instantiate_standard_library: Creating the Target Standard Library from OMOP Concepts

In meerapatelmd/amphora: Manipulate Clinical Ontologies

Description

Filter the current OMOP vocabulary for the elements most relevant to the RWD domain.

Usage

instantiate_standard_library(
  conn,
  standard_library_schema,
  verbose = TRUE,
  render_sql = TRUE,
  render_only = FALSE
)

Arguments

conn	PARAM_DESCRIPTION
standard_library_schema	PARAM_DESCRIPTION
verbose	PARAM_DESCRIPTION, Default: TRUE
render_sql	PARAM_DESCRIPTION, Default: TRUE
render_only	PARAM_DESCRIPTION, Default: FALSE

Details

1. Identify a valid Concept in the vocabulary schema. A hash will be created for concepts that do not presently exist.

2. Provide the class it belongs to. If the Class does not currently exist, it will be made and added to the Concept table.

3. Copy the Concept to the Standard Library.

4. Add the "Has concept" relationship to the Class

5. Add that "Concept of" relationship to the Concept

Value

OUTPUT_DESCRIPTION

See Also

schema_exists,create_schema,send render typewrite

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

meerapatelmd/amphora documentation built on Feb. 5, 2021, 12:53 a.m.