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Merge pull request #16 from inbo/checklist
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‎.Rbuildignore‎

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.travis.yml
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^.*\.Rproj$
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^CITATION\.cff$
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^LICENSE.md$
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^README\.Rmd$
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^\.Rproj\.user$
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^man-roxygen$
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.travis.yml
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appveyor.yml
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tic.R
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^\.github$
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^\.httr-oauth$
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^\.zenodo\.json$
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^_pkgdown.yml$
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^_pkgdown\.yml$
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^checklist.yml$
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^codecov\.yml$
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^data-raw$
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^docs$
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^man-roxygen$
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^pkgdown$
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^data-raw$
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appveyor.yml
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tic.R

‎.github/CODE_OF_CONDUCT.md‎

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# Contributor Code of Conduct
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As contributors and maintainers of this project, we pledge to respect all people who
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contribute through reporting issues, posting feature requests, updating documentation,
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submitting pull requests or patches, and other activities.
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We are committed to making participation in this project a harassment-free experience for
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everyone, regardless of level of experience, gender, gender identity and expression,
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sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
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Examples of unacceptable behaviour by participants include the use of sexual language or
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imagery, derogatory comments or personal attacks, trolling, public or private harassment,
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insults, or other unprofessional conduct.
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Project maintainers have the right and responsibility to remove, edit, or reject comments,
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commits, code, wiki edits, issues, and other contributions that are not aligned to this
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Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
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from the project team.
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Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by
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opening an issue or contacting one or more of the project maintainers.
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This Code of Conduct is adapted from the Contributor Covenant
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(http://contributor-covenant.org), version 1.0.0, available at
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http://contributor-covenant.org/version/1/0/0/

‎.github/CONTRIBUTING.md‎

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# CONTRIBUTING #
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### Fixing typos
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Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
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E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
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### Prerequisites
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Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem.
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If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
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### Pull request process
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* We recommend that you create a Git branch for each pull request (PR).
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* Look at the GitHub Actions build status before and after making changes.
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The `README` should contain badges for any continuous integration services used by the package.
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* We require the `tidyverse` [style guide](http://style.tidyverse.org).
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You can use the [`styler`](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
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* We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).
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* We use [`testthat`](https://cran.r-project.org/package=testthat).
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Contributions with test cases included are easier to accept.
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* For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
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### Code of Conduct
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Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).
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By contributing to this project you agree to abide by its terms.
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### Prefer to Email?
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Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
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Though note that private discussions over email don't help others - of course
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email is totally warranted if it's a sensitive problem of any kind.
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### Thanks for contributing!
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This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md

‎.github/workflows/check_on_branch.yml‎

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on:
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push:
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branches-ignore:
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- main
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- master
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- ghpages
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name: "check package with checklist"
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jobs:
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check-package:
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runs-on: ubuntu-latest
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name: "check package"
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: read
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steps:
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- uses: inbo/actions/[email protected]

‎.github/workflows/check_on_different_r_os.yml‎

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on:
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push:
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branches:
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- main
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- master
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pull_request:
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branches:
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- main
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- master
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name: R-CMD-check-OS
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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_R_CHECK_SYSTEM_CLOCK_: false
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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extra-repositories: https://inbo.r-universe.dev
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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error-on: '"error"'

‎.github/workflows/check_on_main.yml‎

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on:
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push:
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branches:
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- main
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- master
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permissions:
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contents: write
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name: "check package on main with checklist"
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jobs:
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check-package:
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runs-on: ubuntu-latest
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name: "check package"
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: inbo/actions/[email protected]

‎.github/workflows/release.yml‎

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name: Releases
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on:
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push:
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tags:
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- v*
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workflow_run:
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workflows: ["check package on main with checklist"]
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types:
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- completed
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jobs:
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publish:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v3
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- name: Get tag
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run: |
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git fetch --tags --force
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TAG=$(git tag --contains $(git rev-parse HEAD))
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TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
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echo "tag=$TAG" >> $GITHUB_ENV
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echo "$TAG_BODY" > body.md
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- uses: ncipollo/release-action@v1
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with:
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name: Release ${{ env.tag }}
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tag: ${{ env.tag }}
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bodyFile: body.md

‎.gitignore‎

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.Rproj.user
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.Rhistory
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*.dbf
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*.doc*
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*.gddoc
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*.gdsheet
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*.gpkg
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*.html
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*.mdb
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*.shp*
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*.shx
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*.xls*
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*_files
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.DS_Store
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.RData
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.Renviron
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.Rhistory
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.Rproj.user
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.Ruserdata
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inst/doc
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.httr-oauth
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docs
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inst/doc
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libs
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output
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renv/library

‎.travis.yml‎

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‎.zenodo.json‎

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{
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"title": "effectclass: Classification and Visualisation of Effects",
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"version": "0.1.4",
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"license": "GPL-3.0",
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"upload_type": "software",
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"description": "<p>Classify effects by comparing the confidence intervals with\nthresholds.<\/p>",
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"keywords": [
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"classification",
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"effect size",
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"uncertainty",
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"visualisation"
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],
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"access_right": "open",
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"language": "eng",
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"contributors": [
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{
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"name": "Onkelinx, Thierry",
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"affiliation": "Research Institute for Nature and Forest (INBO)",
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"orcid": "0000-0001-8804-4216",
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"type": "ContactPerson"
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},
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{
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"name": "Research Institute for Nature and Forest (INBO)",
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"type": "RightsHolder"
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}
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],
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"creators": [
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{
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"name": "Onkelinx, Thierry",
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"affiliation": "Research Institute for Nature and Forest (INBO)",
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"orcid": "0000-0001-8804-4216"
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}
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],
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"communities": [
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{
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"identifier": "inbo"
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}
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]
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}

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