Man pages for cleanEHR
The Critical Care Clinical Data Processing Tools
| as.number | Convert standard IDs to numbers (character) which can be used... |
| ccd | Synthetic example dataset |
| ccd_demographic_spell | Create demographic table with spell IDs |
| ccd_demographic_table | Create the demographic tables, which includes all... |
| ccd_select_table | Create the table for ccTable from ccRecord |
| ccd_unique_spell | find the unique spell ID. |
| ccEpisode-class | The S4 class which holds data of a single episode. |
| ccRecord-class | The S4 class which holds all the CCHIC patient record -... |
| ccTable_apply_filters | Apply all the setup filters. |
| ccTable-class | Process the EHR data in table format |
| 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... |
| demg.distribution | demg.distribution Create a plot of the distribution of... |
| 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... |
| 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... |
| 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... |
| is.drugs | Check if the item NHIC code or short name belongs to the... |
| is.laboratory | Check if the item NHIC code or short name belongs to the... |
| is.physiology | Check if the item NHIC code or short name belongs to the... |
| 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-ccEpisode-character-method | Episode chart |
| plot_episode-ccEpisode-missing-method | Episode chart default fields |
| plus-ccRecord-ccEpisode-method | Adding one ccEpisode object to a ccRecord |
| plus-ccRecord-ccRecord-method | Combine two ccRecord objects |
| plus-ccRecord-list-method | Adding a list of ccEpisode to ccRecord |
| plus-ccRecord-NULL-method | Adding nothing to a ccRecord object and return the original... |
| 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. |
| sub-ccRecord-ANY-method | Create a subset of ccRecord object from the original one via... |
| sub-ccRecord-character-method | Create a ccRecord subsetting via selected sites. |
| sub-sub-ccRecord-method | Subsetting a ccRecord object and return a list of ccEpisode... |
| 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" |
| xml2Data | Convert the XML file to ccRecord |
| xml.file.duration.plot | plot the duration of XML files. |
| xmlLoad | load xml clinical data |
| xml.site.duration.plot | Plot the XML duration in terms of sites. |
| xmlTime2POSIX | Convert time from xml to POSIX format. |
