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Extract the outcome cohort counts result

Source: R/CharacterzationQueries.R
getCaseCounts.Rd

This function extracts outcome cohort counts across databases in the results for specified target and outcome cohorts.

Usage

getCaseCounts(
  connectionHandler,
  schema,
  cTablePrefix = "c_",
  cgTablePrefix = "cg_",
  databaseTable = "database_meta_data",
  targetIds = NULL,
  outcomeIds = NULL
)

Arguments

connectionHandler

A connection handler that connects to the database and extracts sql queries. Create a connection handler via `ResultModelManager::ConnectionHandler$new()`.

schema

The result database schema (e.g., 'main' for sqlite)

cTablePrefix

The prefix used for the characterization results tables

cgTablePrefix

The prefix used for the cohort generator results tables

databaseTable

The name of the table with the database details (default 'database_meta_data')

targetIds

A vector of integers corresponding to the target cohort IDs

outcomeIds

A vector of integers corresponding to the outcome cohort IDs

Value

Returns a data.frame with the columns:

  • databaseName the name of the database

  • targetName the target cohort name

  • targetId the target cohort unique identifier

  • outcomeName the outcome name

  • outcomeId the outcome unique identifier

  • rowCount the number of entries in the cohort

  • personCount the number of people in the cohort

  • minPriorObservation the minimum required observation days prior to index for an entry

  • outcomeWashoutDays patients with the outcome occurring within this number of days prior to index are excluded (NA means no exclusion)

  • riskWindowStart the number of days ofset the start anchor that is the start of the time-at-risk

  • startAnchor the start anchor is either the target cohort start or cohort end date

  • riskWindowEnd the number of days ofset the end anchor that is the end of the time-at-risk

  • endAnchor the end anchor is either the target cohort start or cohort end date

Details

Specify the connectionHandler, the schema and the target/outcome cohort IDs

See also

Other Characterization: getBinaryCaseSeries(), getBinaryRiskFactors(), getCaseBinaryFeatures(), getCaseContinuousFeatures(), getCharacterizationDemographics(), getContinuousCaseSeries(), getContinuousRiskFactors(), getDechallengeRechallenge(), getIncidenceRates(), getTargetBinaryFeatures(), getTargetContinuousFeatures(), getTargetCounts(), getTimeToEvent(), plotAgeDistributions(), plotSexDistributions()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver

cc <- getCaseCounts(
connectionHandler = connectionHandler, 
schema = 'main'
)