Merge pull request #4 from PetterHopp/main

OKplan v0.3.0

.Rbuildignore

@@ -6,7 +6,9 @@
 ^build.R
 ^install.R
 ^style.R
-^README.md
+^README\.md
+^README\.Rmd
 ^doc$
 ^Meta$
 ^OKplan.Rcheck\vign_test$
+^CONTRIBUTING\.md

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 *.Rproj
 *.Rcheck
+inst/doc

CONTRIBUTING.md

@@ -0,0 +1,214 @@
+# Contribute to OKplan
+
+<!-- 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 `OKplan`.
+
+`OKplan` 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;">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>
+</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 `OKplan` 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 `OKplan` feature? Take a look at the `OKplan`
+help and [issue
+list](https://github.com/NorwegianVeterinaryInstitute/OKplan/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/OKplan/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 `OKplan` and discovered a bug? Don’t let others have the same
+experience and report it as an [issue on
+GitHub](https://github.com/NorwegianVeterinaryInstitute/OKplan/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/OKplan/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/OKplan/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. Please try to
+adhere to some principles and style convention used for
+`NVIverse`-packages.
+
+-   Please limit the number of package dependencies for `OKplan`. The
+    use of base functions is much appreciated.
+
+-   New code should generally follow the tidyverse [style
+    guide](http://style.tidyverse.org). I recommend to use the
+    [`styler`](https://CRAN.R-project.org/package=styler) package to
+    apply spaces: `styler::style_file(filename, scope = "spaces")`.
+    Please don’t restyle code that has nothing to do with your pull
+    request.
+
+-   You should add a bullet point to `NEWS.md` motivating the change.
+
+-   You should add yourself as a contributor to the `DESCRIPTION`.
+
+-   If you’re adding a new function or new arguments to an existing
+    function, you’ll also need to document them. `NVIverse`-packages use
+    [`roxygen2`](https://cran.r-project.org/package=roxygen2), with
+    [Markdown
+    syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html),
+    for documentation. Make sure to re-run `devtools::document()` on the
+    code before submitting.
+
+-   `NVIverse`-packages use the assert-functions from
+    [`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).
+    Adding argument checking for new functions and/or arguments will be
+    highly appreciated.
+
+-   If you can, also write a test. `NVIverse`-packages use
+    [`testthat`](https://cran.r-project.org/package=testthat) for tests.
+
+-   Also run `devtools::check()` to make sure your function doesn’t
+    imply downstream errors or warnings.
+
+### 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 .

DESCRIPTION

@@ -1,35 +1,42 @@
 Package: OKplan
-Title: Tools facilitating the planning of surveillance programmes for the NFSA
-Version: 0.2.0
-Date: 2021-01-29
-Author: Petter Hopp <[email protected]>
-Maintainer: Petter Hopp <[email protected]>
-Description: The R-package include tools facilitating the planning of surveillance programmes
-    for the Norwegian Food Safety Authority. The package is under development. Included will
-    be tools for:
-    1) Making the target population,
-    2) Random selection,
-    3) generate lists for the NFSA.
+Title: Tools to facilitate the Planning of the annual Surveillance Programmes
+Version: 0.3.0
+Date: 2021-11-29
+Authors@R: 
+  c(person(given = "Petter",
+           family = "Hopp",
+           role = c("aut", "cre"),
+           email = "[email protected]"),
+    person(given = "Norwegian Veterinary Institute",
+           role = "cph"))
+Description: Provide tools to facilitate the planning of the annual surveillance
+    programmes. The main focus is tools for generating standardized lists for 
+    NFSA.
 URL: https://github.com/NorwegianVeterinaryInstitute/OKplan
 BugReports: https://github.com/NorwegianVeterinaryInstitute/OKplan/issues
-Depends: R (>= 3.4.1)
-License: Proprietary. Do not distribute outside the Norwegian Veterinary Institute
+Depends: R (>= 3.5.0)
+License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
+    checkmate,
     poorman,
-    NVIdb,
-    checkmate
-RoxygenNote: 7.1.1
+    stats,
+    NVIdb (>= 0.3.0)
 Suggests:
-    usethis,
+    covr,
+    devtools,
+    knitr,
     remotes,
-    testthat,
+    rmarkdown,
     roxygen2,
-    withr,
-    devtools,
     styler,
-    knitr,
-    rmarkdown
+    testthat,
+    usethis,
+    NVIpackager
+Remotes: 
+    NorwegianVeterinaryInstitute/NVIdb,
+    NorwegianVeterinaryInstitute/NVIpackager
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 Language: en-GB

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(control_OK_selection)
-export(include_generated_date)
+export(adjust_samples_to_budget)
+export(append_date_generated_line)
+export(append_sum_line)
+export(check_OK_selection)
 export(make_random)

NEWS

@@ -1,21 +1,48 @@
+OKplan 0.3.0 - (2021-11-29)
+---------------------------
+
+New features:
+
+- adjust_sample_number adjusts the sample numbers per unit up or down to reach the total sample size in accord with the budget.
+
+- append_sum_line appends a line with the sum of samples to the table in Excel.
+
+
+Bug fixes:
+
+- Included reference to NVIdb at GitHub to correct potential problems when installing the package.
+
+
+Other changes:
+
+  - Updated licence to BSD_3_clause and the copyright holder to Norwegian Veterinary Institute.
+
+  - Updated documentation and help.
+
+
+BREAKING CHANGES:
+
+  - Renamed to append_date_generated_line from include_generated_date.
+
+
 OKplan 0.2.0 - (2021-01-29)
---------------------------
+---------------------------
 
 New features:
 
   - Included a preliminary version of control_OK_selection for control of standard files with OK selection data.
 
 
 OKplan 0.1.1 - (2021-01-01)
---------------------------
+---------------------------
 
 Other changes:
 
   - included argument checking based on checkmate
 
 
 OKplan 0.1.0 - (2020-12-30)
---------------------------
+---------------------------
 
 First release: