chads2vasModel: Apply the existing model CHADs2vas using the standardised...

Description Usage Arguments Details Value

View source: R/chads2vasModel.R

Description

Apply the existing model CHADs2vas using the standardised framework

Usage

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chads2vasModel(
  connectionDetails,
  cdmDatabaseSchema,
  cohortDatabaseSchema,
  outcomeDatabaseSchema,
  cohortTable,
  outcomeTable,
  cohortId,
  outcomeId,
  oracleTempSchema = NULL,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  endDay = -1,
  requireTimeAtRisk = T,
  minTimeAtRisk = 364,
  includeAllOutcomes = T,
  firstExposureOnly = F,
  removePriorOutcome = T,
  recalibrate = T,
  calibrationPopulation = NULL
)

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

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

firstExposureOnly

Whether to restrict to first target cohort start date if people are in target popualtion multiple times

removePriorOutcome

Remove people with prior outcomes from the target population

recalibrate

Recalibrate the model on the new data

calibrationPopulation

A data.frame of subjectId, cohortStartDate, indexes used to recalibrate the model on new data

Details

This function applies CHADs2vas 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.