Add function to generate table of descriptive statistics

[AshlinHarris]

Input: a concept group c

Output:

• A table with columns for individuals in c, individuals outside c, unmatched, and total (number and percentage)
• Rows with totals and breakdowns (sex, age in 5 year bins)

[AshlinHarris]

The function should be run on

• the entire data set
• Covid positive individuals
• vaccinated individuals, broken down by vaccine type

What if individuals have received more than one vaccine type?

[AshlinHarris]

Quote from https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:gender:

The Gender domain captures all concepts about the sex of a person, denoting the biological and physiological characteristics. In fact, the Domain (and field in the PERSON table) should probably should be called “sex” rather than “gender”, as gender refers to behaviors, roles, expectations, and activities in society.

The domain contains only two standard concepts: FEMALE (concept_id=8532) and MALE (concept_id=8507). Many data sources contain other codes, such as “Unknown”, “Refused to tell”, “Hermaphrodite”, as well as transgender constellations (“male to female”, etc.). For the current purposes of the OMOP CDM, the gender concepts are used to stratify patients by their biological make-up or to adjust analytical results for the influence of the biological sex. Therefore, all those other genders are denoted as concept_id=0 (unknown information).

Quote from https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:ethnicity:

The race field contains races and ethnic backgrounds, while for Ethnicity there are only two categories for data on ethnicity: “Hispanic or Latino” (concept_id=38003563) and “Not Hispanic or Latino” (concept_id=38003564). This means, the two categories are orthogonal to each other, and both Latinos and non-Latinos can have any racial or ethnic background.

This is a very US-centric solution, and hence the terminology might be confusing to non-US data owners. If belong to the latter group, you can probably ignore this field entirely.

There are no relationships defined for Ethnicity.

Relevant data fields:

• :ETHNICITY_CONCEPT_ID
  • "Hispanic or Latino": 38003563
  • "Not Hispanic or Latino": 38003564
• :GENDER_CONCEPT_SOURCE
  • Female: 8532
  • Male: 8507
  • Other or Unknown: 0
• :YEAR_OF_BIRTH
• :DRUG_CONCEPT_ID
  • Johnson & Johnson: 739906
  • Pfizer: 37003436
  • Moderna: 37003518

Identifying COVID-positive individuals requires a concept set. How should concept sets be handled in general?