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DARAutils

R CMD Check Coverage Lint

Useful generic functions that can be used in DARApipelines

Overview

DARAutils (part of DARAtools) is an R package that offers generic function that could be useful in DARA pipelines.

Installation and updating

From RIVM GitLab

Most recent version

To install DARAutils from GitLab, first install the graph package by running:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("graph")

You can now download the latest version of DARAutils via the internal Gitlab environment using the remotes package:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_gitlab("dara/DARAutils@main", host = "https://gitlab.rivm.nl", build = FALSE)

Please visit the Wiki to find instructions on how to install older versions of DARAutils.

Development version 

remotes::install_gitlab("dara/DARAutils@develop", host = "https://gitlab.rivm.nl", build = FALSE)

From RIVM-syso GitHub

To install DARAutils from GitHub, first install the graph package by running:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("graph")

You can now download the latest version of DARAutils via GitHub using the remotes package:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("rivm-syso/DARAutils@main", build = FALSE")

From CRAN

TODO add installation via CRAN

Usage

r library(DARAutils) will load the DARAutils package, part of the DARAtools framework. The other packages within DARAtools are:

  • DARAgit, for git functionality.
  • DARAvis, for data visualisation in RIVM-house style.
  • DARAgeo, for loading geographical data.
  • DARApipeline, for running an EPI data pipeline.

Getting help

For detailed documentation, use:

# The function cut_and_label() is used here as an example.
# Please replace it with the specific function for which you want to see documentation.
?cut_and_label

First point of contact for questions: DARAteam ().

Please report a DARAutils issue at GitLab issues.

Authors and acknowledgment

This R package was created by the DARA team (RIVM/CIb/EPI in department DIS).

License

The code can be re-used under license EUPL v.1.2.

Code of Conduct

We want to create a welcoming and respectful environment for everyone.

  • Be kind and respectful to others.
  • Do not use offensive or inappropriate language.
  • Respect differences in opinion, experience, and background.
  • If you experience or witness unacceptable behavior, please report it by contacting the maintainers at .

Disclaimer

This R package was originally developed to meet the specific needs of the EPI (Epidemiology & Surveillance) department within the CIb (Centre for Infectious Disease Control) at the RIVM. However, it is made openly available to all RIVM employees who may find it useful for their work. While we welcome and encourage feedback from users outside the EPI department, please note that the package’s primary development focus remains aligned with the needs of its original user base.

We strive to ensure that the package is reliable and effective for its intended purposes, but we cannot guarantee that every feature or functionality will fully meet the requirements of your specific use case. Additionally, while we appreciate all suggestions and feedback, we cannot guarantee that we will have the time or resources to incorporate every requested feature or fix into future updates.

This package is provided “as is”, without any express or implied warranties of accuracy, completeness, fitness for a particular purpose, or non-infringement. Use of the package, and interpretation of its results, is at your own risk. We encourage users to validate outputs thoroughly before applying them in critical contexts.

If you encounter issues, have suggestions, or wish to share feedback, please report them via the package’s GitHub issue board or by contacting the package maintainer(s): DARAteam (). Your input is highly valuable and helps us improve the package for all users. Thank you for your understanding and cooperation!