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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-method
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.