FUNPACK API reference

FUNPACK is written in the Python programming language. While FUNPACK was designed primarily as a command-line tool, it can also be programmatically called from a Python script. The pages in this section document all of the classes and functions that are contained within the FUNPACK codebase.

• funpack.cleaning
  • applyChildValues()
  • applyCleaningFunctions()
  • applyNAInsertion()
  • applyNewLevels()
  • cleanData()
• funpack.cleaning_functions
  • codeToNumeric()
  • fillMissing()
  • fillVisits()
  • flattenHierarchical()
  • keepVisits()
  • makeNa()
  • parseSpirometryData()
  • remove()
• funpack.config
  • loadConfigFile()
  • makeEpilog()
  • makeParser()
  • parseArgs()
  • parseArgsWithConfigFile()
  • sanitiseArgs()
• funpack.custom
  • PluginRegistry
    • PluginRegistry.args()
    • PluginRegistry.clearRegistry()
    • PluginRegistry.exists()
    • PluginRegistry.get()
    • PluginRegistry.listPlugins()
    • PluginRegistry.loadPluginFile()
    • PluginRegistry.registerPlugin()
    • PluginRegistry.run()
  • args()
  • cleaner()
  • clearRegistry()
  • exists()
  • exporter()
  • formatter()
  • get()
  • listPlugins()
  • loadPluginFile()
  • loader()
  • metaproc()
  • processor()
  • registerBuiltIns()
  • registerPlugin()
  • run()
  • runCleaner()
  • runExporter()
  • runFormatter()
  • runLoader()
  • runMetaproc()
  • runProcessor()
  • runSniffer()
  • sniffer()
• funpack.datatable
  • AUTO_VARIABLE_ID
  • Column
  • DataTable
    • DataTable.addColumns()
    • DataTable.addFlag()
    • DataTable.allColumns
    • DataTable.cattable
    • DataTable.columns()
    • DataTable.dataColumns
    • DataTable.getFlags()
    • DataTable.index
    • DataTable.indexColumns
    • DataTable.instances()
    • DataTable.isSubtable
    • DataTable.manager
    • DataTable.maskSubjects()
    • DataTable.merge()
    • DataTable.njobs
    • DataTable.parallel
    • DataTable.pool()
    • DataTable.present()
    • DataTable.proctable
    • DataTable.removeColumns()
    • DataTable.shape
    • DataTable.subtable()
    • DataTable.variables
    • DataTable.vartable
    • DataTable.visits()
  • MODIFIED_COLUMN
• funpack.dryrun
  • doDryRun()
• funpack.exporting
  • defaultDateTimeFormat()
  • escapeString()
  • exportData()
  • formatColumn()
  • formatCompound()
• funpack.exporting_hdf5
  • HDF5_KEY
  • HDF5_STYLE
  • HDF5_STYLES
  • exportFunpackStyle()
  • exportHDF5()
  • exportPandasStyle()
  • importFunpackStyle()
• funpack.exporting_tsv
  • NUM_ROWS
  • exportCSV()
  • exportTSV()
  • writeDataFrame()
• funpack.fileinfo
  • FileInfo
    • FileInfo.allColumns
    • FileInfo.allVariables
    • FileInfo.columns()
    • FileInfo.datafiles
    • FileInfo.dialect()
    • FileInfo.encoding()
    • FileInfo.header()
    • FileInfo.index()
    • FileInfo.loader()
    • FileInfo.sniffer()
  • fileinfo()
  • has_header()
  • renameDuplicateColumns()
  • sniff()
• funpack.icd10
  • initialise()
  • saveCodes()
  • storeCodes()
  • toNumeric()
• funpack.importing.core
  • MERGE_AXIS
  • MERGE_AXIS_OPTIONS
  • MERGE_STRATEGY
  • MERGE_STRATEGY_OPTIONS
  • NUM_ROWS
  • VariableMissing
  • coerceToNumeric()
  • importData()
  • loadChunk()
  • loadFile()
  • loadFiles()
• funpack.importing.filter
  • REMOVE_DUPLICATE_COLUMN_IDENTIFIER
  • addAuxillaryVariables()
  • columnsToLoad()
  • evaluateSubjectExpression()
  • evaluateSubjectExpressions()
  • filterSubjects()
  • restrictVariables()
• funpack.importing.reindex
  • genReindexedColumns()
  • reindexByVisit()
• funpack.loadtables
  • CATTABLE_COLUMNS
  • CATTABLE_CONVERTERS
  • CATTABLE_DTYPES
  • DCTABLE_COLUMNS
  • DCTABLE_DTYPES
  • IMPLICIT_CATEGORIES
  • PROCTABLE_COLUMNS
  • PROCTABLE_CONVERTERS
  • TYPETABLE_COLUMNS
  • TYPETABLE_CONVERTERS
  • TYPETABLE_DTYPES
  • VARTABLE_COLUMNS
  • VARTABLE_CONVERTERS
  • VARTABLE_DTYPES
  • addImplicitCategories()
  • addNewVariable()
  • categoryVariables()
  • columnTypes()
  • convert_ParentValues()
  • convert_Process()
  • convert_Process_Variable()
  • convert_category_variables()
  • convert_comma_sep_numbers()
  • convert_comma_sep_text()
  • convert_dtype()
  • convert_type()
  • identifyUncategorisedVariables()
  • loadCategoryTable()
  • loadProcessingTable()
  • loadTableBases()
  • loadTables()
  • loadVariableTable()
  • mergeCleanFunctions()
  • mergeDataCodingTable()
  • mergeIntoVariableTable()
  • mergeTableFiles()
  • sanitiseVariableTable()
  • variableCategories()
• funpack.main
  • configLogging()
  • doCleanAndProcess()
  • doDescriptionExport()
  • doExport()
  • doICD10Export()
  • doImport()
  • doSummaryExport()
  • doUnknownsExport()
  • generateDescription()
  • main()
  • splitDataTable()
• funpack.merging
  • mergeDataFrames()
• funpack.metaproc_functions
  • codingDescriptionFromValue()
  • hierarchicalDescriptionFromCode()
  • hierarchicalDescriptionFromNumeric()
• funpack.parsing.process
  • NoSuchProcessError
  • Process
    • Process.args
    • Process.auxillaryVariables()
    • Process.broadcastKwargs
    • Process.filterMissing
    • Process.kwargs
    • Process.name
    • Process.processString
    • Process.run()
  • makeProcessParser()
  • parseProcesses()
• funpack.parsing.value_expression
  • Literal
  • ValueExpression
    • ValueExpression.add()
    • ValueExpression.div()
    • ValueExpression.expression
    • ValueExpression.max()
    • ValueExpression.min()
    • ValueExpression.mul()
    • ValueExpression.sub()
  • makeValueExpressionParser()
  • parseValueExpressions()
• funpack.parsing.variable_expression
  • SYMBOLS
  • VariableExpression
    • VariableExpression.evaluate()
    • VariableExpression.variables
  • calculateVariableExpressionEvaluationOrder()
  • makeParser()
  • parseBinary()
  • parseCondition()
  • parseUnary()
  • parseVariable()
  • parseVariableExpression()
  • variablesInExpression()
• funpack.plugins.fmrib
  • columns_FMRIBImaging()
  • load_FMRIBImaging()
  • normalisedAcquisitionTime()
  • normalisedDate()
• funpack.processing
  • The processing table
  • Broadcasting arguments
  • processData()
  • retrieveProcess()
  • runParallelProcess()
  • runProcess()
  • unpackResults()
• funpack.processing_functions
  • binariseCategorical()
  • createDiagnosisColumns()
  • expandCompound()
  • removeField()
  • removeIfRedundant()
  • removeIfSparse()
• funpack.processing_functions_core
  • binariseCategorical()
  • expandCompound()
  • generateBinaryColumns()
  • isSparse()
  • matrixRedundantColumns()
  • naCorrelation()
  • pairwiseRedundantColumns()
• funpack.schema
  • DOWNLOAD
  • NEVER_DOWNLOAD
  • codingFileUrl()
  • downloadFile()
  • encodingUrl()
  • fieldUrl()
  • loadEnodingDictionaries()
  • loadFieldProperties()
  • shouldDownload()
• funpack.schema.coding
  • getCoding()
  • getCodingFilePath()
  • loadCodingFile()
• funpack.schema.hierarchy
  • CircularError
  • HIERARCHY_DATA_NAMES
  • Hierarchy
    • Hierarchy.coding()
    • Hierarchy.codings
    • Hierarchy.description()
    • Hierarchy.get()
    • Hierarchy.index()
    • Hierarchy.parentIDs()
    • Hierarchy.parents()
    • Hierarchy.set()
  • Node
    • Node.attrs
    • Node.coding
    • Node.node_id
    • Node.parent_id
  • codeToNumeric()
  • dataCodingType()
  • getHierarchyCoding()
  • getHierarchyFilePath()
  • loadEncodingTable()
  • loadHierarchyFile()
  • numericToCode()
• funpack.scripts.demo
  • create_funpack_entrypoint()
  • main()
• funpack.util
  • CTYPES
    • CTYPES.categorical_multiple
    • CTYPES.categorical_multiple_non_numeric
    • CTYPES.categorical_single
    • CTYPES.categorical_single_non_numeric
    • CTYPES.compound
    • CTYPES.continuous
    • CTYPES.date
    • CTYPES.integer
    • CTYPES.sequence
    • CTYPES.text
    • CTYPES.time
    • CTYPES.unknown
  • DATA_TYPES
  • Singleton
    • Singleton.instance()
    • Singleton.setInstance()
  • cat()
  • dedup()
  • deprecated()
  • findConfigDir()
  • findConfigDirs()
  • findConfigFile()
  • findPluginFile()
  • findTableFile()
  • generateColumnName()
  • inMainProcess()
  • isna()
  • logIfError()
  • parseColumnName()
  • parseMatlabRange()
  • tempdir()
  • timed()
  • wc()