Merge pull request #5 from PetterHopp/main

NVIpjsr v0.1.0 First release

.Rbuildignore

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

.gitignore

@@ -47,3 +47,6 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+inst/doc
+!vignettes/NVIpjsr.pdf
+

CODE_OF_CONDUCT.md

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+# 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

CONTRIBUTING.md

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+# Contribute to NVIpjsr
+
+<!-- CONTRIBUTING.md and ./vignettes/Contribute_to_NVIpkg.Rmd. are generated 
+     from ./templates/Contribute_to_NVIpkg.Rmd in NVIpackager. 
+     Please edit that file -->
+
+Thank you for considering contributing to `NVIpjsr`.
+
+`NVIpjsr` is one of several packages assembled under the name
+`NVIverse`, a collection of R-packages with tools to facilitate data
+management and data reporting at the Norwegian Veterinary Institute
+(NVI).
+
+### NVIverse packages
+
+<table>
+<colgroup>
+<col style="width: 13%" />
+<col style="width: 8%" />
+<col style="width: 78%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th style="text-align: left;">Package</th>
+<th style="text-align: left;">Status</th>
+<th style="text-align: left;">Description</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td style="text-align: left;">NVIconfig</td>
+<td style="text-align: left;">Private</td>
+<td style="text-align: left;">Configuration information necessary for
+some NVIverse functions</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">NVIdb</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate the use of NVI’s
+databases</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">NVIpjsr</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate working with PJS
+data</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">NVIspatial</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate working with spatial
+data at NVI</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">NVIpretty</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to make R-output pretty in accord
+with NVI’s graphical profile</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">NVIbatch</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate the running of
+R-scripts in batch mode at NVI</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">OKplan</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate the planning of
+surveillance programmes for the NFSA</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">OKcheck</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate checking of data from
+national surveillance programmes</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">NVIcheckmate</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Extension of checkmate with argument
+checking adapted for NVIverse</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">NVIpackager</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Tools to facilitate the development of
+NVIverse packages</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">NVIrpackages</td>
+<td style="text-align: left;">Public</td>
+<td style="text-align: left;">Keeps a table of the R packages in
+NVIverse</td>
+</tr>
+</tbody>
+</table>
+
+## How you can contribute
+
+There are several ways you can contribute to this project: ask a
+question, propose an idea, report a bug, improve the documentation, or
+contribute code.
+
+### Ask a question
+
+Using `NVIpjsr` and need help? Browse the package help to see if you can
+find a solution. Still problems? Post your question in R-forum at
+workplace or contact the package maintainer by
+[email](mailto:[email protected]).
+
+### Propose an idea
+
+Have an idea for a new `NVIpjsr` feature? Take a look at the `NVIpjsr`
+help and [issue
+list](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues) to
+see if it isn’t included or suggested yet. If not, suggest your idea as
+an [issue on
+GitHub](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues/new).
+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 `NVIpjsr` and discovered a bug? Don’t let others have the same
+experience and report it as an [issue on
+GitHub](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues/new)
+so we can fix it. A good bug report makes it easier for us to do so, so
+please include:
+
+-   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 function help? Think a function could use a better
+example? Good documentation makes all the difference, so your help to
+improve it is very welcome!
+
+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](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/tree/main/R).
+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 our\_package? Great!
+Have a look at the [issue
+list](https://github.com/NorwegianVeterinaryInstitute/NVIpjsr/issues)
+and leave a comment on the things you want to work on. See also the
+development guidelines below.
+
+## Development guidelines
+
+If you want to contribute code, you are welcome to do so. You will find
+a description of the code conventions, which have been used, in the
+vignette “NVIverse code conventions” in the package `NVIpackager`. A
+summary of the principles and style convention used for
+`NVIverse`-packages is given below.
+
+-   Please limit the number of package dependencies for `NVIpjsr`. The
+    use of base functions is much appreciated.
+
+-   New code should generally follow the tidyverse [style
+    guide](http://style.tidyverse.org) with some modifications.
+
+    -   use snake\_case for variable names, column names, function names
+        etc.
+    -   function names should start with a verb and should be
+        descriptive and can be long. Avoid strange abbreviations.
+    -   to indent the code you may use the short cut keys Ctrl+a (select
+        all) and Ctrl+i (indent) when you are in R-studio.
+    -   I recommend to use the
+        [`styler`](https://CRAN.R-project.org/package=styler) package to
+        apply spaces:
+        `styler::style_file(filename, scope = c("spaces", "line_breaks"))`.
+        Please don’t restyle code that has nothing to do with your pull
+        request.
+
+-   You should add a bullet point to `NEWS` motivating the change.
+
+-   You should add yourself as a contributor to the `DESCRIPTION`.
+
+Although not expected from all contributors, it will be highly
+appreciated if you also are willing to suggest:
+
+-   documentation for new functions or new arguments to existing
+    functions The `NVIverse`-packages use
+    [`roxygen2`](https://cran.r-project.org/package=roxygen2) for
+    documentation.
+
+-   argument checking of the function arguments. The `NVIverse`-packages
+    use the assert-functions from the
+    [`checkmate`](https://CRAN.R-project.org/package=checkmate) package
+    for argument checking as well as some additional assert-functions in
+    [`NVIcheckmate`](https://github.com/NorwegianVeterinaryInstitute/NVIcheckmate).
+
+-   one or more tests ensuring that the function works as intended. The
+    `NVIverse`-packages use
+    [`testthat`](https://cran.r-project.org/package=testthat) for tests.
+
+### Git commit standards
+
+We follow the commit message style guide maintained within the
+angular.js project.
+
+The start of commit messages should be one of the following:
+
+-   feat: A new feature
+-   fix: A bug fix
+-   doc: Documentation only changes
+-   style: Changes that do not affect the meaning of the code
+    (white-space, formatting, missing semi-colons, etc)
+-   refactor: A code change that neither fixes a bug or adds a feature
+-   perf: A code change that improves performance
+-   test: Adding missing tests
+-   chore: Changes to the build process or auxiliary tools and libraries
+    such as documentation generation
+
+Do not capitalize the first letter.
+
+## Code of conduct
+
+Please note that this project is released with a [Contributor Code of
+Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+By participating to this project, you agree to abide by its terms.
+
+## References
+
+This document is adapted from a
+[template](https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c)
+by @peterdesmet .