Man pages for cleanEHR
The Critical Care Clinical Data Processing Tools

as.numberConvert standard IDs to numbers (character) which can be used...
ccdSynthetic example dataset
ccd_demographic_spellCreate demographic table with spell IDs
ccd_demographic_tableCreate the demographic tables, which includes all...
ccd_select_tableCreate the table for ccTable from ccRecord
ccd_unique_spellfind the unique spell ID.
ccEpisode-classThe S4 class which holds data of a single episode.
ccRecord-classThe S4 class which holds all the CCHIC patient record -...
ccTable_apply_filtersApply all the setup filters.
ccTable-classProcess the EHR data in table format
ccTable_cleanApply all the filters
ccTable_create_cctableCreate a ccTable object
ccTable_export_csvExport the clean table as a CSV file
ccTable_filter_categoriesCategorical data filter
ccTable_filter_missingnessData missing filter
ccTable_filter_nodataNo data filter
ccTable_filter_rangeNumerical range filter
ccTable_reload_confReload the YAML configuration file
ccTable_resetReset the ccTable
code2stnameConvert NHIC codes to the short names
create2dcleanClean table - low memory
create_cctableCreate a ccTable object
data.checklistThis a reference table of NHIC data items.
data.quality.reportCreate the data quality report the data quality report
deltaTimeConvert calendar date-time to the time difference comparing...
demg.distributiondemg.distribution Create a plot of the distribution of... a demographic completeness table (in pander table)
extract_file_originExtract the original file name from a path and file removing...
extract_infoExtract information from data.checklist
file.summaryProduce a file summary table
for_each_episodeloop over all episodes of a ccRecord object
getEpisodePeriodGet the length of stay based on the first and the last data...
getXmlepisodeget the episode data from xml
icnarc2diagnosisConvert ICNARC codes to diagnosis (text)
icnarc_tableICNARC diagnosis reference table
inrangeCheck if the values of a vector v is in the given ranges.
is.demographicCheck if the item NHIC code or short name belongs to the...
is.drugsCheck if the item NHIC code or short name belongs to the...
is.laboratoryCheck if the item NHIC code or short name belongs to the...
is.physiologyCheck if the item NHIC code or short name belongs to the...
ITEM_REFField reference table
lenstayCalculate the length of stay in the ICU.
long2stnameConvert long names to short names.
lookup.itemsLookup items information by keywords
new.episodeCreate a new episode
physio.distributionPlot the physiological data distribution.
plot_episodeIndividual episode chart
plot_episode-ccEpisode-character-methodEpisode chart
plot_episode-ccEpisode-missing-methodEpisode chart default fields
plus-ccRecord-ccEpisode-methodAdding one ccEpisode object to a ccRecord
plus-ccRecord-ccRecord-methodCombine two ccRecord objects
plus-ccRecord-list-methodAdding a list of ccEpisode to ccRecord
plus-ccRecord-NULL-methodAdding nothing to a ccRecord object and return the original...
reallocateTimeRecordPropagate a numerical delta time interval record.
samplerate2dProduce a pander table of sample rate of longitudinal data.
site.infoProduce a site id reference table.
StdIdS4 class to hold standard IDs such as "NIHR_HIC_ICU_0001"
stname2codeConvert short names to NHIC codes
stname2longnameConvert short names to long names.
sub-ccRecord-ANY-methodCreate a subset of ccRecord object from the original one via...
sub-ccRecord-character-methodCreate a ccRecord subsetting via selected sites.
sub-sub-ccRecord-methodSubsetting a ccRecord object and return a list of ccEpisode...
table1Produce the item specified table one. total data point of the ccRecord object.
which.classificationIdentify the classification - classification1
whichIsCodegive id number from NHIC code like "NIHR_HIC_ICU_xxxx"
xml2DataConvert the XML file to ccRecord
xml.file.duration.plotplot the duration of XML files.
xmlLoadload xml clinical data the XML duration in terms of sites.
xmlTime2POSIXConvert time from xml to POSIX format.
cleanEHR documentation built on May 2, 2019, 6:40 a.m.