This function extracts all incidence rates across databases in the results for specified target and outcome cohorts.
Usage
getIncidenceRates(
connectionHandler,
schema,
ciTablePrefix = "ci_",
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$new()`.
- schema
The result database schema (e.g., 'main' for sqlite)
- ciTablePrefix
The prefix used for the cohort incidence results tables
- cgTablePrefix
The prefix used for the cohort generator results tables
- databaseTable
The name of the table with the database details (default 'database_meta_data')
- targetIds
A vector of integers corresponding to the target cohort IDs
- outcomeIds
A vector of integers corresponding to the outcome cohort IDs
Value
Returns a data.frame with the columns:
databaseName the name of the database
targetName the target cohort name
targetId the target cohort unique identifier
outcomeName the outcome name
outcomeId the outcome unique identifier
cleanWindow clean windown around outcome
subgroupName name for the result subgroup
ageGroupName name for the result age group
genderName name for the result gender group
startYear name for the result start year
tarStartWith time at risk start reference
tarStartOffset time at risk start offset from reference
tarEndWith time at risk end reference
tarEndOffset time at risk end offset from reference
personsAtRiskPe persons at risk per event
personsAtRisk persons at risk
personDaysPe person days per event
personDays person days
personOutcomesPe person outcome per event
personOutcomes persons outcome
outcomesPe number of outcome per event
outcomes number of outcome
incidenceProportionP100p incidence proportion per 100 persons
incidenceRateP100py incidence rate per 100 person years
See also
Other Characterization:
getBinaryCaseSeries(),
getBinaryRiskFactors(),
getCaseBinaryFeatures(),
getCaseContinuousFeatures(),
getCaseCounts(),
getCharacterizationDemographics(),
getContinuousCaseSeries(),
getContinuousRiskFactors(),
getDechallengeRechallenge(),
getTargetBinaryFeatures(),
getTargetContinuousFeatures(),
getTargetCounts(),
getTimeToEvent(),
plotAgeDistributions(),
plotSexDistributions()
Examples
conDet <- getExampleConnectionDetails()
connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver
ir <- getIncidenceRates(
connectionHandler = connectionHandler,
schema = 'main'
)