Function reference • cleanEHR

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.