Create a parameter object for the function createEvaluationCohort

createCreateEvaluationCohortArgs(
  xSpecCohortId,
  daysFromxSpec = 0,
  xSensCohortId = prevalenceCohortId,
  prevalenceCohortId,
  caseCohortId = prevalenceCohortId,
  caseFirstOccurrenceOnly = TRUE,
  xSpecCohortSize = 5000,
  covariateSettings = createDefaultCovariateSettings(excludedCovariateConceptIds = c(),
    addDescendantsToExclude = TRUE),
  modelPopulationCohortId = 0,
  modelPopulationCohortIdStartDay = 0,
  modelPopulationCohortIdEndDay = 0,
  inclusionEvaluationCohortId = 0,
  inclusionEvaluationDaysFromStart = 0,
  inclusionEvaluationDaysFromEnd = 0,
  duringInclusionEvaluationOnly = FALSE,
  exclusionEvaluationCohortId = 0,
  exclusionEvaluationDaysFromStart = 0,
  exclusionEvaluationDaysFromEnd = 0,
  minimumOffsetFromStart = 0,
  minimumOffsetFromEnd = 30,
  modelBaseSampleSize = 25000,
  baseSampleSize = 2e+06,
  lowerAgeLimit = 0,
  upperAgeLimit = 120,
  visitLength = 0,
  visitType = c(9201, 9202, 9203, 581477, 262),
  gender = c(8507, 8532),
  race = 0,
  ethnicity = 0,
  startDate = "19001010",
  endDate = "21000101",
  falsePositiveNegativeSubjects = 10,
  modelId = "main",
  evaluationCohortId = "main",
  randomVisitTable = "",
  excludeModelFromEvaluation = FALSE,
  removeSubjectsWithFutureDates = TRUE,
  saveEvaluationCohortPlpData = FALSE
)

Arguments

xSpecCohortId: The number of the "extremely specific (xSpec)" cohortdefinition id in the cohort table (for noisy positives).
daysFromxSpec: Number of days from xSpec condition until analyzed visit
xSensCohortId: The number of the "extremely sensitive (xSens)" cohortdefinition id in the cohort table (for noisy negatives).
prevalenceCohortId: The number of the cohort definition id to determine the disease prevalence.
caseCohortId: The number of the cohort definition id to determine cases in the evaluation cohort
caseFirstOccurrenceOnly: Set to true if only the first occurrence per subject in the case cohort is to be used
xSpecCohortSize: Maximum xSpec sample size to use in the analysis
covariateSettings: A covariateSettings object as generated using createCovariateSettings().
modelPopulationCohortId: The number of the cohort to be used as a base population for the model. If set to 0, the entire database population will be used.
modelPopulationCohortIdStartDay: The number of days relative to the mainPopulationCohortId cohort start date to begin including visits.
modelPopulationCohortIdEndDay: The number of days relative to the mainPopulationCohortId cohort start date to end including visits.
inclusionEvaluationCohortId: The number of the cohort of the population to be used to designate which visits are are eligible to be in the evaluation cohort
inclusionEvaluationDaysFromStart: The number of days from the cohort start date of the inclusionEvaluationCohortId to start eligible included visits
inclusionEvaluationDaysFromEnd: The number of days from the cohort start date of the inclusionEvaluationCohortId to end eligible included visits
duringInclusionEvaluationOnly: Only include visits that are within the cohort start and end dates
exclusionEvaluationCohortId: The number of the cohort of the population to be used to designate which visits are NOT eligible to be in the evaluation cohort
exclusionEvaluationDaysFromStart: The number of days from the cohort start date of the exclusionEvaluationCohortId to start ineligible included visits
exclusionEvaluationDaysFromEnd: The number of days from the cohort start date of the exclusionEvaluationCohortId to end ineligible included visits
minimumOffsetFromStart: Minimum number of days to offset for the analysis visit from the start of the observation period
minimumOffsetFromEnd: Minimum number of days to offset for the analysis visit from the end of the observation period
modelBaseSampleSize: The number of non-xSpec subjects to include in the model
baseSampleSize: The maximum number of subjects in the evaluation cohort.
lowerAgeLimit: The lower age for subjects in the model.
upperAgeLimit: The upper age for subjects in the model.
visitLength: The minimum length of index visit for acute outcomes.
visitType: The concept_id for the visit type.
gender: The gender(s) to be included.
race: The race(s) to be included.
ethnicity: The ethnicity(s) to be included.
startDate: The starting date for including subjects in the model.
endDate: The ending date for including subjects in the model.
falsePositiveNegativeSubjects: Number of subjects to include for evaluating false positives and negatives
modelId: A string used to generate the file names for this model.
evaluationCohortId: A string used to generate the file names for this evaluation cohort.
randomVisitTable: Table stored in work directory with pre-selected random visits in format of visit_occurrence table
excludeModelFromEvaluation: Should subjects used in the model be excluded from the evaluation cohort?
removeSubjectsWithFutureDates: For buggy data with data in the future: ignore subjects with dates in the future?
saveEvaluationCohortPlpData: Should the large PLP file for the evaluation cohort be saved? To be used for debugging purposes.

Details

Create an object defining the parameter values.