createVocabTable: Write the Vocabulary Table

In meerapatelmd/OncoRegimenFinder: Derive Oncology Treatment Regimens from the OMOP CDM

Description

The Vocabulary Table takes all the HemOnc Regimens in the OMOP Concept Table, maps the RxNorm Ingredients that comprise each Regimen, and calculates the number of unique ingredients per Regimen in an ingredient_count field and a string aggregate ingredient_combination. The ingredient_combination field combines the names of all the ingredients in a comma-separated string when the ingredient_count is greater than 2, an "and" concatenation when the ingredient_count is 2, or simply the ingredient name when ingredient_count is 1. Since a set of RxNorm Ingredients can map to more than 1 HemOnc Regimen, the table also is filtered for the shortest ingredient_combination string by character count by the concept id of the regimen, excluding abbreviations assumed to be of character counts of 5 or less.

Usage

createVocabTable(
  conn,
  writeDatabaseSchema,
  cdmDatabaseSchema,
  vocabularyTable,
  renameTable
)

Arguments

conn	PARAM_DESCRIPTION
writeDatabaseSchema	PARAM_DESCRIPTION
cdmDatabaseSchema	PARAM_DESCRIPTION
vocabularyTable	PARAM_DESCRIPTION

Value

A Vocabulary Table in the designated schema.

See Also

lsTables,appendDate,renameTable,dropTable,execute,readTable,writeTable render,readSql press_enter group_by,summarise,arrange,rename,mutate-joins,mutate,select group_by_unique_aggregate,arrange_by_nchar str_replace fct_collapse

meerapatelmd/OncoRegimenFinder documentation built on Jan. 1, 2021, 9:25 a.m.