performTemporalCharacterization

performTemporalCharacterization Perform temporal characterization on a concept or family of concepts belonging to a supported Achilles analysis.

performTemporalCharacterization(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  analysisIds = NULL,
  conceptId = NULL,
  outputFile = "temporal-characterization.csv"
)

Arguments

connectionDetails

An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.

cdmDatabaseSchema

Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.

resultsDatabaseSchema

Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.

analysisIds

(OPTIONAL) A vector containing the set of Achilles analysisIds for which results will be returned. The following are supported: 202,402,602,702,802,1802,2102. If not specified, data for all analysis will be returned. Ignored if conceptId is given.

conceptId

(OPTIONAL) A SNOMED concept_id from the CONCEPT table for which a monthly Achilles analysis exists. If not specified, all concepts for a given analysis will be returned.

outputFile

CSV file where temporal characterization will be written. Default is temporal-characterization.csv.

Value

A csv file with temporal analyses for each time series

Details

performTemporalAnalyses Assumes achilles has been run.

Currently supported Achilles analyses for temporal analyses are:
202  - Visit Occurrence
402  - Condition occurrence
602  - Procedure Occurrence
702  - Drug Exposure
802  - Observation
1802 - Measurement
2102 - Device

Examples

if (FALSE) {
# Example 1:
pneumonia <- 255848
performTemporalCharacterization(
  connectionDetails     = connectionDetails,
  cdmDatabaseSchema     = "cdm",
  resultsDatabaseSchema = "results",
  conceptId             = pneumonia,
 outputFolder          = "output/pneumoniaTemporalChar.csv")

# Example 2:
performTemporalCharacterization(
  connectionDetails     = connectionDetails,
  cdmDatabaseSchema     = "cdm",
  resultsDatabaseSchema = "results",
  analysisIds           = c(402,702),
 outputFolder          = "output/conditionAndDrugTemporalChar.csv")

# Example 3:
performTemporalCharacterization(
  connectionDetails     = connectionDetails,
  cdmDatabaseSchema     = "cdm",
  resultsDatabaseSchema = "results",
 outputFolder          = "output/CompleteTemporalChar.csv")
}