The Critical Care Clinical Data Processing Tools


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Documentation for package ‘cleanEHR’ version 1.0

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+-method Adding nothing to a ccRecord object and return the original ccRecord
+-method Adding one ccEpisode object to a ccRecord
+-method Combine two ccRecord objects
+-method Adding a list of ccEpisode to ccRecord
as.number Convert standard IDs to numbers (character) which can be used for indexing.
ccd Synthetic example dataset
ccd_demographic_spell Create demographic table with spell IDs
ccd_demographic_table Create the demographic tables, which includes all non-time-varying variables.
ccd_select_table Create the table for ccTable from ccRecord
ccd_unique_spell find the unique spell ID.
ccEpisode The S4 class which holds data of a single episode.
ccEpisode-class The S4 class which holds data of a single episode.
ccRecord The S4 class which holds all the CCHIC patient record - served as a database.
ccRecord-class The S4 class which holds all the CCHIC patient record - served as a database.
ccTable Process the EHR data in table format
ccTable-class Process the EHR data in table format
ccTable_apply_filters Apply all the setup filters.
ccTable_clean Apply all the filters
ccTable_create_cctable Create a ccTable object
ccTable_export_csv Export the clean table as a CSV file
ccTable_filter_categories Categorical data filter
ccTable_filter_missingness Data missing filter
ccTable_filter_nodata No data filter
ccTable_filter_range Numerical range filter
ccTable_reload_conf Reload the YAML configuration file
ccTable_reset Reset the ccTable
code2stname Convert NHIC codes to the short names
create2dclean Clean table - low memory
create_cctable Create a ccTable object
data.checklist This a reference table of NHIC data items.
data.quality.report Create the data quality report
data.quality.report.brc Create the data quality report
deltaTime Convert calendar date-time to the time difference comparing to the ICU admission time.
demg.distribution demg.distribution Create a plot of the distribution of numerical demographic data.
demographic.data.completeness Create a demographic completeness table (in pander table)
extract_file_origin Extract the original file name from a path and file removing all the suffixes.
extract_info Extract information from data.checklist
file.summary Produce a file summary table
for_each_episode loop over all episodes of a ccRecord object
getEpisodePeriod Get the length of stay based on the first and the last data point.
getXmlepisode get the episode data from xml
icnarc2diagnosis Convert ICNARC codes to diagnosis (text)
icnarc_table ICNARC diagnosis reference table
inrange Check if the values of a vector v is in the given ranges.
is.demographic Check if the item NHIC code or short name belongs to the demographic category.
is.drugs Check if the item NHIC code or short name belongs to the drugs category.
is.laboratory Check if the item NHIC code or short name belongs to the Laboratory category.
is.physiology Check if the item NHIC code or short name belongs to the physiology category.
ITEM_REF Field reference table
lenstay Calculate the length of stay in the ICU.
long2stname Convert long names to short names.
lookup.items Lookup items information by keywords
new.episode Create a new episode
physio.distribution Plot the physiological data distribution.
plot_episode Individual episode chart
plot_episode-method Episode chart
plot_episode-method Episode chart default fields
reallocateTimeRecord Propagate a numerical delta time interval record.
samplerate2d Produce a pander table of sample rate of longitudinal data.
site.info Produce a site id reference table.
StdId S4 class to hold standard IDs such as "NIHR_HIC_ICU_0001"
stname2code Convert short names to NHIC codes
stname2longname Convert short names to long names.
table1 Produce the item specified table one.
total.data.point Return total data point of the ccRecord object.
which.classification Identify the classification - classification1
whichIsCode give id number from NHIC code like "NIHR_HIC_ICU_xxxx"
xml.file.duration.plot plot the duration of XML files.
xml.site.duration.plot Plot the XML duration in terms of sites.
xml2Data Convert the XML file to ccRecord
xmlLoad load xml clinical data
xmlTime2POSIX Convert time from xml to POSIX format.
[-method Create a subset of ccRecord object from the original one via specifying the row number of episodes.
[-method Create a ccRecord subsetting via selected sites.
[[-method Subsetting a ccRecord object and return a list of ccEpisode objects.