qstrokeModel: Apply the existing model Qstroke stroke risk using the...

In OHDSI/PredictionComparison: Package for comparing patient level predictions developed using OHDSI's PatientLevelPreidiction package

Description

Apply the existing model Qstroke stroke risk using the standardised framework

Usage

qstrokeModel(
  connectionDetails,
  cdmDatabaseSchema,
  cohortDatabaseSchema,
  outcomeDatabaseSchema,
  cohortTable,
  outcomeTable,
  cohortId,
  outcomeId,
  oracleTempSchema = NULL,
  cdmVersion = 5,
  analysisId = "Q-stroke-female",
  sampleSize = NULL,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  endDay = -1,
  requireTimeAtRisk = T,
  minTimeAtRisk = 1,
  includeAllOutcomes = T,
  removePriorOutcome = T,
  priorOutcomeLookback = 9999,
  calibrationPopulation = NULL,
  createCovariateCohorts = T,
  overwriteExistingCohorts = T,
  covariateDatabaseSchema = cohortDatabaseSchema,
  covariateCohortTable = "PredictionComp"
)

Arguments

connectionDetails	The connection details for extracting the data
cdmDatabaseSchema	A string specifying the database containing the cdm
cohortDatabaseSchema	A string specifying the database containing the target population cohort
outcomeDatabaseSchema	A string specifying the database containing the outcome cohort
cohortTable	A string specifying the table containing the target population cohort
outcomeTable	A string specifying the table containing the outcome cohort
cohortId	An iteger specifying the cohort id for the target population cohorts
outcomeId	An iteger specifying the cohort id for the outcome cohorts
oracleTempSchema	The temp schema require is using oracle
cdmVersion	The CDM version you are using
analysisId	An id to give to the study
sampleSize	The size to sample from T when applying the existing model
riskWindowStart	The start of the period to predict the risk of the outcome occurring start relative to the target cohort start date
startAnchor	Is the risk start relative to cohort_start or cohort_end
riskWindowEnd	The end of the period to predict the risk of the outcome occurring start relative to the target cohort start date
endAnchor	Is the risk end relative to cohort_start or cohort_end
endDay	The last day relative to index for the covariates
requireTimeAtRisk	Require a minimum number of days observed in the time at risk period?
minTimeAtRisk	If requireTimeAtRisk is true, the minimum number of days at risk
includeAllOutcomes	Whether to include people with outcome who do not satify the minTimeAtRisk
removePriorOutcome	Remove people with prior outcomes from the target population
priorOutcomeLookback	Time prior to index to remove people if they have the outcome
calibrationPopulation	A data.frame of subjectId, cohortStartDate, indexes used to recalibrate the model on new data
createCovariateCohorts	Create the cohorts used for the covariates in the model
overwriteExistingCohorts	Overwrite cohorts that already exist in the covariateCohortTable table
covariateDatabaseSchema	A read/write database to keep the covariate cohorts
covariateCohortTable	A read/write table to keep the covariate cohorts

Details

This function applies Qstroke stroke risk to a target cohort and validates the performance

Value

A list containing the model performance and the personal predictions for each subject in the target population

OHDSI/PredictionComparison documentation built on July 14, 2020, 6:16 p.m.