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Create a dummy database

Source: R/database-dummy.R
create_dummy_database.Rd

Sets up an example database for codeminer with dummy data and sets the environment variable CODEMINER_DB_PATH. Any subsequent codeminer actions will use this database.

Usage

create_dummy_database(
  db_path = tempfile(fileext = ".duckdb"),
  ...,
  .envir = parent.frame()
)

Arguments

db_path

Path to the database file. Defaults to a temporary file. This is to avoid writing the dummy data to an already existing database.

...

These dots are for future extensions and must be empty.

.envir

Environment in which to set the CODEMINER_DB_PATH variable. Defaults to the calling environment.

Value

The path to the created database file, invisibly.

Examples

# Create dummy database in a temporary location
temp_db <- tempfile(fileext = ".duckdb")
create_dummy_database(temp_db)
#> Creating new database at /tmp/RtmpRK6Py7/file1bd354e6ace.duckdb
#> Reading 17 selected tables from UKB Resource 592
#> 
#> Extending read_v2_drugs_bnf with BNF hierarchy and descriptions
#> Extending read_v2_icd10 by expanding ICD-10 code ranges
#> Adding tables to database
#> ✔ Lookup table BNF_UKB v4 added successfully.
#> ✔ Relationship table BNF_relationship_UKB v4 added successfully.
#> ✔ Lookup table DM+D_UKB v4 added successfully.
#> ✔ Lookup table ICD-9_UKB v4 added successfully.
#> ✔ Relationship table ICD-9_relationship_UKB v4 added successfully.
#> ✔ Lookup table ICD-10_UKB v4 added successfully.
#> ✔ Relationship table ICD-10_relationship_UKB v4 added successfully.
#> ✔ Mapping table ICD-9_ICD-10_UKB v4 added successfully.
#> ✔ Lookup table Read 2_UKB v4 added successfully.
#> ✔ Relationship table Read 2_relationship_UKB v4 added successfully.
#> ✔ Lookup table Read 2, drugs_UKB v4 added successfully.
#> ✔ Mapping table Read 2, drugs_BNF_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 2_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 2_Read 3_UKB v4 added successfully.
#> ✔ Lookup table Read 3_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 3_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 3_Read 2_UKB v4 added successfully.
#> ✔ Dummy database ready to use!

# This also sets the environment variable `CODEMINER_DB_PATH`
Sys.getenv("CODEMINER_DB_PATH")
#> [1] "/tmp/RtmpRK6Py7/file1bd370d34a41.duckdb"