Calculate summary statistics

[milanmlft]

Definition of done

Script that can be run taking an input OMOP dataset and producing summary statistics that will be used in the dashboard (uploading these to a different schema)

For now

• monthly counts
• for numeric data- mean and standard deviation (without any time filtering)
• ignore categorical variables for now

Testing

Using in memory databases, parse example dataset, have tests for a subset of this output to ensure that the statistics are being calculated as expected

• test using one of the synthae datasets available from CDMConnector
• have a final summarised dataset against which we test the script, could potentially also be used for SAF-611

Dependencies

Details

Suggested structure for tables:

• concept ID, concept type (e.g. observation), concept name, vocabulary
• concept_id, date (10th day of month per year), patient count, readings per patient
• concept id, summary_attribute (e.g. mean/sd for numeric or categorical variable 1/categorical variable 2…), value_as_string (if categorical, use readable name with ID in brackets), value_as_double

[linear]

SAF-590 Calculate summary statistics depending on data type

[linear]

SAF-591 Calculate summary statistics depending on data type

[milanmlft]

Closed by #22