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acutelines.datatoolbox

This package can be used to work with data extracted from the Acutelines data- and biobank. It provides tools to parse data extracts and perform calculations in a uniform matter.

https://github.com/umcg-seh/acutelines.datatoolbox

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords

biobank medical research
Last synced: 6 months ago · JSON representation ·

Repository

This package can be used to work with data extracted from the Acutelines data- and biobank. It provides tools to parse data extracts and perform calculations in a uniform matter.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Topics
biobank medical research
Created almost 2 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License Citation

README.md

Acutelines Datatoolbox R Package

GitHub R package version License: MIT DOI <!-- badges: end -->

Full documenation is available at umcg-seh.github.io/acutelines.datatoolbox. Visit GitHub for source code.

Introduction

This package can be used to work with data extracted from the Acutelines data- and biobank. It provides tools to parse data extracts and perform calculations in a uniform matter.

Acutelines is a multi-disciplinary prospective hospital-based cohort study examining 24/7 the complete acute patient journey admitted to the ED of the University Medical Centre Groningen (UMCG), a tertiary care teaching hospital in the Netherlands. It employs a broad range of investigative procedures in assessing the pre-hospital, in-hospital, and long-term health factors that affect outcome in patients with acute conditions. The cohort population is broadly representative of the people living in the Northern Netherlands with acute medical conditions. Detailed information about the cohort and participant selection can be found elsewhere [1] [2]. Participants were asked for written informed consent, when applicable by proxy. The Acutelines cohort study is approved by the medical ethics committee of the UMCG, the Netherlands and registered under trial registration number NCT04615065 at ClinicalTrials.gov [3].

  1. www.acutelines.nl
  2. ter Avest E, van Munster BC, van Wijk RJ, et al Cohort profile of Acutelines: a large data/biobank of acute and emergency medicine. BMJ Open 2021;11:e047349. doi: 10.1136/bmjopen-2020-047349
  3. https://clinicaltrials.gov/study/NCT04615065

Installation

To install a package from Github, first install and load the devtools packages:

R install.packages('devtools') library(devtools)

Install the acutelines.datatoolbox package from GitHub:

R install_github("UMCG-SEH/acutelines.datatoolbox")

Load the package:

R library(acutelines.datatoolbox)

Install specific version

If you want to install a specific version of the package for legacy purposes, mention the version number with @ in the install_github command:

R install_github("UMCG-SEH/acutelines.datatoolbox@v0.0.0.6")

After that load and use the package as you normally do.

Getting started

After installation, you can process the data depending on your data extract. Refer to the Articles section in the documentation for a general introduction.

Start by importing your dataset from CSV, for example:

R df <- read.csv("path/to/data/file.csv", header = TRUE, # Import CSV header (first line) as column names sep = ";", # Set CSV columns separator dec = ".", # Set CSV decimal separator for numbers fileEncoding = "UTF-8-BOM", # Set file encoding format, change or ommit according to file type na.strings=c("NA","NaN", " ", "\\N", "NULL")) # Set which values are considered NA

Then run the desired functions from the Acutelines Datatoolbox, eg: sofa_magic_wrapper().

Owner

  • Name: UMCG-SEH
  • Login: UMCG-SEH
  • Kind: organization

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "acutelines.datatoolbox" in publications use:'
type: software
license: MIT
title: 'acutelines.datatoolbox: Toolbox to work with Acutelines biobank data.'
version: 1.0.1
doi: 10.5281/zenodo.14824083
abstract: This package can be used to work with data extracted from the Acutelines
  data- and biobank. It provides tools to parse data extracts and perform calculations
  in a uniform matter.
authors:
- family-names: Wijk
  given-names: Raymond J.
  name-particle: van
  email: r.j.van.wijk@umcg.nl
  orcid: https://orcid.org/0000-0002-2106-7699
- family-names: Hincapié-Osorno
  given-names: Carolina
  orcid: https://orcid.org/0000-0001-8582-1614
repository-code: https://github.com/UMCG-SEH/acutelines.datatoolbox
url: https://umcg-seh.github.io/acutelines.datatoolbox/
date-released: '2025-02-05'
contact:
- family-names: Wijk
  given-names: Raymond J.
  name-particle: van
  email: r.j.van.wijk@umcg.nl
  orcid: https://orcid.org/0000-0002-2106-7699
keywords:
- biobank
- medical
- research
references:
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
  version: '>= 1.1.4'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown

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