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| --- | ||
| title: "Oncology extension package for ADaM in R Asset Library" | ||
| output: md_document | ||
| date: '2022-10-04' | ||
| --- | ||
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| <!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file --> | ||
| <!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively --> | ||
| <!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") --> | ||
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| # admiralonco <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/> | ||
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| <!-- badges: start --> | ||
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| [<img src="http://pharmaverse.org/shields/admiralonco.svg">](https://pharmaverse.org) | ||
| [](https://CRAN.R-project.org/package=admiralonco) | ||
| [](https://github.com/pharmaverse/admiralonco/actions/workflows/code-coverage.yml) | ||
| [](https://CRAN.R-project.org/package=admiralonco) | ||
| [](https://github.com/pharmaverse/admiralonco/actions/workflows/code-coverage.yml) | ||
| <!-- badges: end --> | ||
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| Oncology extension package for ADaM in R Asset Library `{admiral}` | ||
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| ## Purpose | ||
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| To provide a complementary (to `{admiral}`) toolbox that enables users to develop oncology disease area specifics. | ||
| To provide a complementary (to `{admiral}`) toolbox that enables users | ||
| to develop oncology disease area specifics. | ||
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| ## Installation | ||
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| The package is available from CRAN and can be installed by running `install.packages("admiralonco")`. | ||
| The package is available from CRAN and can be installed by running | ||
| `install.packages("admiralonco")`. | ||
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| To install the latest development version of the package directly from | ||
| GitHub use the following code: | ||
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| if (!requireNamespace("remotes", quietly = TRUE)) { | ||
| install.packages("remotes") | ||
| } | ||
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| remotes::install_github("pharmaverse/admiraldev", ref = "devel") # This is a required dependency of {admiralonco} | ||
| remotes::install_github("pharmaverse/admiral", ref = "devel") # This is a required dependency of {admiralonco} | ||
| remotes::install_github("pharmaverse/admiralonco", ref = "devel") | ||
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| To install the latest development version of the package directly from GitHub use the following code: | ||
| ### Dependencies | ||
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| ```r | ||
| if (!requireNamespace("remotes", quietly = TRUE)) { | ||
| install.packages("remotes") | ||
| } | ||
| The latest version of the package works with the latest versions of the | ||
| packages stated in `DESCRIPTION`. | ||
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| remotes::install_github("pharmaverse/admiralonco", ref = "devel") | ||
| ``` | ||
| If a previous version of the package should be used, it is recommended | ||
| to use latest version of the dependencies at the point of time when the | ||
| previous version of {admiralonco} was released. For example, admiralonco | ||
| 0.3.0 was released on 2023-03-14. I.e., it will work with the latest | ||
| version of packages available at that date, e.g., admiral 0.10. | ||
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| ## Scope | ||
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| * Build a toolbox of re-usable functions and utilities to create oncology-specific ADaM datasets in R in a modular manner. | ||
| * All functions are created based upon the ADaM Implementation Guide and aim to facilitate the programming of ADaM dataset standards. | ||
| * Initially the package will focus on the most common efficacy endpoint needs for solid tumor (using RECIST v1.1 response criteria), | ||
| but over time we will look to add extra areas such as: endpoints for targeted indications, baseline disease characteristics, common | ||
| sensitivity analyses and questionnaires. | ||
| - Build a toolbox of re-usable functions and utilities to create | ||
| oncology-specific ADaM datasets in R in a modular manner. | ||
| - All functions are created based upon the ADaM Implementation Guide | ||
| and aim to facilitate the programming of ADaM dataset standards. | ||
| - Initially the package will focus on the most common efficacy | ||
| endpoint needs for solid tumor (using RECIST v1.1 response | ||
| criteria), but over time we will look to add extra areas such as: | ||
| endpoints for targeted indications, baseline disease | ||
| characteristics, common sensitivity analyses and questionnaires. | ||
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| ## Expectations | ||
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| `{admiralonco}` is expected to complement `{admiral}` and provide functions to help with the creation of the efficacy endpoints required for oncology ADaMs. | ||
| `{admiralonco}` is expected to complement `{admiral}` and provide | ||
| functions to help with the creation of the efficacy endpoints required | ||
| for oncology ADaMs. | ||
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| ## References and Documentation | ||
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| * Please refer to the [{admiral} References and Documentation](https://pharmaverse.github.io/admiral/cran-release/index.html#references-and-documentation) | ||
| - Please refer to the [{admiral} References and | ||
| Documentation](https://pharmaverse.github.io/admiral/main/index.html#references-and-documentation) | ||
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| ## R Versions | ||
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| Here's a summary of our strategy for this package related to R versions: | ||
| Here’s a summary of our strategy for this package related to R versions: | ||
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| * R versions for developers and users will follow the same as `{admiral}` core package. | ||
| * For development the `devel` branch of `{admiral}` core is used as a dependency. For releasing a new `{admiralonco}` version it must run using the latest released `{admiral}` core version, i.e., `main` branch of `{admiral}` core. | ||
| - R versions for developers and users will follow the same as | ||
| `{admiral}` core package. | ||
| - For development the `devel` branch of `{admiral}` core is used as a | ||
| dependency. For releasing a new `{admiralonco}` version it must run | ||
| using the latest released `{admiral}` core version, i.e., `main` | ||
| branch of `{admiral}` core. | ||
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| ## Contact | ||
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| We use the following for support and communications between user and developer community: | ||
| We use the following for support and communications between user and | ||
| developer community: | ||
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| * [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) - for informal discussions, Q&A and building our user community. If you don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) to join the pharmaverse Slack workspace | ||
| * [GitHub Issues](https://github.com/pharmaverse/admiralonco/issues) - for direct feedback, enhancement requests or raising bugs | ||
| - [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) - for | ||
| informal discussions, Q&A and building our user community. If you | ||
| don’t have access, use this | ||
| [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) | ||
| to join the pharmaverse Slack workspace | ||
| - [GitHub Issues](https://github.com/pharmaverse/admiralonco/issues) - | ||
| for direct feedback, enhancement requests or raising bugs |