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