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cleanEHR (version 1.0)

The Critical Care Clinical Data Processing Tools

Description

An electronic health care record (EHR) data cleaning and processing platform. It focus on heterogeneous high resolution longitudinal data. It works with Critical Care Health Informatics Collaborative (CCHIC) dataset. It is created to address various data reliability and accessibility problems of EHRs as such.

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Version

Install

install.packages('cleanEHR')

Monthly Downloads

9

Version

1.0

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

December 16th, 2017

Functions in cleanEHR (1.0)

Process the EHR data in table format

ccTable_filter_categories

Categorical data filter

Field reference table

ccTable_filter_missingness

Data missing filter

S4 class to hold standard IDs such as "NIHR_HIC_ICU_0001"

ccTable_filter_nodata

ccTable_create_cctable

Create a ccTable object

ccTable_export_csv

Export the clean table as a CSV file

ccTable_filter_range

Numerical range filter

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

Synthetic example dataset

ccEpisode-class

The S4 class which holds data of a single episode.

ccTable_apply_filters

Apply all the setup filters.

ccd_demographic_spell

Create demographic table with spell IDs

Apply all the filters

ccd_select_table

Create the table for ccTable from ccRecord

data.quality.report.brc

Create the data quality report

ccd_unique_spell

find the unique spell ID.

Convert calendar date-time to the time difference comparing to the ICU admission time.

extract_file_origin

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

Convert NHIC codes to the short names

This a reference table of NHIC data items.

Produce a pander table of sample rate of longitudinal data.

data.quality.report

Create the data quality report

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

Produce a site id reference table.

ccd_demographic_table

Create the demographic tables, which includes all non-time-varying variables.

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

icnarc2diagnosis

Convert ICNARC codes to diagnosis (text)

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

ICNARC diagnosis reference table

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

Calculate the length of stay in the ICU.

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

+,ccRecord,list-method

Adding a list of ccEpisode to ccRecord

+,ccRecord,ccEpisode-method

Adding one ccEpisode object to a ccRecord

reallocateTimeRecord

Propagate a numerical delta time interval record.

+,ccRecord,ccRecord-method

Combine two ccRecord objects

[[,ccRecord-method

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

[,ccRecord,ANY-method

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

Produce the item specified table one.

[,ccRecord,character-method

Create a ccRecord subsetting via selected sites.

ccTable_reload_conf

Reload the YAML configuration file

Reset the ccTable

demg.distribution

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

Extract information from data.checklist

Clean table - low memory

Create a new episode

Create a ccTable object

physio.distribution

Plot the physiological data distribution.

Produce a file summary table

for_each_episode

loop over all episodes of a ccRecord object

Convert short names to NHIC codes

xml.site.duration.plot

Plot the XML duration in terms of sites.

stname2longname

Convert short names to long names.

Convert the XML file to ccRecord

which.classification

Identify the classification - classification1

plot_episode,ccEpisode,character-method

Lookup items information by keywords

plot_episode,ccEpisode,missing-method

Episode chart default fields

give id number from NHIC code like "NIHR_HIC_ICU_xxxx"

Individual episode chart

xml.file.duration.plot

plot the duration of XML files.

load xml clinical data

+,ccRecord,NULL-method

Adding nothing to a ccRecord object and return the original ccRecord

Convert time from xml to POSIX format.

total.data.point

Return total data point of the ccRecord object.

demographic.data.completeness

Create a demographic completeness table (in pander table)

getEpisodePeriod

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

get the episode data from xml

Convert long names to short names.

The S4 class which holds all the CCHIC patient record - served as a database.