Initialize package

.Rbuildignore

@@ -0,0 +1,5 @@
+^camtrapdp\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$
+^README\.Rmd$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# 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 [email protected]. 
+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>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+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>.
+
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

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+# Contributing to camtrapdp
+
+<!-- This CONTRIBUTING.md is adapted from https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c -->
+
+First of all, thanks for considering contributing to camtrapdp! 👍 It's people like you that make it rewarding for us - the project maintainers - to work on camtrapdp. 😊
+
+camtrapdp is an open source project, maintained by people who care. We are not directly funded to do so.
+
+[repo]: https://github.com/inbo/camtrapdp
+[issues]: https://github.com/inbo/camtrapdp/issues
+[new_issue]: https://github.com/inbo/camtrapdp/issues/new
+[website]: https://inbo.github.io/camtrapdp
+[citation]: https://inbo.github.io/camtrapdp/authors.html
+[email]: mailto:[email protected]
+
+## Code of conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
+
+## How you can contribute
+
+There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this [Open Source Guide](https://opensource.guide/how-to-contribute/).
+
+### Share the love ❤️
+
+Think camtrapdp is useful? Let others discover it, by telling them in person, via Twitter or a blog post.
+
+Using camtrapdp for a paper you are writing? Consider [citing it][citation].
+
+### Ask a question ⁉️
+
+Using camtrapdp and got stuck? Browse the [documentation][website] to see if you can find a solution. Still stuck? Post your question as an [issue on GitHub][new_issue]. While we cannot offer user support, we'll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs.
+
+Want to ask a question in private? Contact the package maintainer by [email][mailto:email].
+
+### Propose an idea 💡
+
+Have an idea for a new camtrapdp feature? Take a look at the [documentation][website] and [issue list][issues] to see if it isn't included or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. While we can't promise to implement your idea, it helps to:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible.
+
+See below if you want to contribute code for your idea as well.
+
+### Report a bug 🐛
+
+Using camtrapdp and discovered a bug? That's annoying! Don't let others have the same experience and report it as an [issue on GitHub][new_issue] so we can fix it. A good bug report makes it easier for us to do so, so please include:
+
+* Your operating system name and version (e.g. Mac OS 10.13.6).
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Improve the documentation 📖
+
+Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!
+
+#### The website
+
+[This website][website] is generated with [`pkgdown`](http://pkgdown.r-lib.org/). That means we don't have to write any html: content is pulled together from documentation in the code, vignettes, [Markdown](https://guides.github.com/features/mastering-markdown/) files, the package `DESCRIPTION` and `_pkgdown.yml` settings. If you know your way around `pkgdown`, you can [propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to improve documentation. If not, [report an issue][new_issue] and we can point you in the right direction.
+
+#### Function documentation
+
+Functions are described as comments near their code and translated to documentation using [`roxygen2`](https://klutometis.github.io/roxygen/). If you want to improve a function description:
+
+1. Go to `R/` directory in the [code repository][repo].
+2. Look for the file with the name of the function.
+3. [Propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to update the function documentation in the roxygen comments (starting with `#'`).
+
+### Contribute code 📝
+
+Care to fix bugs or implement new functionality for camtrapdp? Awesome! 👏 Have a look at the [issue list][issues] and leave a comment on the things you want to work on. See also the development guidelines below.
+
+## Development guidelines
+
+We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development.
+
+1. Fork [this repo][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
+2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`.
+3. Open the RStudio project file (`.Rproj`).
+4. Make your changes:
+    * Write your code.
+    * Test your code (bonus points for adding unit tests).
+    * Document your code (see function documentation above).
+    * Check your code with `devtools::check()` and aim for 0 errors and warnings.
+5. Commit and push your changes.
+6. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request).

.github/workflows/R-CMD-check.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -47,3 +47,4 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+.Rproj.user

DESCRIPTION

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+Package: camtrapdp
+Title: Read and Convert Camera Trap Data Packages (Camtrap DP)
+Version: 0.0.0.9000
+Authors@R: c(
+    person("Damiano", "Oldoni", email = "[email protected]",
+           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),
+    person("Research Institute for Nature and Forest (INBO)",
+           role = "cph", comment = "https://www.vlaanderen.be/inbo/en-gb/"),
+    person("LifeWatch Belgium",
+           role = "fnd", comment = "https://lifewatch.be")
+  )
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.0
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2024 Research Institute for Nature and Forest (INBO)
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: Research Institute for Nature and Forest (INBO)

LICENSE.md

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+# MIT License
+
+Copyright (c) 2024 Research Institute for Nature and Forest (INBO)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+