prepareBRData: Create data object based on era tables

In sverchkov/BaselineRegularization: Baseline Regularization

Description

Creates the data object for running Baseline Regularization

Usage

prepareBRData(con = NULL, observation_period = "observation_period",
  drug_era = "drug_era", condition_era = "condition_era",
  drug_exposure = "drug_exposure",
  condition_occurrence = "condition_occurrence",
  visit_occurrence = "visit_occurrence", response_event,
  tying = "occurrence", risk_window = 0L, minimum_duration = 0L,
  drug_concept_processor = passthroughConceptProcessor,
  condition_concept_processor = passthroughConceptProcessor)

Arguments

con	A DBI Connection to an OMOP CDM database used if the OMOP tables are provided as table names.
observation_period	Either the name of the 'observation_period' table in the database specified by 'con' or the table itself in a dataframe-like R object. If this is specified it defines the observation periods; if it is not, the observation periods are inferred from the other tables in the data, assuming one all-encompassing observation period per patient.
drug_era	A dataframe-like view or the table name of the OMOP DRUG_ERA table
condition_era	A dataframe-like view or the table name of the OMOP CONDITION_ERA table
drug_exposure	Either the name of the 'drug_exposure' table in the database specified by 'con' or the table itself in a dataframe-like R object
condition_occurrence	Either the name of the 'condition_occurrence' table in the database specified by 'con' or the table itself in a dataframe-like R object
visit_occurrence	(optional) Either the name of the 'visit_occurrence' table in the database specified by 'con' or the table itself in a dataframe-like R object, only used to infer observation periods if needed.
response_event	The condition_concept_id of the condition of interest
tying	Parameter tying mode, "interval", or "occurence" (default)
risk_window	The number of days right after a drug era during which the patient is considered still under exposure.
minimum_duration	The number of days a patient must be under observation to be included in the analysis.
drug_concept_processor	A processor function for drug concepts
condition_concept_processor	A processor function for conditions

Value

An object containing the matrices X, Z, y

Author(s)

Yuriy Sverchkov

sverchkov/BaselineRegularization documentation built on May 9, 2019, 1:26 p.m.