NVIdb: Tools to facilitate the use of NVI’s databases

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

Overview

NVIdbprovides tools to facilitate downloading and processing of data from the Norwegian Veterinary Institute’s databases. The package comprises several categories of functions. 1) Manage credentials (i.e. password and username), 2) Login functions for database services, 3) Read, copy and update various in-house data registers, 4) Translate codes into descriptions. NVIdb is dependant of NVIconfig which has to be installed manually from GitHub. All PJS and EOS related functions are moved to NVIpjsr.

NVIdb 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 NVIdb for more information.

Installation

NVIdb is available at GitHub. To install NVIdb 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 NVIdb package without vignettes, run the following code:

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

To install (or update) the NVIdb 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/NVIdb",
    upgrade = FALSE,
    build = TRUE,
    build_vignettes = TRUE)

In addition, you will also need to install the private package NVIconfig that keep specific information on NVI’s paths and databases. NVIconfig is expected to be relatively stable and you will not need to update NVIconfig every time NVIdb is updated.

To install (or update) the NVIconfig package, run the following code:

remotes::install_github("NorwegianVeterinaryInstitute/NVIconfig",
    auth_token = "PAT",
    upgrade = FALSE,
    build = TRUE,
    build_vignettes = TRUE)

where PAT is your personal access token.

Usage

The NVIdb package needs to be attached.

library(NVIdb)

NVIdb provides tools to facilitate downloading and processing of data from the Norwegian Veterinary Institute’s databases, in particular PJS and EOS. The package comprises several categories of functions:

1. Manage credentials (i.e. password and username),
2. Login functions for database services,
3. Select PJS-data,
4. Initial cleaning of PJS-data,
5. Read, copy and update various in-house data registers,
6. Translate codes into descriptions.

By combining the functions for managing username and password and the login functions, you are able to login to PJS and EOS (and potentially other databases) without hard coding the password in the script. Thereafter, you may extract data from PJS and EOS using the R-package RODBC.

The read copy and update functions for data from NVI’s internal databases gives you access to these data without any need of knowing where the data are stored. Currently you get access to registers of administrative regions (Kommune, Fylke, Postnummer, Mattilsynets avdelinger og regioner), produsentinformasjon (Produksjonstilskuddsregister and new and old prodnr) and translation tables for PJS-codes into descriptive text.

There are also functions to use these registers to translate variables with codes into names and others. You can translate

• PJS-codes into descriptive text,
• kommunenr into kommune, fylke, as well as current kommunenr, kommune, fylkenr and fylke
• kommunenr into Mattilsynets avdeling and region
• postnr into poststed and poststedets kommunenr
• old produsentnr into current produsentnr

Further documentation

Help

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

help(package = "NVIdb")

Vignettes

Consult the vignettes for task-oriented help.

vignette(package = "NVIdb")

Vignettes in package NVIdb:

• Contribute to NVIdb (html)
• NVIdb reference manual (pdf)
• Retrieve and standardise PJS-data (html)

NEWS

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

Copyright and license

Copyright (c) 2019 - 2024 Norwegian Veterinary Institute.
Licensed under the BSD_3_clause License. See License for details.

Contributing

Contributions to develop NVIdb 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 NVIdb for more information.

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