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.