createCreateEvaluationCohortArgs: Create a parameter object for the function...
In OHDSI/PheValuator: Rapid Phenotype Evaluation

createCreateEvaluationCohortArgs

R Documentation

Create a parameter object for the function createEvaluationCohort

Description

Create a parameter object for the function createEvaluationCohort

Usage

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.