Initialize the package

.Rbuildignore

@@ -0,0 +1,23 @@
+^renv$
+^renv\.lock$
+CODE_OF_CONDUCT.md
+SECURITY.md
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^vignettes/hello\.Rmd$
+^docs$
+^\.github$
+README.*
+^\.lintr$
+^staged_dependencies\.yaml$
+coverage.*
+^\.pre-commit-config\.yaml$
+^codemeta\.json$
+init.sh
+workflows.md
+images
+^pkgdown$
+^.revdeprefs\.yaml$
+^revdep$
+^\.covrignore$

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @pawelru

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* 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
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## 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
+
+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
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**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
+
+**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
+
+**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
+
+**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
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

.github/CONTRIBUTING.md

@@ -0,0 +1,136 @@
+# 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
+
+[👶 Getting started](#getting-started)
+
+[📔 Code of Conduct](#code-of-conduct)
+
+[🗃 License](#license)
+
+[📜 Issues](#issues)
+
+[🚩 Pull requests](#pull-requests)
+
+[💻 Coding guidelines](#coding-guidelines)
+
+[🏆 Recognition model](#recognition-model)
+
+[❓ Questions](#questions)
+
+## Getting started
+
+Please refer the project [documentation][docs] for a brief introduction. Please also see other [articles][articles] within the project documentation for additional information.
+
+## Code of Conduct
+
+A [Code of Conduct](CODE_OF_CONDUCT.md) governs this project. Participants and contributors are expected to follow the rules outlined therein.
+
+## License
+
+All your contributions will be covered by this project's [license][license].
+
+## 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
+
+### GitHub Flow
+
+This repository uses the [GitHub Flow](https://docs.github.com/en/get-started/quickstart/github-flow) model for collaboration. To submit a pull request:
+
+1. Create a branch
+
+   Please see the [branch naming convention](#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
+    * 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.
+
+4. Address review comments, if any
+
+5. Post approval
+
+   Merge your PR if you have write access. Otherwise, the reviewer will merge the PR on your behalf.
+
+6. Pat yourself on the back
+
+   Congratulations! 🎉
+   You are now an official contributor to this project! We are grateful for your contribution.
+
+### 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`](https://github.com/openpharma/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](https://openpharma.github.io/staged.dependencies/) for more details.
+
+## 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
+
+This repository follows the standard [`tidyverse` style guide](https://style.tidyverse.org/) and uses [`lintr`](https://github.com/r-lib/lintr) for lint checks. Customized lint configurations are available in this repository's `.lintr` file.
+
+### Dependency management
+
+Lightweight is the right weight. This repository follows [tinyverse](https://www.tinyverse.org/) recommedations of limiting dependencies to minimum.
+
+### 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
+
+#### 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`
+
+We highly recommend that you use the [`pre-commit`](https://pre-commit.com/) tool combined with [`R hooks for pre-commit`](https://github.com/lorenzwalthert/precommit) 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
+
+As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the [repository insights][insights], to recognize a _significant_ contribution and hence add the contributor to the package authors list, the following rules are enforced:
+
+* Minimum 5% of lines of code authored* (determined by `git blame` query) OR
+* Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*
+
+*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
+
+If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.
+
+<!-- urls -->
+[docs]: https://insightsengineering.github.io/r.pkg.template/index.html
+[articles]: https://insightsengineering.github.io/r.pkg.template/main/articles/index.html
+[license]: https://insightsengineering.github.io/r.pkg.template/main/LICENSE-text.html
+[insights]: https://github.com/insightsengineering/r.pkg.template/pulse

.github/ISSUE_TEMPLATE/bug.yml

@@ -0,0 +1,51 @@
+---
+name: 🐞 Bug Report
+description: File a bug report
+title: "[Bug]: <title>"
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: Tell us what you see!
+      value: "A bug happened!"
+    validations:
+      required: true
+  - type: dropdown
+    id: r-version
+    attributes:
+      label: Which version(s) of R were you using?
+      multiple: true
+      options:
+        - "3.6.x"
+        - "4.1.x"
+        - "4.2.x"
+        - "Other"
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: R
+  - type: checkboxes
+    id: code-of-conduct
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct](https://insightsengineering.github.io/r.pkg.template/CODE_OF_CONDUCT.html)
+      options:
+        - label: I agree to follow this project's Code of Conduct.
+          required: true
+  - type: checkboxes
+    id: contributor-guidelines
+    attributes:
+      label: Contribution Guidelines
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines](https://insightsengineering.github.io/r.pkg.template/CONTRIBUTING.html)
+      options:
+        - label: I agree to follow this project's Contribution Guidelines.
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,10 @@
+---
+blank_issues_enabled: true
+
+contact_links:
+  - name: We are hiring!
+    url: https://careers.gene.com/
+    about: Genentech and Roche are hiring!
+  - name: Pharmaverse
+    url: https://pharmaverse.org/
+    about: Related projects @ Pharmaverse.org

.github/ISSUE_TEMPLATE/feature.yml

@@ -0,0 +1,27 @@
+---
+name: ✨ Feature Request
+description: Request or propose a new feature
+title: "[Feature Request]: <title>"
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+    validations:
+      required: true
+  - type: checkboxes
+    id: code-of-conduct
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct](https://insightsengineering.github.io/r.pkg.template/CODE_OF_CONDUCT.html)
+      options:
+        - label: I agree to follow this project's Code of Conduct.
+          required: true
+  - type: checkboxes
+    id: contributor-guidelines
+    attributes:
+      label: Contribution Guidelines
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines](https://insightsengineering.github.io/r.pkg.template/CONTRIBUTING.html)
+      options:
+        - label: I agree to follow this project's Contribution Guidelines.
+          required: true