version 0.1.16.9031, https://github.com/insightsengineering/teal.osprey/, https://insightsengineering.github.io/teal.osprey/.","code":"@Manual{, title = {teal.osprey: 'teal' Modules for TLG Functions in Osprey}, author = {Nina Qi and Dawid Kaledkowski and Chendi Liao and Liming Li and Konrad Pagacz}, year = {2024}, note = {R package version 0.1.16.9031, https://github.com/insightsengineering/teal.osprey/}, url = {https://insightsengineering.github.io/teal.osprey/}, }"},{"path":"https://insightsengineering.github.io/teal.osprey/index.html","id":"tealosprey","dir":"","previous_headings":"","what":"teal Modules for TLG Functions in Osprey","title":"teal Modules for TLG Functions in Osprey","text":"teal.osprey provides community contributed teal modules analysis functions osprey package. enables teal app developers easily create applications making use osprey.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"teal Modules for TLG Functions in Osprey","text":"","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.osprey@*release\") # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.osprey\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Arguments — argument_convention","title":"Standard Arguments — argument_convention","text":"documentation function lists arguments teal modules used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Arguments — argument_convention","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. paramcd (character(1) choices_selected) variable value designating studied parameter. See teal.transform::choices_selected() details. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/argument_convention.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Arguments — argument_convention","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Arguments — argument_convention","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/as_numeric_from_comma_sep_str.html","id":null,"dir":"Reference","previous_headings":"","what":"takes input_string, splits by ","title":"takes input_string, splits by ","text":"takes input_string, splits \",\" returns numeric vector NAs split-strings numeric. e.g. as_numeric_from_comma_separated_string(\"4 ,hello,5,, 3\") c(4, NA, 5, NA, 3). input argument NULL just whitespace NULL returned","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/as_numeric_from_comma_sep_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"takes input_string, splits by ","text":"","code":"as_numeric_from_comma_sep_str(input_string)"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/as_numeric_from_comma_sep_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"takes input_string, splits by ","text":"input_string string split numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/reference/label_aevar.html","id":null,"dir":"Reference","previous_headings":"","what":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"Automatically switch variable labels standard AE variables AE osprey functions","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/label_aevar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"","code":"label_aevar(x)"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/label_aevar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"x variable key","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/name_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"retrieve name of ci method — name_ci","title":"retrieve name of ci method — name_ci","text":"retrieve name ci method retrieve detailed name ci method","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/name_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"retrieve name of ci method — name_ci","text":"","code":"name_ci(x = ci_choices) name_ci(x = ci_choices)"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/name_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"retrieve name of ci method — name_ci","text":"x ci method retrieve name","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/reference/plot_decorate_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to plot decorated output UI — plot_decorate_output","text":"","code":"plot_decorate_output(id)"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/plot_decorate_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to plot decorated output UI — plot_decorate_output","text":"id (character) id element","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/quick_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function for quick filter — quick_filter","title":"Utility function for quick filter — quick_filter","text":"Utility function quick filter","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/quick_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function for quick filter — quick_filter","text":"","code":"quick_filter(filter_opt, ANL)"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/quick_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function for quick filter — quick_filter","text":"filter_opt vector string names flag variable filter (keep Y rows ) ANL input dataset","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/quick_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function for quick filter — quick_filter","text":"filtered dataframe","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/quick_filter.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Utility function for quick filter — quick_filter","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/shared_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Shared Parameters — shared_params","title":"Shared Parameters — shared_params","text":"Contains arguments shared multiple functions package avoid repetition using inheritParams.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/shared_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shared Parameters — shared_params","text":"plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. label (character) module label teal app. Please note module developed based ADaM data structure ADaM variables.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/srv_g_decorate.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper server function to decorate plot output — srv_g_decorate","title":"Helper server function to decorate plot output — srv_g_decorate","text":"used tm_g_ae_oview() tm_g_events_term_id().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/srv_g_decorate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper server function to decorate plot output — srv_g_decorate","text":"","code":"srv_g_decorate( id, plot_id = \"out\", plt = reactive(NULL), plot_height, plot_width )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/srv_g_decorate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper server function to decorate plot output — srv_g_decorate","text":"id (character) id module plot_id (character) id plot output plt (reactive) reactive object graph object plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/teal.osprey-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","title":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","text":"teal.osprey provides community contributed teal modules analysis functions osprey package. See package website. enables teal app developers easily create applications making use osprey analysis functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/reference/teal.osprey-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","text":"Maintainer: Nina Qi qit3@gene.com Authors: Dawid Kaledkowski dawid.kaledkowski@roche.com Chendi Liao chendi.liao@roche.com Liming Li liming.li@roche.com Konrad Pagacz contributors: Molly [contributor] Carolyn Zhang [contributor] Tina Cho [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_oview.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal module for the AE overview — tm_g_ae_oview","title":"Teal module for the AE overview — tm_g_ae_oview","text":"Display AE overview plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_oview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal module for the AE overview — tm_g_ae_oview","text":"","code":"tm_g_ae_oview( label, dataname, arm_var, flag_var_anl, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_oview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal module for the AE overview — tm_g_ae_oview","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. flag_var_anl (teal.transform::choices_selected) choices_selected object variables used count adverse event sub-groups (e.g. Serious events, Related events, etc.) fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_oview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal module for the AE overview — tm_g_ae_oview","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_oview.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal module for the AE overview — tm_g_ae_oview","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE .add_event_flags <- function(dat) { dat <- dat |> mutate( TMPFL_SER = AESER == \"Y\", TMPFL_REL = AEREL == \"Y\", TMPFL_GR5 = AETOXGR == \"5\", AEREL1 = (AEREL == \"Y\" & ACTARM == \"A: Drug X\"), AEREL2 = (AEREL == \"Y\" & ACTARM == \"B: Placebo\") ) labels <- c( \"Serious AE\", \"Related AE\", \"Grade 5 AE\", \"AE related to A: Drug X\", \"AE related to B: Placebo\" ) cols <- c(\"TMPFL_SER\", \"TMPFL_REL\", \"TMPFL_GR5\", \"AEREL1\", \"AEREL2\") for (i in seq_along(labels)) { attr(dat[[cols[i]]], \"label\") <- labels[i] } dat } ADAE <- .add_event_flags(ADAE) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADAE <- data[[\"ADAE\"]] app <- init( data = data, modules = modules( tm_g_ae_oview( label = \"AE Overview\", dataname = \"ADAE\", arm_var = choices_selected( selected = \"ACTARM\", choices = c(\"ACTARM\", \"ACTARMCD\") ), flag_var_anl = choices_selected( selected = \"AEREL1\", choices = variable_choices( ADAE, c(\"TMPFL_SER\", \"TMPFL_REL\", \"TMPFL_GR5\", \"AEREL1\", \"AEREL2\") ), ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_ae_oview #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":null,"dir":"Reference","previous_headings":"","what":"teal module for the AE by subgroups — tm_g_ae_sub","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"Display AE subgroups plot teal module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"","code":"tm_g_ae_sub( label, dataname, arm_var, group_var, plot_height = c(600L, 200L, 2000L), plot_width = NULL, fontsize = c(5, 3, 7) )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. group_var (choices_selected) subgroups variables. See teal.transform::choices_selected() details. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"Liming Li (Lil128) liming.li@roche.com Molly (hey59) hey59@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_ae_sub.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_ae_sub( label = \"AE by Subgroup\", dataname = \"ADAE\", arm_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"ACTARM\", \"ACTARMCD\") ), group_var = choices_selected( selected = c(\"SEX\", \"REGION1\", \"RACE\"), choices = c(\"SEX\", \"REGION1\", \"RACE\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_ae_sub #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":null,"dir":"Reference","previous_headings":"","what":"Butterfly plot Teal Module — tm_g_butterfly","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"Display butterfly plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"","code":"tm_g_butterfly( label, dataname, filter_var = NULL, right_var, left_var, category_var, color_by_var, count_by_var, facet_var = NULL, sort_by_var = teal.transform::choices_selected(selected = \"count\", choices = c(\"count\", \"alphabetical\")), legend_on = TRUE, plot_height = c(600L, 200L, 2000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). filter_var (choices_selected) variable name data filter, please see details regarding expected values, default isNULL.choices vector filter_var choices, default NULL right_var (choices_selected) dichotomization variable right side left_var (choices_selected) dichotomization variable left side category_var (choices_selected) category (y axis) variable color_by_var (choices_selected) variable defines color blocks within bar count_by_var (choices_selected) variable defines x axis calculated facet_var (choices_selected) variable row facets sort_by_var (choices_selected) argument order class term elements table, default \"count\" legend_on (boolean) value whether legend displayed plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/reference/tm_g_butterfly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"filter_var option designed work conjunction filtering function provided teal (encoding panel right hand side shiny app). can used quick access predefined subsets domain datasets (subject-level dataset) used analysis, denoted value \"Y\". variable within filter_var_choices expected contain values either \"Y\" \"N\". multiple variables selected filter_var, observations \"Y\" value every selected variables used subsequent analysis. Flag variables (ADaM datasets) can used directly filter.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu Chendi Liao (liaoc10) chendi.liao@roche.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_butterfly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ library(dplyr) set.seed(23) ADSL <- rADSL ADAE <- rADAE ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), \"UG\")) ADAE <- mutate( ADAE, flag1 = ifelse(AETOXGR == 1, 1, 0), flag2 = ifelse(AETOXGR == 2, 1, 0), flag3 = ifelse(AETOXGR == 3, 1, 0), flag1_filt = rep(\"Y\", n()) ) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_butterfly( label = \"Butterfly Plot\", dataname = \"ADAE\", right_var = choices_selected( selected = \"SEX\", choices = c(\"SEX\", \"ARM\", \"RACE\") ), left_var = choices_selected( selected = \"RACE\", choices = c(\"SEX\", \"ARM\", \"RACE\") ), category_var = choices_selected( selected = \"AEBODSYS\", choices = c(\"AEDECOD\", \"AEBODSYS\") ), color_by_var = choices_selected( selected = \"AETOXGR\", choices = c(\"AETOXGR\", \"None\") ), count_by_var = choices_selected( selected = \"# of patients\", choices = c(\"# of patients\", \"# of AEs\") ), facet_var = choices_selected( selected = NULL, choices = c(\"RACE\", \"SEX\", \"ARM\") ), sort_by_var = choices_selected( selected = \"count\", choices = c(\"count\", \"alphabetical\") ), legend_on = TRUE, plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_butterfly #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Events by Term Plot Teal Module — tm_g_events_term_id","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"Display Events Term plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"","code":"tm_g_events_term_id( label, dataname, term_var, arm_var, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). term_var teal.transform::choices_selected object available choices pre-selected option names can used specify term events arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"Liming Li (lil128) liming.li@roche.com Molly (hey59) hey59@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_events_term_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_events_term_id( label = \"Common AE\", dataname = \"ADAE\", term_var = choices_selected( selected = \"AEDECOD\", choices = c( \"AEDECOD\", \"AETERM\", \"AEHLT\", \"AELLT\", \"AEBODSYS\" ) ), arm_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"ACTARM\", \"ACTARMCD\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_events_term_id #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_heat_bygrade.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal module for the heatmap by grade — tm_g_heat_bygrade","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"Display heatmap grade shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_heat_bygrade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"","code":"tm_g_heat_bygrade( label, sl_dataname, ex_dataname, ae_dataname, cm_dataname = NA, id_var, visit_var, ongo_var, anno_var, heat_var, conmed_var = NULL, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_heat_bygrade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"label (character(1)) menu item label module teal app. sl_dataname (character) subject level dataset name, needs available list passed data argument teal::init() ex_dataname (character) exposures dataset name, needs available list passed data argument teal::init() ae_dataname (character) adverse events dataset name, needs available list passed data argument teal::init() cm_dataname (character) concomitant medications dataset name, needs available list passed data argument teal::init() specify NA concomitant medications data available id_var (choices_seleced) unique subject ID variable visit_var (choices_seleced) analysis visit variable ongo_var (choices_seleced) study ongoing status variable. variable derived logical variable. Usually can derived EOSSTT. anno_var (choices_seleced) annotation variable heat_var (choices_seleced) heatmap variable conmed_var (choices_seleced) concomitant medications variable, specify NA concomitant medications data available fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_heat_bygrade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_heat_bygrade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"","code":"data <- teal_data() |> within({ library(dplyr) ADSL <- rADSL %>% slice(1:30) ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID) ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID) ADCM <- rADCM %>% filter(USUBJID %in% ADSL$USUBJID) # This preprocess is only to force legacy standard on ADCM ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique() # function to derive AVISIT from ADEX .add_visit <- function(data_need_visit) { visit_dates <- ADEX %>% filter(PARAMCD == \"DOSE\") %>% distinct(USUBJID, AVISIT, ASTDTM) %>% group_by(USUBJID) %>% arrange(ASTDTM) %>% mutate(next_vis = lead(ASTDTM), is_last = ifelse(is.na(next_vis), TRUE, FALSE)) %>% rename(this_vis = ASTDTM) data_visit <- data_need_visit %>% select(USUBJID, ASTDTM) %>% left_join(visit_dates, by = \"USUBJID\") %>% filter(ASTDTM > this_vis & (ASTDTM < next_vis | is_last == TRUE)) %>% left_join(data_need_visit) %>% distinct() return(data_visit) } # derive AVISIT for ADAE and ADCM ADAE <- .add_visit(ADAE) ADCM <- .add_visit(ADCM) # derive ongoing status variable for ADEX ADEX <- ADEX %>% filter(PARCAT1 == \"INDIVIDUAL\") %>% mutate(ongo_status = (EOSSTT == \"ONGOING\")) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADCM <- data[[\"ADCM\"]] app <- init( data = data, modules = modules( tm_g_heat_bygrade( label = \"Heatmap by grade\", sl_dataname = \"ADSL\", ex_dataname = \"ADEX\", ae_dataname = \"ADAE\", cm_dataname = \"ADCM\", id_var = choices_selected( selected = \"USUBJID\", choices = c(\"USUBJID\", \"SUBJID\") ), visit_var = choices_selected( selected = \"AVISIT\", choices = c(\"AVISIT\") ), ongo_var = choices_selected( selected = \"ongo_status\", choices = c(\"ongo_status\") ), anno_var = choices_selected( selected = c(\"SEX\", \"COUNTRY\"), choices = c(\"SEX\", \"COUNTRY\", \"USUBJID\") ), heat_var = choices_selected( selected = \"AETOXGR\", choices = c(\"AETOXGR\") ), conmed_var = choices_selected( selected = \"CMDECOD\", choices = c(\"CMDECOD\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_heat_bygrade #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":null,"dir":"Reference","previous_headings":"","what":"Patient Profile plot teal module — tm_g_patient_profile","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"Display patient profile plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"","code":"tm_g_patient_profile( label = \"Patient Profile Plot\", patient_id, sl_dataname, ex_dataname = NA, ae_dataname = NA, rs_dataname = NA, cm_dataname = NA, lb_dataname = NA, sl_start_date, ex_var = NULL, ae_var = NULL, ae_line_col_var = NULL, ae_line_col_opt = NULL, rs_var = NULL, cm_var = NULL, lb_var = NULL, x_limit = \"-28, 365\", plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"label (character(1)) menu item label module teal app. patient_id (choices_seleced) unique subject ID variable sl_dataname (character) subject level dataset name, needs available list passed data argument teal::init() ex_dataname, ae_dataname, rs_dataname, cm_dataname, lb_dataname (character(1)) names exposure, adverse events, response, concomitant medications, labs datasets, respectively; must available list passed data argument teal::init() set NA (default) omit analysis sl_start_date choices_selected study start date variable, usually set treatment start date randomization date ex_var choices_selected exposure variable plot line leave unspecified set NULL exposure data available ae_var choices_selected adverse event variable plot line leave unspecified set NULL adverse events data available ae_line_col_var choices_selected variable coloring AE lines leave unspecified set NULL adverse events data available ae_line_col_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values ae_line_col_var values. leave unspecified set NULL adverse events data available rs_var choices_selected response variable plot line leave unspecified set NULL response data available cm_var choices_selected concomitant medication variable plot line leave unspecified set NULL concomitant medications data available lb_var choices_selected lab variable plot line leave unspecified set NULL labs data available x_limit single character string two numbers separated comma indicating x-axis limit, default \"-28, 365\" plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/reference/tm_g_patient_profile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"patient profile module plots different domains one plot, study day (x-axis) derived consistency based start date user's choice app (example, ADSL.RANDDT ADSL.TRTSDT): ADAE, ADEX, ADCM, study day based ASTDT /AENDT reference start date ADRS ADLB, study day based ADT reference start date","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"Xuefeng Hou (houx14) houx14@gene.com Tina Cho (chot) tina.cho@roche.com Molly (hey59) hey59@gene.com Ting Qi (qit3) qit3@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_patient_profile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADCM <- rADCM %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) # The step below is to pre-process ADCM to legacy standard ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique() ADRS <- rADRS %>% mutate(ADT = as.Date(ADTM)) ADEX <- rADEX %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADLB <- rADLB %>% mutate(ADT = as.Date(ADTM), LBSTRESN = as.numeric(LBSTRESC)) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADSL <- data[[\"ADSL\"]] app <- init( data = data, modules = modules( tm_g_patient_profile( label = \"Patient Profile Plot\", patient_id = choices_selected( choices = unique(ADSL$USUBJID), selected = unique(ADSL$USUBJID)[1] ), sl_dataname = \"ADSL\", ex_dataname = \"ADEX\", ae_dataname = \"ADAE\", rs_dataname = \"ADRS\", cm_dataname = \"ADCM\", lb_dataname = \"ADLB\", sl_start_date = choices_selected( selected = \"TRTSDTM\", choices = c(\"TRTSDTM\", \"RANDDT\") ), ex_var = choices_selected( selected = \"PARCAT2\", choices = \"PARCAT2\" ), ae_var = choices_selected( selected = \"AEDECOD\", choices = c(\"AEDECOD\", \"AESOC\") ), ae_line_col_var = choices_selected( selected = \"AESER\", choices = c(\"AESER\", \"AEREL\") ), ae_line_col_opt = c(\"Y\" = \"red\", \"N\" = \"blue\"), rs_var = choices_selected( selected = \"PARAMCD\", choices = \"PARAMCD\" ), cm_var = choices_selected( selected = \"CMDECOD\", choices = c(\"CMDECOD\", \"CMCAT\") ), lb_var = choices_selected( selected = \"LBTESTCD\", choices = c(\"LBTESTCD\", \"LBCAT\") ), x_limit = \"-28, 750\", plot_height = c(1200, 400, 5000) ) ) ) #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_spiderplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Spider plot Teal Module — tm_g_spiderplot","title":"Spider plot Teal Module — tm_g_spiderplot","text":"Display spider plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_spiderplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spider plot Teal Module — tm_g_spiderplot","text":"","code":"tm_g_spiderplot( label, dataname, paramcd, x_var, y_var, marker_var, line_colorby_var, xfacet_var = NULL, yfacet_var = NULL, vref_line = NULL, href_line = NULL, anno_txt_var = TRUE, legend_on = FALSE, plot_height = c(600L, 200L, 2000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_spiderplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spider plot Teal Module — tm_g_spiderplot","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). paramcd (character(1) choices_selected) variable value designating studied parameter. See teal.transform::choices_selected() details. x_var x-axis variables y_var y-axis variables marker_var variable dictates marker symbol line_colorby_var variable dictates line color xfacet_var variable x facets yfacet_var variable y facets vref_line vertical reference lines href_line horizontal reference lines anno_txt_var annotation text legend_on boolean value whether legend displayed plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/reference/tm_g_spiderplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spider plot Teal Module — tm_g_spiderplot","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_spiderplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spider plot Teal Module — tm_g_spiderplot","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu Chendi Liao (liaoc10) chendi.liao@roche.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_spiderplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spider plot Teal Module — tm_g_spiderplot","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ ADSL <- rADSL ADTR <- rADTR }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_spiderplot( label = \"Spider plot\", dataname = \"ADTR\", paramcd = choices_selected( choices = \"SLDINV\", selected = \"SLDINV\" ), x_var = choices_selected( choices = \"ADY\", selected = \"ADY\" ), y_var = choices_selected( choices = c(\"PCHG\", \"CHG\", \"AVAL\"), selected = \"PCHG\" ), marker_var = choices_selected( choices = c(\"SEX\", \"RACE\", \"USUBJID\"), selected = \"SEX\" ), line_colorby_var = choices_selected( choices = c(\"SEX\", \"USUBJID\", \"RACE\"), selected = \"SEX\" ), xfacet_var = choices_selected( choices = c(\"SEX\", \"ARM\"), selected = \"SEX\" ), yfacet_var = choices_selected( choices = c(\"SEX\", \"ARM\"), selected = \"ARM\" ), vref_line = \"10, 37\", href_line = \"-20, 0\" ) ) ) #> Initializing tm_g_spiderplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Swimlane Plot — tm_g_swimlane","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"teal module generates swimlane plot (bar plot markers) ADaM data","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"","code":"tm_g_swimlane( label, dataname, bar_var, bar_color_var = NULL, sort_var = NULL, marker_pos_var = NULL, marker_shape_var = NULL, marker_shape_opt = NULL, marker_color_var = NULL, marker_color_opt = NULL, anno_txt_var = NULL, vref_line = NULL, plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL, x_label = \"Time from First Treatment (Day)\" )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"label (character(1)) menu item label module teal app. dataname analysis data used plotting, needs available list passed data argument teal::init(). markers plotted module, \"ADSL\" input. markers plotted, data name marker data input bar_var teal.transform::choices_selected subject-level numeric variable dataset plot bar length bar_color_var teal.transform::choices_selected color variable (subject-level) sort_var choices_selected sort variable (subject-level) marker_pos_var teal.transform::choices_selected variable marker position marker data (Note: make sure marker position relative start day bar length variable bar_var marker_shape_var teal.transform::choices_selected marker shape variable marker data marker_shape_opt aesthetic values map shape values (named vector map shape values name). NULL, please make sure contains possible values marker_shape_var values, otherwise shape assigned ggplot default marker_color_var marker color variable marker data marker_color_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values marker_color_var values, otherwise color assigned ggplot default anno_txt_var character vector subject-level variable names selected annotation vref_line vertical reference lines plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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. x_label label x axis","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"Ting Qi (qit3) qit3@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_swimlane.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ library(dplyr) ADSL <- rADSL %>% mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>% filter(STRATA1 == \"A\" & ARMCD == \"ARM A\") ADRS <- rADRS %>% filter(PARAMCD == \"LSTASDI\" & DCSREAS == \"Death\") %>% mutate(AVALC = DCSREAS, ADY = EOSDY) %>% rbind(rADRS %>% filter(PARAMCD == \"OVRINV\" & AVALC != \"NE\")) %>% arrange(USUBJID) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADSL <- data[[\"ADSL\"]] ADRS <- data[[\"ADRS\"]] app <- init( data = data, modules = modules( tm_g_swimlane( label = \"Swimlane Plot\", dataname = \"ADRS\", bar_var = choices_selected( selected = \"TRTDURD\", choices = c(\"TRTDURD\", \"EOSDY\") ), bar_color_var = choices_selected( selected = \"EOSSTT\", choices = c(\"EOSSTT\", \"ARM\", \"ARMCD\", \"ACTARM\", \"ACTARMCD\", \"SEX\") ), sort_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"USUBJID\", \"SITEID\", \"ACTARMCD\", \"TRTDURD\") ), marker_pos_var = choices_selected( selected = \"ADY\", choices = c(\"ADY\") ), marker_shape_var = choices_selected( selected = \"AVALC\", c(\"AVALC\", \"AVISIT\") ), marker_shape_opt = c(\"CR\" = 16, \"PR\" = 17, \"SD\" = 18, \"PD\" = 15, \"Death\" = 8), marker_color_var = choices_selected( selected = \"AVALC\", choices = c(\"AVALC\", \"AVISIT\") ), marker_color_opt = c( \"CR\" = \"green\", \"PR\" = \"blue\", \"SD\" = \"goldenrod\", \"PD\" = \"red\", \"Death\" = \"black\" ), vref_line = c(30, 60), anno_txt_var = choices_selected( selected = c(\"ACTARM\", \"SEX\"), choices = c( \"ARM\", \"ARMCD\", \"ACTARM\", \"ACTARMCD\", \"AGEGR1\", \"SEX\", \"RACE\", \"COUNTRY\", \"DCSREAS\", \"DCSREASP\" ) ) ) ) ) #> Initializing tm_g_swimlane #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Waterfall Plot — tm_g_waterfall","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"teal module generates waterfall plot ADaM data","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"","code":"tm_g_waterfall( label, dataname_tr = \"ADTR\", dataname_rs = \"ADRS\", bar_paramcd, bar_var, bar_color_var, bar_color_opt = NULL, sort_var, add_label_var_sl, add_label_paramcd_rs, anno_txt_var_sl, anno_txt_paramcd_rs, facet_var, ytick_at = 20, href_line = NULL, gap_point_val = NULL, show_value = TRUE, plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"label (character(1)) menu item label module teal app. dataname_tr tumor burden analysis data used teal module plot bar height, needs available list passed data argument teal::init() dataname_rs response analysis data used teal module label response parameters, needs available list passed data argument teal::init() bar_paramcd choices_selected parameter tumor burden data plotted bar height bar_var choices_selected numeric variable dataset plot bar height, e.g., PCHG bar_color_var choices_selected color variable (subject level), None corresponds NULL bar_color_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values bar_color_var values, otherwise color assigned ggplot default, please note NULL needs specified case sort_var choices_selected sort variable (subject level), None corresponds NULL add_label_var_sl choices_selected add label bars (subject level), None corresponds NULL add_label_paramcd_rs choices_selected add label bars (response dataset), None corresponds NULL. least one add_label_var_sl add_label_paramcd_rs needs NULL anno_txt_var_sl choices_selected subject level variables displayed annotation table, default NULL anno_txt_paramcd_rs choices_selected analysis dataset variables displayed annotation table, default NULL facet_var choices_selected facet variable (subject level), None corresponds NULL ytick_at bar height axis interval, default 20 href_line numeric vector plot horizontal reference lines, default NULL gap_point_val singular numeric value adding bar break bars significantly higher others, default NULL show_value boolean whether value bar height shown, default TRUE plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/reference/tm_g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_waterfall.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"Ting Qi (qit3) qit3@gene.com houx14 houx14@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/tm_g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADRS <- rADRS ADTR <- rADTR ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX)) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_waterfall( label = \"Waterfall\", dataname_tr = \"ADTR\", dataname_rs = \"ADRS\", bar_paramcd = choices_selected(c(\"SLDINV\"), \"SLDINV\"), bar_var = choices_selected(c(\"PCHG\", \"AVAL\"), \"PCHG\"), bar_color_var = choices_selected(c(\"ARMCD\", \"SEX\"), \"ARMCD\"), bar_color_opt = NULL, sort_var = choices_selected(c(\"ARMCD\", \"SEX\"), NULL), add_label_var_sl = choices_selected(c(\"SEX\", \"EOSDY\"), NULL), add_label_paramcd_rs = choices_selected(c(\"BESRSPI\", \"OBJRSPI\"), NULL), anno_txt_var_sl = choices_selected(c(\"SEX\", \"ARMCD\", \"BMK1\", \"BMK2\"), NULL), anno_txt_paramcd_rs = choices_selected(c(\"BESRSPI\", \"OBJRSPI\"), NULL), facet_var = choices_selected(c(\"SEX\", \"ARMCD\", \"STRATA1\", \"STRATA2\"), NULL), href_line = \"-30, 20\" ) ) ) #> Initializing tm_g_waterfall #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/ui_g_decorate.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper UI function to decorate plot output UI — ui_g_decorate","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"used tm_g_ae_oview() tm_g_events_term_id().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/reference/ui_g_decorate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"","code":"ui_g_decorate( id, titles = \"Titles\", footnotes = \"footnotes\", fontsize = c(5, 4, 11) )"},{"path":"https://insightsengineering.github.io/teal.osprey/reference/ui_g_decorate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"id (character) id module. set NULL want make identical module called . titles (character) default titles footnotes (character) default footnotes fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-01169031","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.16.9031","title":"teal.osprey 0.1.16.9031","text":"Removed Show Warnings modals modules. Moved teal.data Suggests Imports. Changed examples cdisc_data() teal_data().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"breaking-changes-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.osprey 0.1.16.9031","text":"Adapted modules use teal_data objects.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.16.9031","text":"Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.16.9031","text":"Specified minimal version package dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-0116","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.16","title":"teal.osprey 0.1.16","text":"Removed scda package dependency examples. Fixed crash tm_g_heat_bygrade plotting Conmed. Added validation tm_g_spiderplot.R checks duplicates X Y facet variables. Improved input validation used teal::validate_inputs mechanism send validation messages output panel. Removed purrr dependencies. Added argument checks tm_g_patient_profile. Modified example apps use new teal_data join_keys solutions.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"breaking-changes-0-1-16","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.16","text":"Replaced chunks simpler qenv class. tm_xyz_srv modules datasets argument containing FilteredData replaced new argument data (tdata object) filter_panel_api (FilterPanelAPI). Updated arm_var point factor column ANL. can’t character column anymore. Removed redundant formal arguments tm_g_patient_profile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"breaking-changes-0-1-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.15","text":"Soft deprecate function label_aevar().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.15","text":"Added teal.reporter modules. Updated shiny::validate calls shinyvalidate better UI overview. Implemented nestcolor slight refactoring tm_g_swimlane. Added nestcolor examples.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.15","text":"Added names id parameter teal.code::chunks_push modules. Updated modules use datasets names suffix _FILTERED package works breaking changes teal.slice.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.14","text":"Removed unneeded chunk evaluations tm_g_patient_profile module.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.14","text":"Added template pkgdown site. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-13","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.13","text":"Added basic logging modules. label select input widget choose paramcd longer hard coded ADTR tm_g_spiderplot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.13","text":"Rewrote module 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. Functions imported packages now fully specified.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"breaking-changes-0-1-12","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.12","text":"Refactored tm_g_ae_oview remove flag variables generated module default replace parameter add_flag flag_var_anl.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-12","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.12","text":"Added new parameter x_label allowing change label x axis tm_g_swimlane module plot. Updated tm_g_ae_sub longer displays label inputs group variables values selected.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"bug-fixes-0-1-12","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.12","text":"Fixed bug tm_g_waterfall Tumor Burden Parameter UI element now respected.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.12","text":"Updated R version requirement R >= 3.6. Removed function teal::keys examples tm_g_spiderplot tm_g_waterfall modules. Removed dependency test.nest package. Removed dependency utils.nest package replaced functions equivalents checkmate package.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-0111","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.11","title":"teal.osprey 0.1.11","text":"Updated LICENCE README new package references. Updated document tests scda synthetic data replace random.cdisc.data. Added error_on_lint: TRUE .lintr. Removed unnecessary importFrom statements. Updated tm_g_patient_profile module’s study days range accept infinite values. Fixed disappearing plots webpage zoom /.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.10","text":"Added Shiny feature tm_g_swimlane prevent needless re-render output user completely provided inputs vertical lines widget.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.10","text":"Altered Choose 2: inputs widget Encoding Panel independent Filtering Panel tm_g_butterfly. Updated warning message Tumor Burden Parameter selected tm_g_waterfall.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"bug-fixes-0-1-10","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.10","text":"Fixed bug tm_g_butterfly displays filtering faceting widgets despite provided arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"new-features-0-1-9","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.osprey 0.1.9","text":"Added new teal module tm_g_heat_bygrade heatmap grade plot. Added new teal module tm_g_ae_sub AE subgroups plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"bug-fixes-0-1-9","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.9","text":"Fixed misleading validate message tm_g_ae_oview either Control Treatment variable filtered . Added validate statement output better error message left right dichotomization values filtered data.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-9","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.9","text":"Improved reactivity dependencies across modules.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-018","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.8","title":"teal.osprey 0.1.8","text":"Added validation message dataset contain subjects control treatment arms tm_g_events_term_id. Improved validation message subject filtered dataset used tm_g_patient_profile. Fixed modules due changes plot_with_settings latest teal.devel release. Updated study day duration derivation tm_g_patient_profile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.7","text":"Added additional validation horizontal vertical reference lines tm_g_spider_plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"bug-fixes-0-1-7","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.osprey 0.1.7","text":"Fixed tm_g_patient_profile adverse event line color variable selected. Fixed issue unknown date format established minimum number observation threshold tm_g_patient_profile.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"miscellaneous-0-1-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.7","text":"Teal module AE overview summary table - can replaced teal.modules.clinical::tm_t_events_summary. Teal module AE summary table preferred terms - can replaced teal.modules.clinical::tm_t_events. Teal module AE summary table highest NCI-CTCAE grade - can replaced teal.modules.clinical::tm_t_events_by_grade. Teal module Disposition table - can replaced teal.modules.clinical::tm_t_summary. Moved code argument cdisc_dataset (cdisc_data) examples.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-016","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.6","title":"teal.osprey 0.1.6","text":"graph modules now accept plot_width argument specifies plot width renders slider adjust width interactively module. Replaced plot_with_height plot_with_settings module throughout package. Show R Code now produces code generating datasets needed current module, datasets included data argument teal::init. Evaluate chunks chunks_safe_eval rather chunks_eval.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-015","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.5","title":"teal.osprey 0.1.5","text":"Added new teal modules: Teal module events term summary plot. Teal module AE overview summary plot. Teal module patient profile plot","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-014","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.4","title":"teal.osprey 0.1.4","text":"Minor changes tests.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-013","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.3","title":"teal.osprey 0.1.3","text":"Technical release updated dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-012","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.2","title":"teal.osprey 0.1.2","text":"New waterfall module. Refactored due recent changes utils.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-011","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.1","title":"teal.osprey 0.1.1","text":"Included test.nest tests. Fixed outdated modules according current teal functionality. Fixed documentation examples example_app.R. Simplified dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/news/index.html","id":"tealosprey-010","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.0","title":"teal.osprey 0.1.0","text":"Teal module AE overview summary table. Teal module AE summary table preferred terms. Teal module AE summary table highest NCI-CTCAE grade. Teal module Disposition table. Teal module AE butterfly plot. Teal module Swimlane plot. Teal module Spider plot.","code":""}] +[{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nina Qi. Author, maintainer. Dawid Kaledkowski. Author. Chendi Liao. Author. Liming Li. Author. Konrad Pagacz. Author. Molly . Contributor. Carolyn Zhang. Contributor. Tina Cho. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Qi N, Kaledkowski D, Liao C, Li L, Pagacz K (2024). teal.osprey: 'teal' Modules TLG Functions Osprey. R package version 0.1.16.9031, https://github.com/insightsengineering/teal.osprey/, https://insightsengineering.github.io/teal.osprey/main/.","code":"@Manual{, title = {teal.osprey: 'teal' Modules for TLG Functions in Osprey}, author = {Nina Qi and Dawid Kaledkowski and Chendi Liao and Liming Li and Konrad Pagacz}, year = {2024}, note = {R package version 0.1.16.9031, https://github.com/insightsengineering/teal.osprey/}, url = {https://insightsengineering.github.io/teal.osprey/main/}, }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/index.html","id":"tealosprey","dir":"","previous_headings":"","what":"teal Modules for TLG Functions in Osprey","title":"teal Modules for TLG Functions in Osprey","text":"teal.osprey provides community contributed teal modules analysis functions osprey package. enables teal app developers easily create applications making use osprey.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"teal Modules for TLG Functions in Osprey","text":"","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.osprey@*release\") # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.osprey\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Arguments — argument_convention","title":"Standard Arguments — argument_convention","text":"documentation function lists arguments teal modules used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Arguments — argument_convention","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. paramcd (character(1) choices_selected) variable value designating studied parameter. See teal.transform::choices_selected() details. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/argument_convention.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Arguments — argument_convention","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Arguments — argument_convention","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/as_numeric_from_comma_sep_str.html","id":null,"dir":"Reference","previous_headings":"","what":"takes input_string, splits by ","title":"takes input_string, splits by ","text":"takes input_string, splits \",\" returns numeric vector NAs split-strings numeric. e.g. as_numeric_from_comma_separated_string(\"4 ,hello,5,, 3\") c(4, NA, 5, NA, 3). input argument NULL just whitespace NULL returned","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/as_numeric_from_comma_sep_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"takes input_string, splits by ","text":"","code":"as_numeric_from_comma_sep_str(input_string)"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/as_numeric_from_comma_sep_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"takes input_string, splits by ","text":"input_string string split numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/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.osprey/main/reference/label_aevar.html","id":null,"dir":"Reference","previous_headings":"","what":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"Automatically switch variable labels standard AE variables AE osprey functions","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/label_aevar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"","code":"label_aevar(x)"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/label_aevar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Automatically switch variable labels for standard AE variables in AE osprey functions — label_aevar","text":"x variable key","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/name_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"retrieve name of ci method — name_ci","title":"retrieve name of ci method — name_ci","text":"retrieve name ci method retrieve detailed name ci method","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/name_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"retrieve name of ci method — name_ci","text":"","code":"name_ci(x = ci_choices) name_ci(x = ci_choices)"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/name_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"retrieve name of ci method — name_ci","text":"x ci method retrieve name","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/plot_decorate_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to plot decorated output UI — plot_decorate_output","text":"","code":"plot_decorate_output(id)"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/plot_decorate_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to plot decorated output UI — plot_decorate_output","text":"id (character) id element","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/quick_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function for quick filter — quick_filter","title":"Utility function for quick filter — quick_filter","text":"Utility function quick filter","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/quick_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function for quick filter — quick_filter","text":"","code":"quick_filter(filter_opt, ANL)"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/quick_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function for quick filter — quick_filter","text":"filter_opt vector string names flag variable filter (keep Y rows ) ANL input dataset","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/quick_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function for quick filter — quick_filter","text":"filtered dataframe","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/quick_filter.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Utility function for quick filter — quick_filter","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/shared_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Shared Parameters — shared_params","title":"Shared Parameters — shared_params","text":"Contains arguments shared multiple functions package avoid repetition using inheritParams.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/shared_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shared Parameters — shared_params","text":"plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. label (character) module label teal app. Please note module developed based ADaM data structure ADaM variables.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/srv_g_decorate.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper server function to decorate plot output — srv_g_decorate","title":"Helper server function to decorate plot output — srv_g_decorate","text":"used tm_g_ae_oview() tm_g_events_term_id().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/srv_g_decorate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper server function to decorate plot output — srv_g_decorate","text":"","code":"srv_g_decorate( id, plot_id = \"out\", plt = reactive(NULL), plot_height, plot_width )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/srv_g_decorate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper server function to decorate plot output — srv_g_decorate","text":"id (character) id module plot_id (character) id plot output plt (reactive) reactive object graph object plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/teal.osprey-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","title":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","text":"teal.osprey provides community contributed teal modules analysis functions osprey package. See package website. enables teal app developers easily create applications making use osprey analysis functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/teal.osprey-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.osprey: teal modules for 'osprey' — teal.osprey-package","text":"Maintainer: Nina Qi qit3@gene.com Authors: Dawid Kaledkowski dawid.kaledkowski@roche.com Chendi Liao chendi.liao@roche.com Liming Li liming.li@roche.com Konrad Pagacz contributors: Molly [contributor] Carolyn Zhang [contributor] Tina Cho [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_oview.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal module for the AE overview — tm_g_ae_oview","title":"Teal module for the AE overview — tm_g_ae_oview","text":"Display AE overview plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_oview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal module for the AE overview — tm_g_ae_oview","text":"","code":"tm_g_ae_oview( label, dataname, arm_var, flag_var_anl, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_oview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal module for the AE overview — tm_g_ae_oview","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. flag_var_anl (teal.transform::choices_selected) choices_selected object variables used count adverse event sub-groups (e.g. Serious events, Related events, etc.) fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_oview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal module for the AE overview — tm_g_ae_oview","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_oview.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal module for the AE overview — tm_g_ae_oview","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE .add_event_flags <- function(dat) { dat <- dat |> mutate( TMPFL_SER = AESER == \"Y\", TMPFL_REL = AEREL == \"Y\", TMPFL_GR5 = AETOXGR == \"5\", AEREL1 = (AEREL == \"Y\" & ACTARM == \"A: Drug X\"), AEREL2 = (AEREL == \"Y\" & ACTARM == \"B: Placebo\") ) labels <- c( \"Serious AE\", \"Related AE\", \"Grade 5 AE\", \"AE related to A: Drug X\", \"AE related to B: Placebo\" ) cols <- c(\"TMPFL_SER\", \"TMPFL_REL\", \"TMPFL_GR5\", \"AEREL1\", \"AEREL2\") for (i in seq_along(labels)) { attr(dat[[cols[i]]], \"label\") <- labels[i] } dat } ADAE <- .add_event_flags(ADAE) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADAE <- data[[\"ADAE\"]] app <- init( data = data, modules = modules( tm_g_ae_oview( label = \"AE Overview\", dataname = \"ADAE\", arm_var = choices_selected( selected = \"ACTARM\", choices = c(\"ACTARM\", \"ACTARMCD\") ), flag_var_anl = choices_selected( selected = \"AEREL1\", choices = variable_choices( ADAE, c(\"TMPFL_SER\", \"TMPFL_REL\", \"TMPFL_GR5\", \"AEREL1\", \"AEREL2\") ), ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_ae_oview #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":null,"dir":"Reference","previous_headings":"","what":"teal module for the AE by subgroups — tm_g_ae_sub","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"Display AE subgroups plot teal module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"","code":"tm_g_ae_sub( label, dataname, arm_var, group_var, plot_height = c(600L, 200L, 2000L), plot_width = NULL, fontsize = c(5, 3, 7) )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. group_var (choices_selected) subgroups variables. See teal.transform::choices_selected() details. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"Liming Li (Lil128) liming.li@roche.com Molly (hey59) hey59@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_ae_sub.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal module for the AE by subgroups — tm_g_ae_sub","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_ae_sub( label = \"AE by Subgroup\", dataname = \"ADAE\", arm_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"ACTARM\", \"ACTARMCD\") ), group_var = choices_selected( selected = c(\"SEX\", \"REGION1\", \"RACE\"), choices = c(\"SEX\", \"REGION1\", \"RACE\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_ae_sub #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":null,"dir":"Reference","previous_headings":"","what":"Butterfly plot Teal Module — tm_g_butterfly","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"Display butterfly plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"","code":"tm_g_butterfly( label, dataname, filter_var = NULL, right_var, left_var, category_var, color_by_var, count_by_var, facet_var = NULL, sort_by_var = teal.transform::choices_selected(selected = \"count\", choices = c(\"count\", \"alphabetical\")), legend_on = TRUE, plot_height = c(600L, 200L, 2000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). filter_var (choices_selected) variable name data filter, please see details regarding expected values, default isNULL.choices vector filter_var choices, default NULL right_var (choices_selected) dichotomization variable right side left_var (choices_selected) dichotomization variable left side category_var (choices_selected) category (y axis) variable color_by_var (choices_selected) variable defines color blocks within bar count_by_var (choices_selected) variable defines x axis calculated facet_var (choices_selected) variable row facets sort_by_var (choices_selected) argument order class term elements table, default \"count\" legend_on (boolean) value whether legend displayed plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/main/reference/tm_g_butterfly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"filter_var option designed work conjunction filtering function provided teal (encoding panel right hand side shiny app). can used quick access predefined subsets domain datasets (subject-level dataset) used analysis, denoted value \"Y\". variable within filter_var_choices expected contain values either \"Y\" \"N\". multiple variables selected filter_var, observations \"Y\" value every selected variables used subsequent analysis. Flag variables (ADaM datasets) can used directly filter.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu Chendi Liao (liaoc10) chendi.liao@roche.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_butterfly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Butterfly plot Teal Module — tm_g_butterfly","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ library(dplyr) set.seed(23) ADSL <- rADSL ADAE <- rADAE ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), \"UG\")) ADAE <- mutate( ADAE, flag1 = ifelse(AETOXGR == 1, 1, 0), flag2 = ifelse(AETOXGR == 2, 1, 0), flag3 = ifelse(AETOXGR == 3, 1, 0), flag1_filt = rep(\"Y\", n()) ) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_butterfly( label = \"Butterfly Plot\", dataname = \"ADAE\", right_var = choices_selected( selected = \"SEX\", choices = c(\"SEX\", \"ARM\", \"RACE\") ), left_var = choices_selected( selected = \"RACE\", choices = c(\"SEX\", \"ARM\", \"RACE\") ), category_var = choices_selected( selected = \"AEBODSYS\", choices = c(\"AEDECOD\", \"AEBODSYS\") ), color_by_var = choices_selected( selected = \"AETOXGR\", choices = c(\"AETOXGR\", \"None\") ), count_by_var = choices_selected( selected = \"# of patients\", choices = c(\"# of patients\", \"# of AEs\") ), facet_var = choices_selected( selected = NULL, choices = c(\"RACE\", \"SEX\", \"ARM\") ), sort_by_var = choices_selected( selected = \"count\", choices = c(\"count\", \"alphabetical\") ), legend_on = TRUE, plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_butterfly #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Events by Term Plot Teal Module — tm_g_events_term_id","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"Display Events Term plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"","code":"tm_g_events_term_id( label, dataname, term_var, arm_var, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). term_var teal.transform::choices_selected object available choices pre-selected option names can used specify term events arm_var (choices_selected) object available choices pre-selected option variable names can used arm_var. See teal.transform::choices_selected() details. Column arm_var dataname factor. fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"Liming Li (lil128) liming.li@roche.com Molly (hey59) hey59@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_events_term_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Events by Term Plot Teal Module — tm_g_events_term_id","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_events_term_id( label = \"Common AE\", dataname = \"ADAE\", term_var = choices_selected( selected = \"AEDECOD\", choices = c( \"AEDECOD\", \"AETERM\", \"AEHLT\", \"AELLT\", \"AEBODSYS\" ) ), arm_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"ACTARM\", \"ACTARMCD\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_events_term_id #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_heat_bygrade.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal module for the heatmap by grade — tm_g_heat_bygrade","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"Display heatmap grade shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_heat_bygrade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"","code":"tm_g_heat_bygrade( label, sl_dataname, ex_dataname, ae_dataname, cm_dataname = NA, id_var, visit_var, ongo_var, anno_var, heat_var, conmed_var = NULL, fontsize = c(5, 3, 7), plot_height = c(600L, 200L, 2000L), plot_width = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_heat_bygrade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"label (character(1)) menu item label module teal app. sl_dataname (character) subject level dataset name, needs available list passed data argument teal::init() ex_dataname (character) exposures dataset name, needs available list passed data argument teal::init() ae_dataname (character) adverse events dataset name, needs available list passed data argument teal::init() cm_dataname (character) concomitant medications dataset name, needs available list passed data argument teal::init() specify NA concomitant medications data available id_var (choices_seleced) unique subject ID variable visit_var (choices_seleced) analysis visit variable ongo_var (choices_seleced) study ongoing status variable. variable derived logical variable. Usually can derived EOSSTT. anno_var (choices_seleced) annotation variable heat_var (choices_seleced) heatmap variable conmed_var (choices_seleced) concomitant medications variable, specify NA concomitant medications data available fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot. plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum values.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_heat_bygrade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_heat_bygrade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal module for the heatmap by grade — tm_g_heat_bygrade","text":"","code":"data <- teal_data() |> within({ library(dplyr) ADSL <- rADSL %>% slice(1:30) ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID) ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID) ADCM <- rADCM %>% filter(USUBJID %in% ADSL$USUBJID) # This preprocess is only to force legacy standard on ADCM ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique() # function to derive AVISIT from ADEX .add_visit <- function(data_need_visit) { visit_dates <- ADEX %>% filter(PARAMCD == \"DOSE\") %>% distinct(USUBJID, AVISIT, ASTDTM) %>% group_by(USUBJID) %>% arrange(ASTDTM) %>% mutate(next_vis = lead(ASTDTM), is_last = ifelse(is.na(next_vis), TRUE, FALSE)) %>% rename(this_vis = ASTDTM) data_visit <- data_need_visit %>% select(USUBJID, ASTDTM) %>% left_join(visit_dates, by = \"USUBJID\") %>% filter(ASTDTM > this_vis & (ASTDTM < next_vis | is_last == TRUE)) %>% left_join(data_need_visit) %>% distinct() return(data_visit) } # derive AVISIT for ADAE and ADCM ADAE <- .add_visit(ADAE) ADCM <- .add_visit(ADCM) # derive ongoing status variable for ADEX ADEX <- ADEX %>% filter(PARCAT1 == \"INDIVIDUAL\") %>% mutate(ongo_status = (EOSSTT == \"ONGOING\")) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADCM <- data[[\"ADCM\"]] app <- init( data = data, modules = modules( tm_g_heat_bygrade( label = \"Heatmap by grade\", sl_dataname = \"ADSL\", ex_dataname = \"ADEX\", ae_dataname = \"ADAE\", cm_dataname = \"ADCM\", id_var = choices_selected( selected = \"USUBJID\", choices = c(\"USUBJID\", \"SUBJID\") ), visit_var = choices_selected( selected = \"AVISIT\", choices = c(\"AVISIT\") ), ongo_var = choices_selected( selected = \"ongo_status\", choices = c(\"ongo_status\") ), anno_var = choices_selected( selected = c(\"SEX\", \"COUNTRY\"), choices = c(\"SEX\", \"COUNTRY\", \"USUBJID\") ), heat_var = choices_selected( selected = \"AETOXGR\", choices = c(\"AETOXGR\") ), conmed_var = choices_selected( selected = \"CMDECOD\", choices = c(\"CMDECOD\") ), plot_height = c(600, 200, 2000) ) ) ) #> Initializing tm_g_heat_bygrade #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":null,"dir":"Reference","previous_headings":"","what":"Patient Profile plot teal module — tm_g_patient_profile","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"Display patient profile plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"","code":"tm_g_patient_profile( label = \"Patient Profile Plot\", patient_id, sl_dataname, ex_dataname = NA, ae_dataname = NA, rs_dataname = NA, cm_dataname = NA, lb_dataname = NA, sl_start_date, ex_var = NULL, ae_var = NULL, ae_line_col_var = NULL, ae_line_col_opt = NULL, rs_var = NULL, cm_var = NULL, lb_var = NULL, x_limit = \"-28, 365\", plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"label (character(1)) menu item label module teal app. patient_id (choices_seleced) unique subject ID variable sl_dataname (character) subject level dataset name, needs available list passed data argument teal::init() ex_dataname, ae_dataname, rs_dataname, cm_dataname, lb_dataname (character(1)) names exposure, adverse events, response, concomitant medications, labs datasets, respectively; must available list passed data argument teal::init() set NA (default) omit analysis sl_start_date choices_selected study start date variable, usually set treatment start date randomization date ex_var choices_selected exposure variable plot line leave unspecified set NULL exposure data available ae_var choices_selected adverse event variable plot line leave unspecified set NULL adverse events data available ae_line_col_var choices_selected variable coloring AE lines leave unspecified set NULL adverse events data available ae_line_col_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values ae_line_col_var values. leave unspecified set NULL adverse events data available rs_var choices_selected response variable plot line leave unspecified set NULL response data available cm_var choices_selected concomitant medication variable plot line leave unspecified set NULL concomitant medications data available lb_var choices_selected lab variable plot line leave unspecified set NULL labs data available x_limit single character string two numbers separated comma indicating x-axis limit, default \"-28, 365\" plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/main/reference/tm_g_patient_profile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"patient profile module plots different domains one plot, study day (x-axis) derived consistency based start date user's choice app (example, ADSL.RANDDT ADSL.TRTSDT): ADAE, ADEX, ADCM, study day based ASTDT /AENDT reference start date ADRS ADLB, study day based ADT reference start date","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"Xuefeng Hou (houx14) houx14@gene.com Tina Cho (chot) tina.cho@roche.com Molly (hey59) hey59@gene.com Ting Qi (qit3) qit3@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_patient_profile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Patient Profile plot teal module — tm_g_patient_profile","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADAE <- rADAE %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADCM <- rADCM %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) # The step below is to pre-process ADCM to legacy standard ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique() ADRS <- rADRS %>% mutate(ADT = as.Date(ADTM)) ADEX <- rADEX %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADLB <- rADLB %>% mutate(ADT = as.Date(ADTM), LBSTRESN = as.numeric(LBSTRESC)) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADSL <- data[[\"ADSL\"]] app <- init( data = data, modules = modules( tm_g_patient_profile( label = \"Patient Profile Plot\", patient_id = choices_selected( choices = unique(ADSL$USUBJID), selected = unique(ADSL$USUBJID)[1] ), sl_dataname = \"ADSL\", ex_dataname = \"ADEX\", ae_dataname = \"ADAE\", rs_dataname = \"ADRS\", cm_dataname = \"ADCM\", lb_dataname = \"ADLB\", sl_start_date = choices_selected( selected = \"TRTSDTM\", choices = c(\"TRTSDTM\", \"RANDDT\") ), ex_var = choices_selected( selected = \"PARCAT2\", choices = \"PARCAT2\" ), ae_var = choices_selected( selected = \"AEDECOD\", choices = c(\"AEDECOD\", \"AESOC\") ), ae_line_col_var = choices_selected( selected = \"AESER\", choices = c(\"AESER\", \"AEREL\") ), ae_line_col_opt = c(\"Y\" = \"red\", \"N\" = \"blue\"), rs_var = choices_selected( selected = \"PARAMCD\", choices = \"PARAMCD\" ), cm_var = choices_selected( selected = \"CMDECOD\", choices = c(\"CMDECOD\", \"CMCAT\") ), lb_var = choices_selected( selected = \"LBTESTCD\", choices = c(\"LBTESTCD\", \"LBCAT\") ), x_limit = \"-28, 750\", plot_height = c(1200, 400, 5000) ) ) ) #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_spiderplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Spider plot Teal Module — tm_g_spiderplot","title":"Spider plot Teal Module — tm_g_spiderplot","text":"Display spider plot shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_spiderplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spider plot Teal Module — tm_g_spiderplot","text":"","code":"tm_g_spiderplot( label, dataname, paramcd, x_var, y_var, marker_var, line_colorby_var, xfacet_var = NULL, yfacet_var = NULL, vref_line = NULL, href_line = NULL, anno_txt_var = TRUE, legend_on = FALSE, plot_height = c(600L, 200L, 2000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_spiderplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spider plot Teal Module — tm_g_spiderplot","text":"label (character(1)) menu item label module teal app. dataname (character(1)) analysis data used teal module, needs available list passed data argument teal::init(). paramcd (character(1) choices_selected) variable value designating studied parameter. See teal.transform::choices_selected() details. x_var x-axis variables y_var y-axis variables marker_var variable dictates marker symbol line_colorby_var variable dictates line color xfacet_var variable x facets yfacet_var variable y facets vref_line vertical reference lines href_line horizontal reference lines anno_txt_var annotation text legend_on boolean value whether legend displayed plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/main/reference/tm_g_spiderplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spider plot Teal Module — tm_g_spiderplot","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_spiderplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Spider plot Teal Module — tm_g_spiderplot","text":"Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu Chendi Liao (liaoc10) chendi.liao@roche.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_spiderplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spider plot Teal Module — tm_g_spiderplot","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ ADSL <- rADSL ADTR <- rADTR }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_spiderplot( label = \"Spider plot\", dataname = \"ADTR\", paramcd = choices_selected( choices = \"SLDINV\", selected = \"SLDINV\" ), x_var = choices_selected( choices = \"ADY\", selected = \"ADY\" ), y_var = choices_selected( choices = c(\"PCHG\", \"CHG\", \"AVAL\"), selected = \"PCHG\" ), marker_var = choices_selected( choices = c(\"SEX\", \"RACE\", \"USUBJID\"), selected = \"SEX\" ), line_colorby_var = choices_selected( choices = c(\"SEX\", \"USUBJID\", \"RACE\"), selected = \"SEX\" ), xfacet_var = choices_selected( choices = c(\"SEX\", \"ARM\"), selected = \"SEX\" ), yfacet_var = choices_selected( choices = c(\"SEX\", \"ARM\"), selected = \"ARM\" ), vref_line = \"10, 37\", href_line = \"-20, 0\" ) ) ) #> Initializing tm_g_spiderplot #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Swimlane Plot — tm_g_swimlane","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"teal module generates swimlane plot (bar plot markers) ADaM data","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"","code":"tm_g_swimlane( label, dataname, bar_var, bar_color_var = NULL, sort_var = NULL, marker_pos_var = NULL, marker_shape_var = NULL, marker_shape_opt = NULL, marker_color_var = NULL, marker_color_opt = NULL, anno_txt_var = NULL, vref_line = NULL, plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL, x_label = \"Time from First Treatment (Day)\" )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"label (character(1)) menu item label module teal app. dataname analysis data used plotting, needs available list passed data argument teal::init(). markers plotted module, \"ADSL\" input. markers plotted, data name marker data input bar_var teal.transform::choices_selected subject-level numeric variable dataset plot bar length bar_color_var teal.transform::choices_selected color variable (subject-level) sort_var choices_selected sort variable (subject-level) marker_pos_var teal.transform::choices_selected variable marker position marker data (Note: make sure marker position relative start day bar length variable bar_var marker_shape_var teal.transform::choices_selected marker shape variable marker data marker_shape_opt aesthetic values map shape values (named vector map shape values name). NULL, please make sure contains possible values marker_shape_var values, otherwise shape assigned ggplot default marker_color_var marker color variable marker data marker_color_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values marker_color_var values, otherwise color assigned ggplot default anno_txt_var character vector subject-level variable names selected annotation vref_line vertical reference lines plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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. x_label label x axis","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"Ting Qi (qit3) qit3@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_swimlane.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Swimlane Plot — tm_g_swimlane","text":"","code":"# Example using stream (ADaM) dataset data <- teal_data() |> within({ library(dplyr) ADSL <- rADSL %>% mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>% filter(STRATA1 == \"A\" & ARMCD == \"ARM A\") ADRS <- rADRS %>% filter(PARAMCD == \"LSTASDI\" & DCSREAS == \"Death\") %>% mutate(AVALC = DCSREAS, ADY = EOSDY) %>% rbind(rADRS %>% filter(PARAMCD == \"OVRINV\" & AVALC != \"NE\")) %>% arrange(USUBJID) }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADSL <- data[[\"ADSL\"]] ADRS <- data[[\"ADRS\"]] app <- init( data = data, modules = modules( tm_g_swimlane( label = \"Swimlane Plot\", dataname = \"ADRS\", bar_var = choices_selected( selected = \"TRTDURD\", choices = c(\"TRTDURD\", \"EOSDY\") ), bar_color_var = choices_selected( selected = \"EOSSTT\", choices = c(\"EOSSTT\", \"ARM\", \"ARMCD\", \"ACTARM\", \"ACTARMCD\", \"SEX\") ), sort_var = choices_selected( selected = \"ACTARMCD\", choices = c(\"USUBJID\", \"SITEID\", \"ACTARMCD\", \"TRTDURD\") ), marker_pos_var = choices_selected( selected = \"ADY\", choices = c(\"ADY\") ), marker_shape_var = choices_selected( selected = \"AVALC\", c(\"AVALC\", \"AVISIT\") ), marker_shape_opt = c(\"CR\" = 16, \"PR\" = 17, \"SD\" = 18, \"PD\" = 15, \"Death\" = 8), marker_color_var = choices_selected( selected = \"AVALC\", choices = c(\"AVALC\", \"AVISIT\") ), marker_color_opt = c( \"CR\" = \"green\", \"PR\" = \"blue\", \"SD\" = \"goldenrod\", \"PD\" = \"red\", \"Death\" = \"black\" ), vref_line = c(30, 60), anno_txt_var = choices_selected( selected = c(\"ACTARM\", \"SEX\"), choices = c( \"ARM\", \"ARMCD\", \"ACTARM\", \"ACTARMCD\", \"AGEGR1\", \"SEX\", \"RACE\", \"COUNTRY\", \"DCSREAS\", \"DCSREASP\" ) ) ) ) ) #> Initializing tm_g_swimlane #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Waterfall Plot — tm_g_waterfall","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"teal module generates waterfall plot ADaM data","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"","code":"tm_g_waterfall( label, dataname_tr = \"ADTR\", dataname_rs = \"ADRS\", bar_paramcd, bar_var, bar_color_var, bar_color_opt = NULL, sort_var, add_label_var_sl, add_label_paramcd_rs, anno_txt_var_sl, anno_txt_paramcd_rs, facet_var, ytick_at = 20, href_line = NULL, gap_point_val = NULL, show_value = TRUE, plot_height = c(1200L, 400L, 5000L), plot_width = NULL, pre_output = NULL, post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"label (character(1)) menu item label module teal app. dataname_tr tumor burden analysis data used teal module plot bar height, needs available list passed data argument teal::init() dataname_rs response analysis data used teal module label response parameters, needs available list passed data argument teal::init() bar_paramcd choices_selected parameter tumor burden data plotted bar height bar_var choices_selected numeric variable dataset plot bar height, e.g., PCHG bar_color_var choices_selected color variable (subject level), None corresponds NULL bar_color_opt aesthetic values map color values (named vector map color values name). NULL, please make sure contains possible values bar_color_var values, otherwise color assigned ggplot default, please note NULL needs specified case sort_var choices_selected sort variable (subject level), None corresponds NULL add_label_var_sl choices_selected add label bars (subject level), None corresponds NULL add_label_paramcd_rs choices_selected add label bars (response dataset), None corresponds NULL. least one add_label_var_sl add_label_paramcd_rs needs NULL anno_txt_var_sl choices_selected subject level variables displayed annotation table, default NULL anno_txt_paramcd_rs choices_selected analysis dataset variables displayed annotation table, default NULL facet_var choices_selected facet variable (subject level), None corresponds NULL ytick_at bar height axis interval, default 20 href_line numeric vector plot horizontal reference lines, default NULL gap_point_val singular numeric value adding bar break bars significantly higher others, default NULL show_value boolean whether value bar height shown, default TRUE plot_height (numeric(3)) vector indicate default value, minimum maximum values. plot_width (numeric(3)) vector indicate default value, minimum maximum 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.osprey/main/reference/tm_g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"teal::module() object.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_waterfall.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"Ting Qi (qit3) qit3@gene.com houx14 houx14@gene.com","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/tm_g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Waterfall Plot — tm_g_waterfall","text":"","code":"data <- teal_data() |> within({ ADSL <- rADSL ADRS <- rADRS ADTR <- rADTR ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX)) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_g_waterfall( label = \"Waterfall\", dataname_tr = \"ADTR\", dataname_rs = \"ADRS\", bar_paramcd = choices_selected(c(\"SLDINV\"), \"SLDINV\"), bar_var = choices_selected(c(\"PCHG\", \"AVAL\"), \"PCHG\"), bar_color_var = choices_selected(c(\"ARMCD\", \"SEX\"), \"ARMCD\"), bar_color_opt = NULL, sort_var = choices_selected(c(\"ARMCD\", \"SEX\"), NULL), add_label_var_sl = choices_selected(c(\"SEX\", \"EOSDY\"), NULL), add_label_paramcd_rs = choices_selected(c(\"BESRSPI\", \"OBJRSPI\"), NULL), anno_txt_var_sl = choices_selected(c(\"SEX\", \"ARMCD\", \"BMK1\", \"BMK2\"), NULL), anno_txt_paramcd_rs = choices_selected(c(\"BESRSPI\", \"OBJRSPI\"), NULL), facet_var = choices_selected(c(\"SEX\", \"ARMCD\", \"STRATA1\", \"STRATA2\"), NULL), href_line = \"-30, 20\" ) ) ) #> Initializing tm_g_waterfall #> Initializing reporter_previewer_module if (interactive()) { shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/ui_g_decorate.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper UI function to decorate plot output UI — ui_g_decorate","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"used tm_g_ae_oview() tm_g_events_term_id().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/ui_g_decorate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"","code":"ui_g_decorate( id, titles = \"Titles\", footnotes = \"footnotes\", fontsize = c(5, 4, 11) )"},{"path":"https://insightsengineering.github.io/teal.osprey/main/reference/ui_g_decorate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper UI function to decorate plot output UI — ui_g_decorate","text":"id (character) id module. set NULL want make identical module called . titles (character) default titles footnotes (character) default footnotes fontsize (numeric(1) numeric(3)) Defines initial possible range font-size. fontsize set teal.widgets::optionalSliderInputValMinMax() controls font-size output plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-01169031","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.16.9031","title":"teal.osprey 0.1.16.9031","text":"Removed Show Warnings modals modules. Moved teal.data Suggests Imports. Changed examples cdisc_data() teal_data().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"breaking-changes-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.osprey 0.1.16.9031","text":"Adapted modules use teal_data objects.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.16.9031","text":"Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-16-9031","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.16.9031","text":"Specified minimal version package dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-0116","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.16","title":"teal.osprey 0.1.16","text":"Removed scda package dependency examples. Fixed crash tm_g_heat_bygrade plotting Conmed. Added validation tm_g_spiderplot.R checks duplicates X Y facet variables. Improved input validation used teal::validate_inputs mechanism send validation messages output panel. Removed purrr dependencies. Added argument checks tm_g_patient_profile. Modified example apps use new teal_data join_keys solutions.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"breaking-changes-0-1-16","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.16","text":"Replaced chunks simpler qenv class. tm_xyz_srv modules datasets argument containing FilteredData replaced new argument data (tdata object) filter_panel_api (FilterPanelAPI). Updated arm_var point factor column ANL. can’t character column anymore. Removed redundant formal arguments tm_g_patient_profile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"breaking-changes-0-1-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.15","text":"Soft deprecate function label_aevar().","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.15","text":"Added teal.reporter modules. Updated shiny::validate calls shinyvalidate better UI overview. Implemented nestcolor slight refactoring tm_g_swimlane. Added nestcolor examples.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.15","text":"Added names id parameter teal.code::chunks_push modules. Updated modules use datasets names suffix _FILTERED package works breaking changes teal.slice.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.14","text":"Removed unneeded chunk evaluations tm_g_patient_profile module.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.14","text":"Added template pkgdown site. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-13","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.13","text":"Added basic logging modules. label select input widget choose paramcd longer hard coded ADTR tm_g_spiderplot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.13","text":"Rewrote module 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. Functions imported packages now fully specified.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"breaking-changes-0-1-12","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.osprey 0.1.12","text":"Refactored tm_g_ae_oview remove flag variables generated module default replace parameter add_flag flag_var_anl.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-12","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.12","text":"Added new parameter x_label allowing change label x axis tm_g_swimlane module plot. Updated tm_g_ae_sub longer displays label inputs group variables values selected.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"bug-fixes-0-1-12","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.12","text":"Fixed bug tm_g_waterfall Tumor Burden Parameter UI element now respected.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.12","text":"Updated R version requirement R >= 3.6. Removed function teal::keys examples tm_g_spiderplot tm_g_waterfall modules. Removed dependency test.nest package. Removed dependency utils.nest package replaced functions equivalents checkmate package.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-0111","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.11","title":"teal.osprey 0.1.11","text":"Updated LICENCE README new package references. Updated document tests scda synthetic data replace random.cdisc.data. Added error_on_lint: TRUE .lintr. Removed unnecessary importFrom statements. Updated tm_g_patient_profile module’s study days range accept infinite values. Fixed disappearing plots webpage zoom /.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.10","text":"Added Shiny feature tm_g_swimlane prevent needless re-render output user completely provided inputs vertical lines widget.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.10","text":"Altered Choose 2: inputs widget Encoding Panel independent Filtering Panel tm_g_butterfly. Updated warning message Tumor Burden Parameter selected tm_g_waterfall.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"bug-fixes-0-1-10","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.10","text":"Fixed bug tm_g_butterfly displays filtering faceting widgets despite provided arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"new-features-0-1-9","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.osprey 0.1.9","text":"Added new teal module tm_g_heat_bygrade heatmap grade plot. Added new teal module tm_g_ae_sub AE subgroups plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"bug-fixes-0-1-9","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.osprey 0.1.9","text":"Fixed misleading validate message tm_g_ae_oview either Control Treatment variable filtered . Added validate statement output better error message left right dichotomization values filtered data.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-9","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.9","text":"Improved reactivity dependencies across modules.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-018","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.8","title":"teal.osprey 0.1.8","text":"Added validation message dataset contain subjects control treatment arms tm_g_events_term_id. Improved validation message subject filtered dataset used tm_g_patient_profile. Fixed modules due changes plot_with_settings latest teal.devel release. Updated study day duration derivation tm_g_patient_profile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.osprey 0.1.7","text":"Added additional validation horizontal vertical reference lines tm_g_spider_plot.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"bug-fixes-0-1-7","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.osprey 0.1.7","text":"Fixed tm_g_patient_profile adverse event line color variable selected. Fixed issue unknown date format established minimum number observation threshold tm_g_patient_profile.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"miscellaneous-0-1-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.osprey 0.1.7","text":"Teal module AE overview summary table - can replaced teal.modules.clinical::tm_t_events_summary. Teal module AE summary table preferred terms - can replaced teal.modules.clinical::tm_t_events. Teal module AE summary table highest NCI-CTCAE grade - can replaced teal.modules.clinical::tm_t_events_by_grade. Teal module Disposition table - can replaced teal.modules.clinical::tm_t_summary. Moved code argument cdisc_dataset (cdisc_data) examples.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-016","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.6","title":"teal.osprey 0.1.6","text":"graph modules now accept plot_width argument specifies plot width renders slider adjust width interactively module. Replaced plot_with_height plot_with_settings module throughout package. Show R Code now produces code generating datasets needed current module, datasets included data argument teal::init. Evaluate chunks chunks_safe_eval rather chunks_eval.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-015","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.5","title":"teal.osprey 0.1.5","text":"Added new teal modules: Teal module events term summary plot. Teal module AE overview summary plot. Teal module patient profile plot","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-014","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.4","title":"teal.osprey 0.1.4","text":"Minor changes tests.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-013","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.3","title":"teal.osprey 0.1.3","text":"Technical release updated dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-012","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.2","title":"teal.osprey 0.1.2","text":"New waterfall module. Refactored due recent changes utils.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-011","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.1","title":"teal.osprey 0.1.1","text":"Included test.nest tests. Fixed outdated modules according current teal functionality. Fixed documentation examples example_app.R. Simplified dependencies.","code":""},{"path":"https://insightsengineering.github.io/teal.osprey/main/news/index.html","id":"tealosprey-010","dir":"Changelog","previous_headings":"","what":"teal.osprey 0.1.0","title":"teal.osprey 0.1.0","text":"Teal module AE overview summary table. Teal module AE summary table preferred terms. Teal module AE summary table highest NCI-CTCAE grade. Teal module Disposition table. Teal module AE butterfly plot. Teal module Swimlane plot. Teal module Spider plot.","code":""}]