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NVIpackager: Tools to facilitate Development of NVIverse Packages

Overview

NVIpackagerprovides tools to facilitate development of NVIverse packages. You should use ‘create_NVIpkg_skeleton’ to make a package skeleton in accord with NVIverse standards. For further development and maintenance there are tools for updating documentation and installing development versions. The NVIpackager functions are to a large extent wrappers for devtools and usethis functions. In addition, the templates folder keeps templates for standard files like sections of README and CONTRIBUTING.

NVIpackager is part of NVIverse, a collection of R-packages with tools to facilitate data management and data reporting at the Norwegian Veterinary Institute (NVI). The NVIverse consists of the following packages: NVIconfig, NVIdb, NVIpjsr, NVIspatial, NVIpretty, NVIbatch, OKplan, OKcheck, NVIcheckmate, NVIpackager, NVIrpackages. See Contribute to NVIpackager for more information.

Installation

NVIpackager is available at GitHub. To install NVIpackager you will need:

  • R version > 4.0.0
  • R package remotes
  • Rtools version 4.0, 4.2 or 4.3 depending on R version

First install and attach the remotes package.

install.packages("remotes")
library(remotes)

To install (or update) the NVIpackager package without vignettes, run the following code:

remotes::install_github("NorwegianVeterinaryInstitute/NVIpackager",
    upgrade = FALSE,
    build = TRUE,
    build_vignettes = FALSE)

To install (or update) the NVIpackager package with vignettes, you will need to first install some additional R-packages needed for creating the vignettes. Check README below in the section Vignettes to see which vignettes are available. To install the package with the vignettes, first install the packages: knitr, rmarkdown, R.rsp, and NVIrpackages (from GitHub) if they are missing. Then run the following code:

remotes::install_github("NorwegianVeterinaryInstitute/NVIpackager",
    upgrade = FALSE,
    build = TRUE,
    build_vignettes = TRUE)

Usage

The NVIpackager package needs to be attached.

library(NVIpackager)

NVIpackagerprovides tools to facilitate development of NVIverse packages. You should use ‘create_NVIpkg_skeleton’ to make a package skeleton in accord with NVIverse standards. For further development and maintenance there are tools for updating documentation and installing development versions. The NVIpackager functions are to a large extent wrappers for devtools and usethis functions. In addition, the templates folder keeps templates for standard files like sections of README and CONTRIBUTING.

Create a NVIverse package skeleton

To set up a package skeleton you can follow the following procedure:

  1. Create a repository for the package at the NorwegianVeterinaryInstitute’s GitHub account. Give the repository the name of the package.

    • Make a short descriptive text. This can later be used as the Title in the DESCRIPTION file.
    • Choose between Public or Private. If unsure, start with Private. It is easy to change to Public later.
    • Mark for Add a README file.
    • Choose the .gitignore template for R.
    • Choose a licence, For example MIT, BSD 3-clause

  2. Create the repository.

  3. Fork the repository to your own GitHub account.

  4. Create an R-studio project for the package. In R-studio

    • Choose New project -> Version control
    • Copy the directory at GitHub and paste it where asked in R-studio.
    • Select a directory in your PC for your package.

  5. Create the package skeleton

    NVIpackager::create_NVIpkg_skeleton(license_keyword = "BSD_3_clause")

  6. Modify the DESCRIPTION file

    • Copy the descriptive text into the Title field in the DESCRIPTION file.
    • Copy the descriptive text into the Description field in the DESCRIPTION file and eventually extend it.

  7. Update README and Mypackage-package help with the last changes in the DESCRIPTION file.

    document_NVIpkg(pkg = stringi::stri_extract_last_words(usethis::proj_path()),
    pkg_path = usethis::proj_path(),
    style = FALSE,
    manual = "update",
    contributing = FALSE,
    readme = TRUE)

Maintenance of a NVIverse package

Functions for updating documentation, performing tests, build and install the package are collected in the file “./notes/develop.R”. You can run the different sections stepwise during package maintenance and updating.

Further documentation

Help

The full list of all available functions and datasets can be accessed by typing

help(package = "NVIpackager")
Vignettes

Consult the vignettes for task-oriented help.

vignette(package = "NVIpackager")

Vignettes in package NVIpackager:

  • Contribute to NVIpackager (html)
  • NVIpackager reference manual (pdf)
  • NVIverse coding conventions (html)
NEWS

Please check the NEWS for information on new features, bug fixes and other changes.

Copyright and license

Copyright (c) 2021 - 2024 Norwegian Veterinary Institute.
Licensed under the BSD_3_clause License. See License for details.

Contributing

Contributions to develop NVIpackager is highly appreciated. 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. See Contribute to NVIpackager for more information.

Please note that the NVIpackager project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.