Returns metadata about the lookup, mapping, and relationship tables in the codeminer database.
Usage
get_codeminer_metadata(
type = c("lookup", "mapping", "relationship"),
con = NULL
)Value
If a single type is requested, a data frame. If multiple types are requested, a named list of data frames.
Examples
create_dummy_database()
#> ✔ Dummy database ready to use!
#> ℹ To reconnect to your previous database:
#> `Sys.setenv(CODEMINER_DB_PATH = "/tmp/Rtmp7fg0Bd/file1c7d62102137.duckdb")`
#> `codeminer_connect()`
get_codeminer_metadata()
#> $lookup
#> lookup_table_name code_type lookup_version lookup_code_col
#> 1 BNF_UKB v4 BNF UKB v4 BNF_Code
#> 2 DM+D_UKB v4 DM+D UKB v4 concept_id
#> 3 ICD-9_UKB v4 ICD-9 UKB v4 ICD9
#> 4 ICD-10_UKB v4 ICD-10 UKB v4 ALT_CODE
#> 5 Read 2_UKB v4 Read 2 UKB v4 read_code
#> 6 Read 2, drugs_UKB v4 Read 2, drugs UKB v4 read_code
#> 7 Read 3_UKB v4 Read 3 UKB v4 read_code
#> lookup_description_col lookup_source
#> 1 Description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 2 term https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 3 DESCRIPTION_ICD9 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 4 DESCRIPTION https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 5 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 6 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 7 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> preferred_description_col preferred_description_indicator col_filters
#> 1 <NA> <NA> <NA>
#> 2 <NA> <NA> <NA>
#> 3 <NA> <NA> <NA>
#> 4 <NA> <NA> <NA>
#> 5 term_code 00 <NA>
#> 6 <NA> <NA> <NA>
#> 7 description_type P <NA>
#>
#> $mapping
#> mapping_table_name from_code_type to_code_type map_version from_col
#> 1 ICD-9_ICD-10_UKB v4 ICD-9 ICD-10 UKB v4 ICD9
#> 2 Read 2, drugs_BNF_UKB v4 Read 2, drugs BNF UKB v4 read_code
#> 3 Read 2_ICD-9_UKB v4 Read 2 ICD-9 UKB v4 read_code
#> 4 Read 2_ICD-10_UKB v4 Read 2 ICD-10 UKB v4 read_code
#> 5 Read 2_OPCS4_UKB v4 Read 2 OPCS4 UKB v4 read_code
#> 6 Read 2_Read 3_UKB v4 Read 2 Read 3 UKB v4 READV2_CODE
#> 7 Read 3_ICD-9_UKB v4 Read 3 ICD-9 UKB v4 read_code
#> 8 Read 3_ICD-10_UKB v4 Read 3 ICD-10 UKB v4 read_code
#> 9 Read 3_OPCS4_UKB v4 Read 3 OPCS4 UKB v4 read_code
#> 10 Read 3_Read 2_UKB v4 Read 3 Read 2 UKB v4 READV3_CODE
#> to_col map_source
#> 1 ICD10 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 2 bnf_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 3 icd9_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 4 icd10_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 5 opcs_4.2_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 6 READV3_CODE https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 7 icd9_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 8 icd10_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 9 opcs4_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 10 READV2_CODE https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> col_filters
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 {"icd10_code_def":{"values":["1","15","3","5","7","8","2"],"defaults":["1","15","3","5","7","8"]}}
#> 5 <NA>
#> 6 {"IS_ASSURED":{"values":["1"],"defaults":["1"]}}
#> 7 <NA>
#> 8 {"mapping_status":{"values":["E","G","D","R","A","U"],"defaults":["E","G","D"]},"refine_flag":{"values":["C","P","M"],"defaults":["C","P"]},"element_num":{"values":["0","1","2","3"],"defaults":["0"]},"block_num":{"values":["0","1","2","3","4","5","6","7","8","9","10","11","12","13","14"],"defaults":["0"]}}
#> 9 <NA>
#> 10 {"IS_ASSURED":{"values":["1"],"defaults":["1"]}}
#>
#> $relationship
#> relationship_table_name code_type relationship_version from_col to_col
#> 1 BNF_relationship_UKB v4 BNF UKB v4 from to
#> 2 ICD-9_relationship_UKB v4 ICD-9 UKB v4 from to
#> 3 ICD-10_relationship_UKB v4 ICD-10 UKB v4 from to
#> 4 Read 2_relationship_UKB v4 Read 2 UKB v4 from to
#> type_col child_parent_relationship_code
#> 1 type is a
#> 2 type is a
#> 3 type is a
#> 4 type is a
#> relationship_source col_filters
#> 1 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592 <NA>
#> 2 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592 <NA>
#> 3 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592 <NA>
#> 4 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592 <NA>
#>
get_codeminer_metadata("lookup")
#> lookup_table_name code_type lookup_version lookup_code_col
#> 1 BNF_UKB v4 BNF UKB v4 BNF_Code
#> 2 DM+D_UKB v4 DM+D UKB v4 concept_id
#> 3 ICD-9_UKB v4 ICD-9 UKB v4 ICD9
#> 4 ICD-10_UKB v4 ICD-10 UKB v4 ALT_CODE
#> 5 Read 2_UKB v4 Read 2 UKB v4 read_code
#> 6 Read 2, drugs_UKB v4 Read 2, drugs UKB v4 read_code
#> 7 Read 3_UKB v4 Read 3 UKB v4 read_code
#> lookup_description_col lookup_source
#> 1 Description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 2 term https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 3 DESCRIPTION_ICD9 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 4 DESCRIPTION https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 5 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 6 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 7 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> preferred_description_col preferred_description_indicator col_filters
#> 1 <NA> <NA> <NA>
#> 2 <NA> <NA> <NA>
#> 3 <NA> <NA> <NA>
#> 4 <NA> <NA> <NA>
#> 5 term_code 00 <NA>
#> 6 <NA> <NA> <NA>
#> 7 description_type P <NA>
get_codeminer_metadata(c("lookup", "mapping"))
#> $lookup
#> lookup_table_name code_type lookup_version lookup_code_col
#> 1 BNF_UKB v4 BNF UKB v4 BNF_Code
#> 2 DM+D_UKB v4 DM+D UKB v4 concept_id
#> 3 ICD-9_UKB v4 ICD-9 UKB v4 ICD9
#> 4 ICD-10_UKB v4 ICD-10 UKB v4 ALT_CODE
#> 5 Read 2_UKB v4 Read 2 UKB v4 read_code
#> 6 Read 2, drugs_UKB v4 Read 2, drugs UKB v4 read_code
#> 7 Read 3_UKB v4 Read 3 UKB v4 read_code
#> lookup_description_col lookup_source
#> 1 Description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 2 term https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 3 DESCRIPTION_ICD9 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 4 DESCRIPTION https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 5 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 6 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 7 term_description https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> preferred_description_col preferred_description_indicator col_filters
#> 1 <NA> <NA> <NA>
#> 2 <NA> <NA> <NA>
#> 3 <NA> <NA> <NA>
#> 4 <NA> <NA> <NA>
#> 5 term_code 00 <NA>
#> 6 <NA> <NA> <NA>
#> 7 description_type P <NA>
#>
#> $mapping
#> mapping_table_name from_code_type to_code_type map_version from_col
#> 1 ICD-9_ICD-10_UKB v4 ICD-9 ICD-10 UKB v4 ICD9
#> 2 Read 2, drugs_BNF_UKB v4 Read 2, drugs BNF UKB v4 read_code
#> 3 Read 2_ICD-9_UKB v4 Read 2 ICD-9 UKB v4 read_code
#> 4 Read 2_ICD-10_UKB v4 Read 2 ICD-10 UKB v4 read_code
#> 5 Read 2_OPCS4_UKB v4 Read 2 OPCS4 UKB v4 read_code
#> 6 Read 2_Read 3_UKB v4 Read 2 Read 3 UKB v4 READV2_CODE
#> 7 Read 3_ICD-9_UKB v4 Read 3 ICD-9 UKB v4 read_code
#> 8 Read 3_ICD-10_UKB v4 Read 3 ICD-10 UKB v4 read_code
#> 9 Read 3_OPCS4_UKB v4 Read 3 OPCS4 UKB v4 read_code
#> 10 Read 3_Read 2_UKB v4 Read 3 Read 2 UKB v4 READV3_CODE
#> to_col map_source
#> 1 ICD10 https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 2 bnf_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 3 icd9_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 4 icd10_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 5 opcs_4.2_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 6 READV3_CODE https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 7 icd9_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 8 icd10_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 9 opcs4_code https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> 10 READV2_CODE https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592
#> col_filters
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 {"icd10_code_def":{"values":["1","15","3","5","7","8","2"],"defaults":["1","15","3","5","7","8"]}}
#> 5 <NA>
#> 6 {"IS_ASSURED":{"values":["1"],"defaults":["1"]}}
#> 7 <NA>
#> 8 {"mapping_status":{"values":["E","G","D","R","A","U"],"defaults":["E","G","D"]},"refine_flag":{"values":["C","P","M"],"defaults":["C","P"]},"element_num":{"values":["0","1","2","3"],"defaults":["0"]},"block_num":{"values":["0","1","2","3","4","5","6","7","8","9","10","11","12","13","14"],"defaults":["0"]}}
#> 9 <NA>
#> 10 {"IS_ASSURED":{"values":["1"],"defaults":["1"]}}
#>