NVIbatch: Tools to facilitate the running of R-scripts in batch mode at NVI

• Overview
• Installation
• Usage
• Copyright and license
• Contributing

Overview

NVIbatch provides tools to facilitate the writing of batch R-scripts that should be run automatically at specific times.

NVIbatch 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 NVIbatch for more information.

Installation

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

• R version > 4.1.0
• R package remotes
• Rtools version 4.0, 4.2, 4.3 or 4.4 depending on R version

First install and attach the remotes package.

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

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

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

To install (or update) the NVIbatch package with vignettes, you will need to first install some additional R-packages needed to build 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. If you don’t use R-studio, you will also need to install Pandoc. Then run the following code:

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

Usage

The NVIbatch package needs to be attached.

library(NVIbatch)

NVIbatch provides tools to facilitate the writing of batch R-scripts that should be run automatically at specific times. The vignette “Run R scripts automatically” gives a detailed description on how you can set up an automatic batch job to run an R script on Windows.

Further documentation

Help

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

help(package = "NVIbatch")

Vignettes

Consult the vignettes for task-oriented help.

vignette(package = "NVIbatch")

Vignettes in package NVIbatch:

• Contribute to NVIbatch (html)
• Run R scripts automatically (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 NVIbatch 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 NVIbatch for more information.

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