Load source_to_concept_map table from Usagi mapping Files. — load_source_to_concept

This function loads the source_to_concept_map table using the mapping files created with the OHDSI Usagi (https://github.com/OHDSI/Usagi) application.

Usage

load_source_to_concept_map()

Details

This function requires a configured config.yaml file created using amstel::create_config(). It will use the connection configuration specified in the cdm section to load the source_to_concept tables in the CDM by reading the Usagi csv files in the mappings folder.

This function assumes amstel::create_cdm_tables() and amstel::load_vocabulary_tables() have already been run.

Examples

stcm <- load_source_to_concept_map()
#> Loading source_to_concept_map table...
#> Connecting using PostgreSQL driver
#> Deleting all records from table: source_to_concept_map
#> Executing SQL took 0.0345 secs
#> Reading vocabulary_id from concept vocabulary...
#> Processing Usagi mapping files...
#> - admissions_gender
#>   * 'AUMC Gender' for MAPS_TO mapping
#> - admissions_origin
#>   * 'AUMC Origin' for MAPS_TO mapping
#> - admissions_destination
#>   * 'AUMC Destination' for MAPS_TO mapping
#> - admissions_specialty
#>   * 'AUMC Specialty' for MAPS_TO mapping
#> - drugitems_administeredunit
#>   * 'AUMC Unit' for MAPS_TO mapping
#> - drugitems_item
#>   * 'AUMC Drug' for MAPS_TO mapping
#>   * 'AUMC Drug Route' for MAPS_TO_TYPE mapping
#> - drugitems_ordercategory
#>   * 'AUMC Route' for MAPS_TO mapping
#> - freetextitems_item
#>   * 'AUMC Text' for MAPS_TO mapping
#> - freetextitems_value
#>   * 'AUMC Text Value' for MAPS_TO mapping
#> - listitems_item
#>   * 'AUMC List' for MAPS_TO mapping
#>   * 'AUMC Qualifier' for MAPS_TO_TYPE mapping
#> - listitems_meas_value
#>   * 'AUMC Meas Value' for MAPS_TO mapping
#>   * 'AUMC List Unit' for MAPS_TO_UNIT mapping
#> - listitems_obs_value
#>   * 'AUMC Obs Value' for MAPS_TO mapping
#>   * 'AUMC List Unit' for MAPS_TO_UNIT mapping
#>   * 'AUMC Qualifier' for MAPS_TO_TYPE mapping
#> - listitems_device
#>   * 'AUMC Device' for MAPS_TO mapping
#> - listitems_procedure
#>   * 'AUMC Procedure' for MAPS_TO mapping
#> - listitems_condition
#>   * 'AUMC Condition' for MAPS_TO mapping
#> - numericitems_lab
#>   * 'AUMC Laboratory' for MAPS_TO mapping
#>   * 'AUMC Numeric Unit' for MAPS_TO_UNIT mapping
#> - numericitems_other
#>   * 'AUMC Numeric' for MAPS_TO mapping
#>   * 'AUMC Numeric Unit' for MAPS_TO_UNIT mapping
#> - numericitems_tag
#>   * 'AUMC Tag' for MAPS_TO mapping
#> - numericitems_unit
#>   * 'AUMC Unit' for MAPS_TO mapping
#> - procedureorderitems_item
#>   * 'AUMC Procedure Order' for MAPS_TO mapping
#>   * 'AUMC Qualifier' for MAPS_TO_TYPE mapping
#> - processitems_item
#>   * 'AUMC Process' for MAPS_TO mapping
#>   * 'AUMC Anatomic Site' for MAPS_TO_VALUE mapping
#> - providers
#>   * 'AUMC Provider' for MAPS_TO mapping
#> - reason_for_admission
#>   * 'AUMC Diagnosis' for MAPS_TO mapping
#> - specimen_source
#>   * 'AUMC Specimen Source' for MAPS_TO mapping
#> Saving source_to_concept_map.csv in mappings folder...
#> Loading mapping records into table: source_to_concept_map
#> Inserting data took 1.73 secs
#> Loading source_to_value_map table...
#> Connecting using PostgreSQL driver
#> Deleting source_to_value_map table: source_to_value_map
#> Executing SQL took 0.0235 secs
#> Creating source_to_value_map table: source_to_value_map
#> Executing SQL took 0.0112 secs
#> Loading mapping records into table: source_to_value_map
#> Inserting data took 0.0261 secs
#> Success: source_to_value_map loaded.
#> Success: source_to_concept_map loaded.
stcm
#> # A tibble: 9,907 × 9
#>    source_code     source_concept_id source_vocabulary_id source_code_descript…¹
#>    <chr>                       <dbl> <chr>                <chr>                 
#>  1 Vrouw                           0 AUMC Gender          Vrouw                 
#>  2 Man                             0 AUMC Gender          Man                   
#>  3 Huis                            0 AUMC Origin          Huis                  
#>  4 CCU/IC zelfde …                 0 AUMC Origin          CCU/IC zelfde ziekenh…
#>  5 Eerste Hulp af…                 0 AUMC Origin          Eerste Hulp afdeling …
#>  6 Recovery ander…                 0 AUMC Origin          Recovery ander zieken…
#>  7 Eerste Hulp af…                 0 AUMC Origin          Eerste Hulp afdeling …
#>  8 Operatiekamer …                 0 AUMC Origin          Operatiekamer vanaf v…
#>  9 Special/Medium…                 0 AUMC Origin          Special/Medium care a…
#> 10 Operatiekamer …                 0 AUMC Origin          Operatiekamer vanaf E…
#> # ℹ 9,897 more rows
#> # ℹ abbreviated name: ¹source_code_description
#> # ℹ 5 more variables: target_concept_id <dbl>, target_vocabulary_id <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <lgl>