calculateMappingStatus

Calculates the mapping status for code counts in different databases and vocabularies.

Usage

calculateMappingStatus(
  pathToCodeCountsFolder,
  connectionDetails,
  vocabularyDatabaseSchema,
  includeCountForAllDatabases = TRUE,
  skipValidation = TRUE
)

Arguments

pathToCodeCountsFolder

The path to the vocabularies coverage file.

connectionDetails

The connection details for the OMOP tables.

vocabularyDatabaseSchema

The database schema for the OMOP vocabulary.

includeCountForAllDatabases

Logical value indicating whether to include code counts for all databases (default is TRUE).

skipValidation

Logical value indicating whether to skip validation of the input parameters (default is TRUE).

Value

A list containing two tables: concepts_to_match and code_counts_matched, representing the mapping status for code counts.

Details

This function calculates the mapping status for code counts in different databases and vocabularies. The calculation involves the following steps:

1. Validating the input parameters to ensure they meet the required format.

2. Reading and validating the provided vocabularies coverage file.

3. Creating a table called concepts_to_match that collects concepts in OMOP with mapping relationships and synonyms.

4. Creating a table called all_code_counts that contains all code counts in the vocabularies coverage, optionally ignoring databases with failed rules.

5. Creating a new database called "all_databases" with normalized event counts across all databases.

6. Calculating the percentage of codes per database and vocabulary.

7. Calculating the mapping status for code counts based on whether they have mappings and codes.

8. Returning the mapping status information in the form of two tables: concepts_to_match and code_counts_matched.