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cleanEHR (version 0.1)

The Critical Care Clinical Data Processing Tools

Description

A toolset to deal with the Critical Care Health Informatics Collaborative dataset. It is created to address various data reliability and accessibility problems of electronic healthcare records (EHR). It provides a unique platform which enables data manipulation, transformation, reduction, anonymisation, cleaning and validation.

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Install

install.packages('cleanEHR')

Monthly Downloads

9

Version

0.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/CC-HIC/cleanEHR

Homepage

http://www.hic.nihr.ac.uk

Maintainer

Sinan Shi

Last Published

February 2nd, 2017

Functions in cleanEHR (0.1)

add.record.to.record

Combine two ccRecord objects

Create a 2D wide clean table - low memory

construct function of ccTable object

This a reference table of NHIC data items.

Convert standard IDs to numbers (character) which can be used for indexing.

extract_file_origin

Extract the original file name from a path and file removing all the suffixes.

extractIndexTable

get indexing tables for time label, time-wise value, meta data label, and meta data.

demographic.data.completeness

Create a demographic completeness table (in pander table)

demg.distribution

demg.distribution Create a plot of the distribution of numerical demographic data.

extract information from data.checklist

Produce a file summary table

get the episode data from xml

Retrieve information of the query code/item names from data.checklist

get the dfilter

ICNARC diagnosis reference table

+,ccRecord,list-method

Adding a list of ccEpisode objects to a ccRecord

+,ccRecord,NULL-method

Adding nothing to a ccRecord object.

for_each_episode

loop over all episodes of a ccRecord object

Check if the item NHIC code or short name belongs to the physiology category.

getEpisodePeriod

Get the length of stay based on the first and the last data point.

Check if the item NHIC code or short name belongs to the Laboratory category.

[[,ccRecord-method

Subseting a ccRecord object and return a list of ccEpisode objects.

[,ccRecord,character-method

Create a ccRecord subset via selected sites.

load xml clinical data

Convert the XML file to ccRecord

convert calendar time data in a record to delta time comparing to the ICU admission time.

data.quality.report

Create the data quality report

icnarc2diagnosis

Convert the ICNARC code to human readable diagnosis

Check if the values of a vector v is in the given ranges.

+,ccRecord,ccEpisode-method

Adding one ccEpisode object to a ccRecord

stname2longname

Convert short names to long names.

+,ccRecord,ccRecord-method

Combine two ccRecord objects

update_database

Update the critical care database (RData)

physio.distribution

Plot the physiological data distribution.

find the unique spell ID.

[,ccRecord,ANY-method

Create a subset of ccRecord object from the original one via specifying the row number of episodes.

Update the RData database

Produce a pander table of sample rate of longitudinal data.

reallocateTimeRecord

Propagate a numerical delta time interval record.

which.classification

Identify the classification - classification1

give id number from NHIC code like "NIHR_HIC_ICU_xxxx"

Create a new episode

sql.demographic.table

Create demographic SQL tables. The data type of each column is in its corresponding data type.

Lookup items information by keywords

Produce the item specified table one.

Convert short names to NHIC codes

total.data.point

Return total data point of the ccRecord object.

demographic.patient.spell

Assign unique spell ID to the demographic table

Convert time from xml to POSIX format.

Individual episode graph

Check if the item NHIC code or short name belongs to the demographic category.

Produce a site id reference table.

Create wide table from ccRecord

Check if the item NHIC code or short name belongs to the drugs category.

xml.site.duration.plot

Plot the XML duration in terms of sites.

xml.file.duration.plot

plot the duration of XML files.

data.quality.report.brc

Create the data quality report

ccRecord_subset_files

Subset episodes from the specified XML files.

add.episode.list.to.record

Adding a list of ccEpisode to ccRecord

add.episode.to.record

Adding one ccEpisode object to ccRecord object.

Convert NHIC codes to the short names

ccEpisode-class

The S3 class which holds data of a single episode.

The S3 class which holds all the CCHIC patient record - served as a database.

Rearrange and clean the critical care record into a 2D table.

S4 class to hold standard IDs such as "NIHR_HIC_ICU_0001"