Essential tools and utility functions to facilitate the data processing pipeline, data cleaning and data analysing of clinical data from CC-HIC
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README.md

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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 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

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
  • Data cleaning and wrangling with cleanEHR here

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 (s.shi@ucl.ac.uk). 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. 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.

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