# The Critical Care Clinical Data Processing Tools

## Documentation for package ‘cleanEHR’ version 1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

+-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.