|
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`>)
|
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. |
