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NVIpjsr v0.1.0 First release
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‎.Rbuildignore‎

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^\.git$
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^\.gitignore$
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^\.Rhistory$
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^CODE_OF_CONDUCT\.md$
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^CONTRIBUTING\.md$
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^data-raw$
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^man-roxygen$
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^notes$
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^README\.md
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^README\.Rmd$
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^.*\.Rproj$
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^\.Rproj\.user$
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‎.gitignore‎

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# RStudio Connect folder
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rsconnect/
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inst/doc
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!vignettes/NVIpjsr.pdf
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‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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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
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at Petter.Hopp@vetinst.no.
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
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For answers to common questions about this code of conduct, see the FAQ at
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<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
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[homepage]: https://www.contributor-covenant.org

‎CONTRIBUTING.md‎

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# Contribute to NVIpjsr
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<!-- CONTRIBUTING.md and ./vignettes/Contribute_to_NVIpkg.Rmd. are generated
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from ./templates/Contribute_to_NVIpkg.Rmd in NVIpackager.
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Please edit that file -->
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Thank you for considering contributing to `NVIpjsr`.
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`NVIpjsr` is one of several packages assembled under the name
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`NVIverse`, a collection of R-packages with tools to facilitate data
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management and data reporting at the Norwegian Veterinary Institute
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(NVI).
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### NVIverse packages
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<table>
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<colgroup>
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<col style="width: 13%" />
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<col style="width: 8%" />
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<col style="width: 78%" />
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</colgroup>
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<thead>
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<tr class="header">
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<th style="text-align: left;">Package</th>
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<th style="text-align: left;">Status</th>
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<th style="text-align: left;">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr class="odd">
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<td style="text-align: left;">NVIconfig</td>
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<td style="text-align: left;">Private</td>
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<td style="text-align: left;">Configuration information necessary for
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some NVIverse functions</td>
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</tr>
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<tr class="even">
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<td style="text-align: left;">NVIdb</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate the use of NVI’s
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databases</td>
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</tr>
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<tr class="odd">
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<td style="text-align: left;">NVIpjsr</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate working with PJS
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data</td>
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</tr>
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<tr class="even">
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<td style="text-align: left;">NVIspatial</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate working with spatial
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data at NVI</td>
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</tr>
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<tr class="odd">
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<td style="text-align: left;">NVIpretty</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to make R-output pretty in accord
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with NVI’s graphical profile</td>
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</tr>
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<tr class="even">
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<td style="text-align: left;">NVIbatch</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate the running of
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R-scripts in batch mode at NVI</td>
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</tr>
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<tr class="odd">
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<td style="text-align: left;">OKplan</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate the planning of
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surveillance programmes for the NFSA</td>
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</tr>
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<tr class="even">
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<td style="text-align: left;">OKcheck</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate checking of data from
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national surveillance programmes</td>
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</tr>
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<tr class="odd">
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<td style="text-align: left;">NVIcheckmate</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Extension of checkmate with argument
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checking adapted for NVIverse</td>
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</tr>
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<tr class="even">
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<td style="text-align: left;">NVIpackager</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Tools to facilitate the development of
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NVIverse packages</td>
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</tr>
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<tr class="odd">
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<td style="text-align: left;">NVIrpackages</td>
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<td style="text-align: left;">Public</td>
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<td style="text-align: left;">Keeps a table of the R packages in
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NVIverse</td>
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</tr>
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</tbody>
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</table>
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## How you can contribute
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There are several ways you can contribute to this project: ask a
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question, propose an idea, report a bug, improve the documentation, or
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contribute code.
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### Ask a question
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Using `NVIpjsr` and need help? Browse the package help to see if you can
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find a solution. Still problems? Post your question in R-forum at
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workplace or contact the package maintainer by
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[email](mailto:petter.hopp@vetinst.no).
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### Propose an idea
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Have an idea for a new `NVIpjsr` feature? Take a look at the `NVIpjsr`
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help and [issue
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list](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues) to
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see if it isn’t included or suggested yet. If not, suggest your idea as
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an [issue on
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GitHub](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues/new).
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While we can’t promise to implement your idea, it helps to:
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- Explain in detail how it would work.
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- Keep the scope as narrow as possible.
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See below if you want to contribute code for your idea as well.
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### Report a bug
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Using `NVIpjsr` and discovered a bug? Don’t let others have the same
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experience and report it as an [issue on
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GitHub](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues/new)
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so we can fix it. A good bug report makes it easier for us to do so, so
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please include:
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- Any details about your local setup that might be helpful in
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troubleshooting.
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- Detailed steps to reproduce the bug.
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### Improve the documentation
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Noticed a typo on the function help? Think a function could use a better
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example? Good documentation makes all the difference, so your help to
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improve it is very welcome!
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Functions are described as comments near their code and translated to
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documentation using [`roxygen2`](https://klutometis.github.io/roxygen/).
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If you want to improve a function description:
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1. Go to `R/` directory in the [code
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repository](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/tree/main/R).
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2. Look for the file with the name of the function.
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3. [Propose a file
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change](https://help.github.com/articles/editing-files-in-another-user-s-repository/)
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to update the function documentation in the roxygen comments
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(starting with `#'`).
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### Contribute code
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Care to fix bugs or implement new functionality for our\_package? Great!
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Have a look at the [issue
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list](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues)
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and leave a comment on the things you want to work on. See also the
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development guidelines below.
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## Development guidelines
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If you want to contribute code, you are welcome to do so. You will find
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a description of the code conventions, which have been used, in the
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vignette “NVIverse code conventions” in the package `NVIpackager`. A
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summary of the principles and style convention used for
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`NVIverse`-packages is given below.
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- Please limit the number of package dependencies for `NVIpjsr`. The
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use of base functions is much appreciated.
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- New code should generally follow the tidyverse [style
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guide](http://style.tidyverse.org) with some modifications.
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- use snake\_case for variable names, column names, function names
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etc.
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- function names should start with a verb and should be
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descriptive and can be long. Avoid strange abbreviations.
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- to indent the code you may use the short cut keys Ctrl+a (select
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all) and Ctrl+i (indent) when you are in R-studio.
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- I recommend to use the
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[`styler`](https://CRAN.R-project.org/package=styler) package to
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apply spaces:
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`styler::style_file(filename, scope = c("spaces", "line_breaks"))`.
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Please don’t restyle code that has nothing to do with your pull
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request.
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- You should add a bullet point to `NEWS` motivating the change.
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- You should add yourself as a contributor to the `DESCRIPTION`.
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Although not expected from all contributors, it will be highly
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appreciated if you also are willing to suggest:
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- documentation for new functions or new arguments to existing
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functions The `NVIverse`-packages use
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[`roxygen2`](https://cran.r-project.org/package=roxygen2) for
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documentation.
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- argument checking of the function arguments. The `NVIverse`-packages
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use the assert-functions from the
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[`checkmate`](https://CRAN.R-project.org/package=checkmate) package
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for argument checking as well as some additional assert-functions in
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[`NVIcheckmate`](https://github.com/NorwegianVeterinaryInstitute/NVIcheckmate).
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- one or more tests ensuring that the function works as intended. The
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`NVIverse`-packages use
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[`testthat`](https://cran.r-project.org/package=testthat) for tests.
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### Git commit standards
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We follow the commit message style guide maintained within the
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angular.js project.
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The start of commit messages should be one of the following:
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- feat: A new feature
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- fix: A bug fix
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- doc: Documentation only changes
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- style: Changes that do not affect the meaning of the code
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(white-space, formatting, missing semi-colons, etc)
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- refactor: A code change that neither fixes a bug or adds a feature
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- perf: A code change that improves performance
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- test: Adding missing tests
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- chore: Changes to the build process or auxiliary tools and libraries
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such as documentation generation
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Do not capitalize the first letter.
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## Code of conduct
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Please note that this project is released with a [Contributor Code of
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Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
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By participating to this project, you agree to abide by its terms.
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## References
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This document is adapted from a
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[template](https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c)
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by @peterdesmet .

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