Index

A

add() (funpack.parsing.value_expression.ValueExpression method) addAuxillaryVariables() (in module funpack.importing.filter) addColumns() (funpack.datatable.DataTable method) addFlag() (funpack.datatable.DataTable method) addImplicitCategories() (in module funpack.loadtables) addNewVariable() (in module funpack.loadtables) allColumns (funpack.datatable.DataTable property) (funpack.fileinfo.FileInfo property) allVariables (funpack.fileinfo.FileInfo property)

applyChildValues() (in module funpack.cleaning) applyCleaningFunctions() (in module funpack.cleaning) applyNAInsertion() (in module funpack.cleaning) applyNewLevels() (in module funpack.cleaning) args (funpack.parsing.process.Process property) args() (funpack.custom.PluginRegistry method) (in module funpack.custom) attrs (funpack.schema.hierarchy.Node attribute) AUTO_VARIABLE_ID (in module funpack.datatable) auxillaryVariables() (funpack.parsing.process.Process method)

B

binariseCategorical() (in module funpack.processing_functions) (in module funpack.processing_functions_core)

broadcastKwargs (funpack.parsing.process.Process property)

C

calculateVariableExpressionEvaluationOrder() (in module funpack.parsing.variable_expression) cat() (in module funpack.util) categorical_multiple (funpack.util.CTYPES attribute) categorical_multiple_non_numeric (funpack.util.CTYPES attribute) categorical_single (funpack.util.CTYPES attribute) categorical_single_non_numeric (funpack.util.CTYPES attribute) categoryVariables() (in module funpack.loadtables) cattable (funpack.datatable.DataTable property) CATTABLE_COLUMNS (in module funpack.loadtables) CATTABLE_CONVERTERS (in module funpack.loadtables) CATTABLE_DTYPES (in module funpack.loadtables) CircularError cleanData() (in module funpack.cleaning) cleaner() (in module funpack.custom) clearRegistry() (funpack.custom.PluginRegistry method) (in module funpack.custom) codeToNumeric() (in module funpack.cleaning_functions) (in module funpack.schema.hierarchy) coding (funpack.schema.hierarchy.Node attribute) coding() (funpack.schema.hierarchy.Hierarchy method) codingDescriptionFromValue() (in module funpack.metaproc_functions) codingFileUrl() (in module funpack.schema)

codings (funpack.schema.hierarchy.Hierarchy property) coerceToNumeric() (in module funpack.importing.core) Column (class in funpack.datatable) columns() (funpack.datatable.DataTable method) (funpack.fileinfo.FileInfo method) columns_FMRIBImaging() (in module funpack.plugins.fmrib) columnsToLoad() (in module funpack.importing.filter) columnTypes() (in module funpack.loadtables) compound (funpack.util.CTYPES attribute) configLogging() (in module funpack.main) continuous (funpack.util.CTYPES attribute) convert_category_variables() (in module funpack.loadtables) convert_comma_sep_numbers() (in module funpack.loadtables) convert_comma_sep_text() (in module funpack.loadtables) convert_dtype() (in module funpack.loadtables) convert_ParentValues() (in module funpack.loadtables) convert_Process() (in module funpack.loadtables) convert_Process_Variable() (in module funpack.loadtables) convert_type() (in module funpack.loadtables) create_funpack_entrypoint() (in module funpack.scripts.demo) createDiagnosisColumns() (in module funpack.processing_functions) CTYPES (class in funpack.util)

D

DATA_TYPES (in module funpack.util) dataCodingType() (in module funpack.schema.hierarchy) dataColumns (funpack.datatable.DataTable property) datafiles (funpack.fileinfo.FileInfo property) DataTable (class in funpack.datatable) date (funpack.util.CTYPES attribute) DCTABLE_COLUMNS (in module funpack.loadtables) DCTABLE_DTYPES (in module funpack.loadtables) dedup() (in module funpack.util) defaultDateTimeFormat() (in module funpack.exporting) deprecated() (in module funpack.util) description() (funpack.schema.hierarchy.Hierarchy method)

dialect() (funpack.fileinfo.FileInfo method) div() (funpack.parsing.value_expression.ValueExpression method) doCleanAndProcess() (in module funpack.main) doDescriptionExport() (in module funpack.main) doDryRun() (in module funpack.dryrun) doExport() (in module funpack.main) doICD10Export() (in module funpack.main) doImport() (in module funpack.main) doSummaryExport() (in module funpack.main) doUnknownsExport() (in module funpack.main) DOWNLOAD (in module funpack.schema) downloadFile() (in module funpack.schema)

E

encoding() (funpack.fileinfo.FileInfo method) encodingUrl() (in module funpack.schema) escapeString() (in module funpack.exporting) evaluate() (funpack.parsing.variable_expression.VariableExpression method) evaluateSubjectExpression() (in module funpack.importing.filter) evaluateSubjectExpressions() (in module funpack.importing.filter) exists() (funpack.custom.PluginRegistry method) (in module funpack.custom) expandCompound() (in module funpack.processing_functions) (in module funpack.processing_functions_core)

exportCSV() (in module funpack.exporting_tsv) exportData() (in module funpack.exporting) exporter() (in module funpack.custom) exportFunpackStyle() (in module funpack.exporting_hdf5) exportHDF5() (in module funpack.exporting_hdf5) exportPandasStyle() (in module funpack.exporting_hdf5) exportTSV() (in module funpack.exporting_tsv) expression (funpack.parsing.value_expression.ValueExpression property)

F

fieldUrl() (in module funpack.schema) FileInfo (class in funpack.fileinfo) fileinfo() (in module funpack.fileinfo) fillMissing() (in module funpack.cleaning_functions) fillVisits() (in module funpack.cleaning_functions) filterMissing (funpack.parsing.process.Process property) filterSubjects() (in module funpack.importing.filter) findConfigDir() (in module funpack.util) findConfigDirs() (in module funpack.util) findConfigFile() (in module funpack.util) findPluginFile() (in module funpack.util) findTableFile() (in module funpack.util) flattenHierarchical() (in module funpack.cleaning_functions) formatColumn() (in module funpack.exporting) formatCompound() (in module funpack.exporting) formatter() (in module funpack.custom) funpack.cleaning module funpack.cleaning_functions module funpack.config module funpack.custom module funpack.datatable module funpack.dryrun module funpack.exporting module funpack.exporting_hdf5 module funpack.exporting_tsv module funpack.fileinfo module funpack.icd10 module

funpack.importing.core module funpack.importing.filter module funpack.importing.reindex module funpack.loadtables module funpack.main module funpack.merging module funpack.metaproc_functions module funpack.parsing.process module funpack.parsing.value_expression module funpack.parsing.variable_expression module funpack.plugins.fmrib module funpack.processing module funpack.processing_functions module funpack.processing_functions_core module funpack.schema module funpack.schema.coding module funpack.schema.hierarchy module funpack.scripts.demo module funpack.util module

G

generateBinaryColumns() (in module funpack.processing_functions_core) generateColumnName() (in module funpack.util) generateDescription() (in module funpack.main) genReindexedColumns() (in module funpack.importing.reindex) get() (funpack.custom.PluginRegistry method) (funpack.schema.hierarchy.Hierarchy method) (in module funpack.custom)

getCoding() (in module funpack.schema.coding) getCodingFilePath() (in module funpack.schema.coding) getFlags() (funpack.datatable.DataTable method) getHierarchyCoding() (in module funpack.schema.hierarchy) getHierarchyFilePath() (in module funpack.schema.hierarchy)

H

has_header() (in module funpack.fileinfo) HDF5_KEY (in module funpack.exporting_hdf5) HDF5_STYLE (in module funpack.exporting_hdf5) HDF5_STYLES (in module funpack.exporting_hdf5)

header() (funpack.fileinfo.FileInfo method) hierarchicalDescriptionFromCode() (in module funpack.metaproc_functions) hierarchicalDescriptionFromNumeric() (in module funpack.metaproc_functions) Hierarchy (class in funpack.schema.hierarchy) HIERARCHY_DATA_NAMES (in module funpack.schema.hierarchy)

I

identifyUncategorisedVariables() (in module funpack.loadtables) IMPLICIT_CATEGORIES (in module funpack.loadtables) importData() (in module funpack.importing.core) importFunpackStyle() (in module funpack.exporting_hdf5) index (funpack.datatable.DataTable property) index() (funpack.fileinfo.FileInfo method) (funpack.schema.hierarchy.Hierarchy method) indexColumns (funpack.datatable.DataTable property)

initialise() (in module funpack.icd10) inMainProcess() (in module funpack.util) instance() (funpack.util.Singleton class method) instances() (funpack.datatable.DataTable method) integer (funpack.util.CTYPES attribute) isna() (in module funpack.util) isSparse() (in module funpack.processing_functions_core) isSubtable (funpack.datatable.DataTable property)

K

keepVisits() (in module funpack.cleaning_functions)

kwargs (funpack.parsing.process.Process property)

L

listPlugins() (funpack.custom.PluginRegistry method) (in module funpack.custom) Literal (in module funpack.parsing.value_expression) load_FMRIBImaging() (in module funpack.plugins.fmrib) loadCategoryTable() (in module funpack.loadtables) loadChunk() (in module funpack.importing.core) loadCodingFile() (in module funpack.schema.coding) loadConfigFile() (in module funpack.config) loadEncodingTable() (in module funpack.schema.hierarchy) loadEnodingDictionaries() (in module funpack.schema) loader() (funpack.fileinfo.FileInfo method) (in module funpack.custom)

loadFieldProperties() (in module funpack.schema) loadFile() (in module funpack.importing.core) loadFiles() (in module funpack.importing.core) loadHierarchyFile() (in module funpack.schema.hierarchy) loadPluginFile() (funpack.custom.PluginRegistry method) (in module funpack.custom) loadProcessingTable() (in module funpack.loadtables) loadTableBases() (in module funpack.loadtables) loadTables() (in module funpack.loadtables) loadVariableTable() (in module funpack.loadtables) logIfError() (in module funpack.util)

M

main() (in module funpack.main) (in module funpack.scripts.demo) makeEpilog() (in module funpack.config) makeNa() (in module funpack.cleaning_functions) makeParser() (in module funpack.config) (in module funpack.parsing.variable_expression) makeProcessParser() (in module funpack.parsing.process) makeValueExpressionParser() (in module funpack.parsing.value_expression) manager (funpack.datatable.DataTable property) maskSubjects() (funpack.datatable.DataTable method) matrixRedundantColumns() (in module funpack.processing_functions_core) max() (funpack.parsing.value_expression.ValueExpression method) merge() (funpack.datatable.DataTable method) MERGE_AXIS (in module funpack.importing.core) MERGE_AXIS_OPTIONS (in module funpack.importing.core) MERGE_STRATEGY (in module funpack.importing.core) MERGE_STRATEGY_OPTIONS (in module funpack.importing.core) mergeCleanFunctions() (in module funpack.loadtables) mergeDataCodingTable() (in module funpack.loadtables) mergeDataFrames() (in module funpack.merging) mergeIntoVariableTable() (in module funpack.loadtables) mergeTableFiles() (in module funpack.loadtables) metaproc() (in module funpack.custom) min() (funpack.parsing.value_expression.ValueExpression method) MODIFIED_COLUMN (in module funpack.datatable) module funpack.cleaning funpack.cleaning_functions funpack.config funpack.custom funpack.datatable funpack.dryrun funpack.exporting funpack.exporting_hdf5 funpack.exporting_tsv funpack.fileinfo funpack.icd10 funpack.importing.core funpack.importing.filter funpack.importing.reindex funpack.loadtables funpack.main funpack.merging funpack.metaproc_functions funpack.parsing.process funpack.parsing.value_expression funpack.parsing.variable_expression funpack.plugins.fmrib funpack.processing funpack.processing_functions funpack.processing_functions_core funpack.schema funpack.schema.coding funpack.schema.hierarchy funpack.scripts.demo funpack.util

mul() (funpack.parsing.value_expression.ValueExpression method)

N

naCorrelation() (in module funpack.processing_functions_core) name (funpack.parsing.process.Process property) NEVER_DOWNLOAD (in module funpack.schema) njobs (funpack.datatable.DataTable property) Node (class in funpack.schema.hierarchy) node_id (funpack.schema.hierarchy.Node attribute)

normalisedAcquisitionTime() (in module funpack.plugins.fmrib) normalisedDate() (in module funpack.plugins.fmrib) NoSuchProcessError NUM_ROWS (in module funpack.exporting_tsv) (in module funpack.importing.core) numericToCode() (in module funpack.schema.hierarchy)

P

pairwiseRedundantColumns() (in module funpack.processing_functions_core) parallel (funpack.datatable.DataTable property) parent_id (funpack.schema.hierarchy.Node attribute) parentIDs() (funpack.schema.hierarchy.Hierarchy method) parents() (funpack.schema.hierarchy.Hierarchy method) parseArgs() (in module funpack.config) parseArgsWithConfigFile() (in module funpack.config) parseBinary() (in module funpack.parsing.variable_expression) parseColumnName() (in module funpack.util) parseCondition() (in module funpack.parsing.variable_expression) parseMatlabRange() (in module funpack.util) parseProcesses() (in module funpack.parsing.process) parseSpirometryData() (in module funpack.cleaning_functions)

parseUnary() (in module funpack.parsing.variable_expression) parseValueExpressions() (in module funpack.parsing.value_expression) parseVariable() (in module funpack.parsing.variable_expression) parseVariableExpression() (in module funpack.parsing.variable_expression) PluginRegistry (class in funpack.custom) pool() (funpack.datatable.DataTable method) present() (funpack.datatable.DataTable method) Process (class in funpack.parsing.process) processData() (in module funpack.processing) processor() (in module funpack.custom) processString (funpack.parsing.process.Process property) proctable (funpack.datatable.DataTable property) PROCTABLE_COLUMNS (in module funpack.loadtables) PROCTABLE_CONVERTERS (in module funpack.loadtables)

R

registerBuiltIns() (in module funpack.custom) registerPlugin() (funpack.custom.PluginRegistry method) (in module funpack.custom) reindexByVisit() (in module funpack.importing.reindex) remove() (in module funpack.cleaning_functions) REMOVE_DUPLICATE_COLUMN_IDENTIFIER (in module funpack.importing.filter) removeColumns() (funpack.datatable.DataTable method) removeField() (in module funpack.processing_functions) removeIfRedundant() (in module funpack.processing_functions) removeIfSparse() (in module funpack.processing_functions) renameDuplicateColumns() (in module funpack.fileinfo) restrictVariables() (in module funpack.importing.filter)

retrieveProcess() (in module funpack.processing) run() (funpack.custom.PluginRegistry method) (funpack.parsing.process.Process method) (in module funpack.custom) runCleaner() (in module funpack.custom) runExporter() (in module funpack.custom) runFormatter() (in module funpack.custom) runLoader() (in module funpack.custom) runMetaproc() (in module funpack.custom) runParallelProcess() (in module funpack.processing) runProcess() (in module funpack.processing) runProcessor() (in module funpack.custom) runSniffer() (in module funpack.custom)

S

sanitiseArgs() (in module funpack.config) sanitiseVariableTable() (in module funpack.loadtables) saveCodes() (in module funpack.icd10) sequence (funpack.util.CTYPES attribute) set() (funpack.schema.hierarchy.Hierarchy method) setInstance() (funpack.util.Singleton class method) shape (funpack.datatable.DataTable property) shouldDownload() (in module funpack.schema)

Singleton (class in funpack.util) sniff() (in module funpack.fileinfo) sniffer() (funpack.fileinfo.FileInfo method) (in module funpack.custom) splitDataTable() (in module funpack.main) storeCodes() (in module funpack.icd10) sub() (funpack.parsing.value_expression.ValueExpression method) subtable() (funpack.datatable.DataTable method) SYMBOLS (in module funpack.parsing.variable_expression)

T

tempdir() (in module funpack.util) text (funpack.util.CTYPES attribute) time (funpack.util.CTYPES attribute) timed() (in module funpack.util)

toNumeric() (in module funpack.icd10) TYPETABLE_COLUMNS (in module funpack.loadtables) TYPETABLE_CONVERTERS (in module funpack.loadtables) TYPETABLE_DTYPES (in module funpack.loadtables)

U

unknown (funpack.util.CTYPES attribute)

unpackResults() (in module funpack.processing)

V

ValueExpression (class in funpack.parsing.value_expression) variableCategories() (in module funpack.loadtables) VariableExpression (class in funpack.parsing.variable_expression) VariableMissing variables (funpack.datatable.DataTable property) (funpack.parsing.variable_expression.VariableExpression property)

variablesInExpression() (in module funpack.parsing.variable_expression) vartable (funpack.datatable.DataTable property) VARTABLE_COLUMNS (in module funpack.loadtables) VARTABLE_CONVERTERS (in module funpack.loadtables) VARTABLE_DTYPES (in module funpack.loadtables) visits() (funpack.datatable.DataTable method)

W

wc() (in module funpack.util)

writeDataFrame() (in module funpack.exporting_tsv)