All functions

ITEM_REF

Field reference table

StdId() StdId()

S4 class to hold standard IDs such as "NIHR_HIC_ICU_0001"

as.number()

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

ccEpisode-class

The S4 class which holds data of a single episode.

ccRecord-class

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

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

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.

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.

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(<ccEpisode>,<character>)

Episode chart

plot_episode(<ccEpisode>,<missing>)

Episode chart default fields

plot_episode()

Individual episode chart

`+`(<ccRecord>,<`NULL`>)

Adding nothing to a ccRecord object and return the original ccRecord

`+`(<ccRecord>,<ccEpisode>)

Adding one ccEpisode object to a ccRecord

`+`(<ccRecord>,<ccRecord>)

Combine two ccRecord objects

`+`(<ccRecord>,<list>)

Adding a list of ccEpisode to ccRecord

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.

stname2code()

Convert short names to NHIC codes

stname2longname()

Convert short names to long names.

`[`(<ccRecord>,<ANY>)

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

`[`(<ccRecord>,<character>)

Create a ccRecord subsetting via selected sites.

`[[`(<ccRecord>)

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

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.