Package index • codeminer

Clinical codes

Functions for looking up clinical codes and mapping between different coding systems.

DESCRIPTION(): Search for codes that match a description
CODES() CODES_LIKE(): Look up descriptions for clinical codes
CHILDREN() PARENTS() N_CHILDREN() N_PARENTS(): Retrieve parent or child codes
ATTRIBUTES_FOR() HAS_ATTRIBUTES(): Get attributes or codes with attributes
RELATIONSHIP_TYPES_FROM() RELATIONSHIP_TYPES_TO(): Get relationship types for codes
MAP(): Map clinical codes from one coding system to another
get_lookup_table(): Get the full lookup table for a code type
get_mapping_table(): Get the full mapping table for a pair of code types
get_relationship_table(): Get the full relationship table for a code type
default_col_filters(): Default column filters
get_col_filters(): Extract column filters from database metadata

Workbench management

Connect to and manage the codeminer workbench (persistent DuckDB connection).

codeminer_connect(): Connect to the codeminer workbench
codeminer_disconnect(): Disconnect the codeminer workbench
codeminer_status(): Show workbench status
codeminer_refresh_cache(): Refresh the metadata cache
codeminer_set_version(): Pin table versions for the session
codeminer_clear_versions(): Clear active version selections
codeminer_set_col_filters(): Pin column filters for the session
codeminer_clear_col_filters(): Clear all pinned column filters
with_col_filters(): Temporarily override column filters
codeminer_snapshot_extra(): Create a snapshot of the extra database

Database management

Build a local database with lookup and mapping tables for various clinical coding systems.

get_ukb_resource_592(): Get UK Biobank resource 592 directly from UK Biobank website
read_ukb_resource_592(): Read UK Biobank Resource 592 clinical code mappings
add_ukb_resource_592(): Add UK Biobank Resource 592 tables to CodeMiner database
get_snomed_ct_uk_monolith(): Get SNOMED CT UK Monolith Edition from NHS TRUD
read_snomed_ct_uk_monolith(): Read the SNOMED CT UK Monolith Edition into R
add_snomed_ct_uk_monolith(): Add SNOMED CT UK Monolith tables to CodeMiner database
get_ukb_codings(): Download the UK Biobank codings file
read_ukb_codings(): Read UK Biobank codings file into lookup tables
add_ukb_codings(): Add UK Biobank codings tables to CodeMiner database
get_phecode(): Download Phecode 1.2 files
read_phecode(): Read Phecode 1.2 files into lookup and mapping tables
add_phecode(): Add Phecode 1.2 tables to CodeMiner database
get_nhsbsa_bnf_snomed(): Download the NHSBSA BNF-SNOMED mapping file
read_nhsbsa_bnf_snomed(): Read the NHSBSA BNF-SNOMED mapping file into a mapping table
add_nhsbsa_bnf_snomed(): Add NHSBSA BNF-SNOMED mapping table to CodeMiner database
get_nhs_data_migration(): Get NHS Data Migration mapping tables from NHS TRUD
read_nhs_data_migration(): Read NHS Data Migration mapping tables into R
add_nhs_data_migration(): Add NHS Data Migration mapping tables to CodeMiner database
get_icd10_trud(): Get ICD-10 coding system files from NHS TRUD
read_icd10_trud(): Read ICD-10 coding files into R
add_icd10_trud(): Add ICD-10 lookup table to CodeMiner database
get_opcs4_trud(): Get OPCS-4 coding system files from NHS TRUD
read_opcs4_trud(): Read OPCS-4 coding files into R
add_opcs4_trud(): Add OPCS-4 lookup table to CodeMiner database
get_read3_trud(): Get Read 3 (CTV3) coding system files from NHS TRUD
read_read3_trud(): Read Read 3 (CTV3) coding files into R
add_read3_trud(): Add Read 3 (CTV3) tables to CodeMiner database
get_read2_trud(): Get Read 2 coding system files from NHS TRUD
read_read2_trud(): Read Read 2 coding files into R
add_read2_trud(): Add Read 2 tables to CodeMiner database
build_database(): Build the Codeminer database
dummy_ukb_resource_592_path(): Get path to dummy UK Biobank Resource 592 file
create_dummy_database(): Create a dummy database
add_lookup_table(): Add a lookup table to the database
remove_lookup_table(): Remove a lookup table from the database
lookup_metadata(): Create lookup metadata
update_lookup_metadata(): Update lookup table metadata
add_mapping_table(): Add a mapping table to the database
remove_mapping_table(): Remove a mapping table from the database
mapping_metadata(): Create mapping metadata
update_mapping_metadata(): Update mapping table metadata
add_relationship_table(): Add a relationship table to the database
remove_relationship_table(): Remove a relationship table from the database
relationship_metadata(): Create relationship metadata
update_relationship_metadata(): Update relationship table metadata
get_codeminer_metadata(): Get codeminer metadata

Dummy data

Dummy data for tests.

read_icd10_phecode_map_dummy(): Read dummy Phecode Map 1.2 with ICD-10 codes (beta) file into R
read_phecode_lkp_dummy(): Read dummy Phecode definitions file into R
read_ukb_codings_dummy(): Read dummy UK Biobank codings into R
dummy_clinical_events_tidy(): Dummy UK Biobank clinical events, tidied
dummy_icd10_phecode_map_path(): Dummy Phecode Map 1.2 with ICD-10 codes (beta) file path
dummy_phecode_lkp_path(): Dummy Phecode definitions file path
dummy_snomed_ct_uk_monolith_path(): Get full path to the dummy SNOMED CT GPS RF2 files
dummy_ukb_codings_path(): Dummy UK Biobank codings file path
dummy_ukb_resource_592_path(): Get path to dummy UK Biobank Resource 592 file
example_ontology: Example ontology data

Utilities

Miscellaneous utility functions.

`%AND%` `%OR%` `%NOT%`: Infix set operations
with_type() icd10() icd9() read3() read2() sct() opcs4() phecode() read2_drugs() bnf() dmd() data_coding_3() data_coding_4() data_coding_5() data_coding_6(): Set code type context
collect_codes_input(): Collect and validate codes input from ... argument