dataquieR 2

dataquieR 2: An updated R package for FAIR data quality assessments in observational studies and electronic health record data - Published in JOSS (2024)

https://gitlab.com/libreumg/dataquier

Keywords

Repository

Data quality assessments <https://doi.org/10.21105/joss.03093> guided by a data quality framework <https://doi.org/10.1186/s12874-021-01252-7> target the data quality dimensions integrity, completeness, consistency, and accuracy.

https://gitlab.com/libreumg/dataquier/blob/master/

# `dataquieR`



[![minimal R
version](https://img.shields.io/badge/R%3E%3D-3.6.0-6666ff.svg)](https://cran.r-project.org/)
[![Pipeline
Status](https://gitlab.com/libreumg/dataquier/badges/master/pipeline.svg?ignore_skipped=true)](https://libreumg.gitlab.io/dataquier/)
[![Coverage](https://codecov.io/gl/libreumg/dataquier/branch/master/graph/badge.svg?token=79TK6GQTMG)](https://app.codecov.io/gl/libreumg/dataquier)
[![CRAN-Version](https://www.r-pkg.org/badges/version/dataquieR)](https://cran.r-project.org/package=dataquieR)
![Latest
Release](https://gitlab.com/libreumg/dataquier/-/badges/release.svg)
[![DOI](https://img.shields.io/badge/DOI-10.32614%2FCRAN.package.dataquieR-00be00.svg)](https://doi.org/10.32614/CRAN.package.dataquieR)
[![CRAN-Downloads](https://cranlogs.r-pkg.org/badges/dataquieR)](https://www.r-pkg.org/pkg/dataquieR)
[![Project Status: Active  The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![`Lifecycle`](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![license](https://img.shields.io/badge/license-BSD_2_clause%20+%20file%20LICENSE-00be00.svg)](https://opensource.org/license/bsd-2-clause)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03093/status.svg)](https://doi.org/10.21105/joss.03093)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06581/status.svg)](https://doi.org/10.21105/joss.06581)



The goal of `dataquieR` is to provide functions for assessing data
quality issues in studies, that can be used alone or in a data quality
pipeline. `dataquieR` also implements one generic pipeline producing
`flexdashboard` based HTML5 reports.

See also

[`https://dataquality.qihs.uni-greifswald.de`](https://dataquality.qihs.uni-greifswald.de)

------------------------------------------------------------------------

## Installation

You can install the released version of `dataquieR` from
[CRAN](https://CRAN.R-project.org/package=dataquieR) with:

``` r
install.packages("dataquieR")
```

The suggested packages can be directly installed by:

``` r
install.packages("dataquieR", dependencies = TRUE)
```

The developer version from
[`GitLab.com`](https://gitlab.com/libreumg/dataquier) can be installed
using:

``` r
if (!requireNamespace("devtools")) {
  install.packages("devtools")
}
devtools::install_gitlab("libreumg/dataquier")
```

For examples and additional documentation, please refer to our
[website](https://dataquality.qihs.uni-greifswald.de).

## Suggested packages

`dataquieR` reports can now use
[`plotly`](https://cran.r-project.org/package=plotly) if installed. That
means that, in the final report, you can zoom in the figures and get
information by hovering on the points, etc. To install `plotly` type:

``` r
install.packages("plotly")
```

To install all suggested packages, run:

``` r
prep_check_for_dataquieR_updates()
```

This command can also check for new beta releases of `dataquieR` from
our own server, so not from `CRAN`:

``` r
prep_check_for_dataquieR_updates(beta = TRUE)
```

***Hint*** If you are running `dataquieR` in an un-trusted setting,
namely, inside a server application, please consider disabling the
import of R-serialization files to prevent users from importing `RData`
(or `RDS` or even `R`) files, that trigger code execution on your
machine, see, e.g., [Ivan Krylovs
blog](https://aitap.github.io/2024/05/02/unserialize.html) for the
reason:

``` r
# prevent rio from reading potentially code-containing files
options(rio.import.trust = FALSE)
```

If you do so, the example data wont be loaded any more.

If you are using a version \>= 2.0.0 of `rio`, this will be the default,
so for running our examples, then, youll have to trust our files by
using e.g.
`withr::with_options(list(rio.import.trust = FALSE), prep_get_data_frame("study_data"))`
for loading our example study data into the data-frame cache, initially
and trusting our files loaded from

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## References

- [Software Paper](https://doi.org/10.21105/joss.06581) [![JOSS
  Article](https://joss.theoj.org/papers/10.21105/joss.06581/status.svg)](https://doi.org/10.21105/joss.06581)
- [Software Paper](https://doi.org/10.21105/joss.03093) [![JOSS
  Article](https://joss.theoj.org/papers/10.21105/joss.03093/status.svg)](https://doi.org/10.21105/joss.03093)
- [Data Quality Concept
  Paper](https://doi.org/10.1186/s12874-021-01252-7)
- [Data Quality Concept and Software Web
  Site](https://dataquality.qihs.uni-greifswald.de)

## Funding  see also [here](https://dataquality.qihs.uni-greifswald.de/Contact.html)

- German Research Foundation (`https://www.dfg.de/`) (DFG:
  `SCHM 2744/31`  initial concept and dataquieR development,
  `SCHM 2744/9-1`  `NFDI` Task Force `COVID-19` use case application;
  `SCHM 2744/3-4`  concept extensions, ongoing )

- [European Unions Horizon 2020 research and innovation
  program](https://research-and-innovation.ec.europa.eu/funding/funding-opportunities/funding-programmes-and-open-calls/horizon-2020_en):
  [euCanSHare, grant agreement No.825903](http://www.eucanshare.eu/) 
  [dataquieR](https://cran.r-project.org/package=dataquieR) refinements
  and implementations in the
  [Square2](https://pubmed.ncbi.nlm.nih.gov/28423853/) web application.

- [National Research Data Infrastructure for Personal Health
  Data](https://www.nfdi4health.de/en/): `NFDI 13/1`  extension based
  on revised metadata concept, ongoing.

- German National Cohort (NAKO Gesundheitsstudie) NAKO
  (`https://nako.de/`): `BMBF` (`https://www.bmbf.de/`): `01ER1301A` and
  `01ER1801A`

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