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https://github.com/ropensci-archive/cleanEHR
:warning: ARCHIVED :warning: Essential tools and utility functions to facilitate the data processing pipeline, data cleaning and data analysing of clinical data from CC-HIC
https://github.com/ropensci-archive/cleanEHR
big-data critical-care electronic-health-record healthcare intensive-care r r-package rstats
Last synced: 3 months ago
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:warning: ARCHIVED :warning: Essential tools and utility functions to facilitate the data processing pipeline, data cleaning and data analysing of clinical data from CC-HIC
- Host: GitHub
- URL: https://github.com/ropensci-archive/cleanEHR
- Owner: ropensci-archive
- License: gpl-3.0
- Archived: true
- Created: 2016-01-27T13:58:00.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2022-08-23T13:13:14.000Z (about 2 years ago)
- Last Synced: 2024-06-12T15:15:13.130Z (5 months ago)
- Topics: big-data, critical-care, electronic-health-record, healthcare, intensive-care, r, r-package, rstats
- Language: R
- Homepage:
- Size: 6.48 MB
- Stars: 54
- Watchers: 15
- Forks: 23
- Open Issues: 0
-
Metadata Files:
- Readme: README-not.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - ropensci-archive/cleanEHR - :warning: ARCHIVED :warning: Essential tools and utility functions to facilitate the data processing pipeline, data cleaning and data analysing of clinical data from CC-HIC (R)
README
[](https://travis-ci.org/ropensci/cleanEHR)
[](https://codecov.io/gh/ropensci/cleanEHR)
[]()
[](https://cran.r-project.org/package=cleanEHR)
[](http://www.r-pkg.org/pkg/cleanEHR)
[](https://zenodo.org/badge/latestdoi/50511003)
[](https://github.com/ropensci/onboarding/issues/102)
cleanEHR is an electronic health care record (EHR) data cleaning and
processing platform, which works with the Critical Care Health Informatics
Collaborative's data set. The purpose of the project is to enable researchers
to answer clinical questions that are important to patients, but which are
normally too difficult because data is unstandardised, siloed, and
inaccessible.
Since 2014 data from the critical care units at Cambridge, Guys/Kings/St
Thomas', Imperial, Oxford, and University College London has been extracted and
stored securely in a standardised format.
These data are crucially needed by healthcare professionals for the delivery
and continuity of care; by administrators for audit, planning and service
improvement; and by academic and industry researchers for the translation of
scientific progress into patient benefit. Through this process, CC-HIC can
improve patient outcomes, reduce the costs of care, and accelerate the pace of
translational health research.
The physical database is held at the [UCL
IDHS](http://www.ucl.ac.uk/isd/itforslms/services/handling-sens-data/tech-soln)
within the Information Services Division of University College London (UCL).
UCL manage and ensure that the database and the surrounding governance
structures are appropriate for holding identifiable and sensitive NHS data. The
safe haven is compliant to NHS Information Governance Toolkit Level 2 and
operates to the ISO 27001, the Safe Haven already holds identifiable, sensitive
NHS data for secondary purpose. The Critical Care HIC management group will
maintain oversight and be the point of contact for researchers wishing to
access data.
The security put in place to ensure the safety of this resource inevitably
creates challenges for the researchers. We have therefore created a three sided
tool to make CCHIC _research ready_.
- this shared code library
- an anonymised development data set
- a virtual machine for simulating work within the safe haven
You request access to the anonymised toy dataset from
[here](https://form.jotformeu.com/80383154562355)
## Required packages
* R (>= 3.1.0),
* XML,
* data.table,
* yaml,
* pander,
* Rcpp,
* methods
## How to install the R package
### From CRAN to get the last stable version
```
install.packages("cleanEHR")
```
### From Github to install the latest development version.
```
install.packages("devtools")
devtools::install_github("CC-HIC/cleanEHR")
```
## Vignette
* Introduction to CCHIC critical care data [here](https://docs.ropensci.org/cleanEHR/articles/cchic_overview.html)
* Data cleaning and wrangling with cleanEHR [here](https://docs.ropensci.org/cleanEHR/articles/data_clean.html)
## How to contribute
The cleanEHR package is currently under development. We wish you will find our
software tools useful to your research project. If you have any question about
the code or the data, please just raise an issue ticket on Github or contact us
via email ([email protected]). As cleanEHR is an open source and community
project, we also welcome contributions of any kind. We would like to make
cleanEHR the platform of collaboration critical care data analysis. If you have
any idea or comment, please feel free to raise the issue ticket [here](https://github.com/ropensci/cleanEHR/issues). We would
also encourage everyone to integrate their code into the cleanEHR repository to
benefit the entire community. Please feel free to contact us when you wish to
contribute your code.
[](https://ropensci.org)