I’m running the CohortMethod code for a PLE study generated by Atlas. It looks like there’s a mismatch in the size of the cohortMethodData objects:
Running CohortMethod analyses
*** Creating cohortMethodData objects ***
| | 0%Thread 1 returns error: “numbers of columns of arguments do not match” when using argument(s): list(args = list(connectionDetails = list(dbms = “redshift”, user = “user”, password = “password”, server = “[redacted]”, oracleDriver = “thin”), cdmDatabaseSchema = “full_201903_omop_v5”, oracleTempSchema = NULL, exposureDatabaseSchema = “study_reference”, exposureTable = “arthro”, outcomeDatabaseSchema = “study_reference”, outcomeTable = “arthro”, cdmVersion = 5, outcomeIds = c(882, 26662, 30234, 30753, 31317, 72715, n72737, 73575, 74725, 75860, 76161, 77139, 78162, 78474, 79864, 80824, 81151, 133729, 136057, 136184, 136661, 136773, 137351, 137951, 138384, 138825, 139099, 140641, 141375, 141932, 194686, 195562, 195603, 196456, 197006, 197381, 197607, 197610, 197911, 198101, 198400, 198803, 199866, 200528, 201061, 201072, 201254, 201322, 201418, 201620, 201826, 257004, 261325, 312950, 313459, 316127, 318736, 318800, 321596, 373478, 374375, 375806, 376065, 376382, 377575, 377910, 379805, 381292, 381295, 381877, n432730, 432738, 432798, 432883, 433163, 433316, 433440, 433753, 433811, 434004, 434005, 434610, 434613, 435243, 435510, 435511, 435515, 435796, 436070, 436118, 436246, 436375, 436940, 436962, 437246, 437264, 437833, 437851, 438120, 438409, 439082, 439147, 440129, 441417, 443211, 443597, 443731, 444367, 4033837, 4084229, 4088920, 4098604, 4103703, 4110815, 4168217, 4172432, 4193704, 4209423, 4211231, 4305080, 4308509, 4311591, 40483107, 45768910), targetId = 880, comparatorId = 881, restrictToCommonPeriod = FALSE, n removeDuplicateSubjects = “remove all”, maxCohortSize = 100000, excludeDrugsFromCovariates = FALSE, covariateSettings = list(list(VisitCountMediumTerm = FALSE, ObservationShortTerm = TRUE, shortTermStartDays = -30, MeasurementRangeGroupShortTerm = FALSE, ConditionOccurrenceLongTerm = FALSE, DrugEraStartLongTerm = FALSE, VisitCountShortTerm = FALSE, Chads2Vasc = TRUE, ConditionGroupEraStartLongTerm = FALSE, ConditionEraShortTerm = FALSE, Dcsi = TRUE, DrugGroupEraLongTerm = TRUE, DrugGroupEraShortTerm = TRUE, n ConditionEraStartLongTerm = FALSE, temporal = FALSE, DemographicsIndexMonth = TRUE, ConditionOccurrencePrimaryInpatientLongTerm = FALSE, ConditionEraAnyTimePrior = FALSE, addDescendantsToInclude = FALSE, ConditionGroupEraStartMediumTerm = FALSE, ProcedureOccurrenceLongTerm = TRUE, DrugExposureLongTerm = FALSE, DrugEraStartShortTerm = FALSE, DistinctIngredientCountMediumTerm = FALSE, DistinctMeasurementCountShortTerm = FALSE, MeasurementRangeGroupLongTerm = TRUE, ConditionGroupEraOverlapping = FALSE, n MeasurementRangeGroupMediumTerm = FALSE, DrugGroupEraStartMediumTerm = FALSE, MeasurementAnyTimePrior = FALSE, MeasurementMediumTerm = FALSE, includedCovariateIds = list(), ConditionOccurrenceAnyTimePrior = FALSE, DistinctConditionCountLongTerm = FALSE, MeasurementValueLongTerm = FALSE, DrugEraShortTerm = FALSE, DrugGroupEraAnyTimePrior = FALSE, DrugEraOverlapping = FALSE, ConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE, ConditionEraMediumTerm = FALSE, ConditionEraOverlapping = FALSE, n ConditionEraStartShortTerm = FALSE, ObservationAnyTimePrior = FALSE, VisitConceptCountShortTerm = FALSE, DemographicsEthnicity = TRUE, DistinctIngredientCountLongTerm = FALSE, ConditionOccurrencePrimaryInpatientShortTerm = FALSE, DemographicsAgeGroup = TRUE, DistinctProcedureCountShortTerm = FALSE, DistinctObservationCountMediumTerm = FALSE, includedCovariateConceptIds = list(), DrugGroupEraStartShortTerm = FALSE, addDescendantsToExclude = TRUE, DrugEraLongTerm = FALSE, DistinctConditionCountShortTerm = FALSE, n ConditionGroupEraShortTerm = TRUE, ConditionEraStartMediumTerm = FALSE, VisitCountLongTerm = FALSE, DemographicsRace = TRUE, ProcedureOccurrenceAnyTimePrior = FALSE, DistinctObservationCountLongTerm = FALSE, ProcedureOccurrenceMediumTerm = FALSE, CharlsonIndex = TRUE, DemographicsPriorObservationTime = FALSE, MeasurementShortTerm = TRUE, DistinctProcedureCountMediumTerm = FALSE, ConditionEraLongTerm = FALSE, DrugGroupEraStartLongTerm = FALSE, DemographicsGender = TRUE, DeviceExposureAnyTimePrior = FALSE, n ObservationLongTerm = TRUE, DemographicsIndexYearMonth = FALSE, ConditionOccurrenceMediumTerm = FALSE, longTermStartDays = -365, DemographicsAge = FALSE, DrugGroupEraOverlapping = TRUE, DistinctMeasurementCountLongTerm = FALSE, MeasurementRangeGroupAnyTimePrior = FALSE, DistinctConditionCountMediumTerm = FALSE, DrugGroupEraMediumTerm = FALSE, ProcedureOccurrenceShortTerm = TRUE, ObservationMediumTerm = FALSE, ConditionGroupEraAnyTimePrior = FALSE, Chads2 = TRUE, DrugExposureAnyTimePrior = FALSE, n DeviceExposureLongTerm = TRUE, DemographicsTimeInCohort = FALSE, DistinctMeasurementCountMediumTerm = FALSE, MeasurementValueShortTerm = FALSE, DeviceExposureMediumTerm = FALSE, ConditionGroupEraStartShortTerm = FALSE, ConditionOccurrencePrimaryInpatientMediumTerm = FALSE, MeasurementLongTerm = TRUE, DemographicsIndexYear = TRUE, MeasurementValueMediumTerm = FALSE, DrugEraStartMediumTerm = FALSE, MeasurementValueAnyTimePrior = FALSE, DistinctObservationCountShortTerm = FALSE, DrugEraMediumTerm = FALSE, n ConditionGroupEraLongTerm = TRUE, DrugExposureShortTerm = FALSE, DistinctIngredientCountShortTerm = FALSE, DeviceExposureShortTerm = TRUE, mediumTermStartDays = -180, DemographicsPostObservationTime = FALSE, VisitConceptCountLongTerm = FALSE, VisitConceptCountMediumTerm = FALSE, excludedCovariateConceptIds = c(19058978, 4001652, 4149198, 2211436, 44514807, 4248555, 320827, 43531648, 4136345, 4138870, 4003142, 40756852, 4326255, 2000025, 44514800, 2005904, 2211717, 2211716, 4253808, 199073, n 37017417, 2105103, 75039, 4062247, 200761, 4076181, 4176868, 4138872, 2006200, 4001650, 4079266, 2771224, 4035487, 2773425, 2773451, 4140294, 2775846, 4076882, 4177835, 35625764, 46272777, 2773435, 44809076, 35625794, 37115753, 2771205, 2773426, 4300754, 4203771, 35610630, 2771691, 2104836, 763946, 2773449, 2771701, 2771684, 44790484, 2773442, 2771220, 4150990, 2005944, 2771225, 44790486, 2771697, 2773453, 4205526, 4144432, 44515517, 2771705, 4079401, 2771215, 42872820, 2104837, 4137703, n 2773424, 4330505, 44515513, 4142076, 4034666, 2771694, 44514793, 4078258, 4142923, 2103716, 4196649, 4077286, 4143687, 2771703, 44790478, 2771702, 46272778, 4076609, 4079260, 2771707, 2771223, 2775859, 2771696, 2771222, 44514777, 44515510, 2771221, 2773443, 2771700, 2771706, 2771219, 44515504, 44514784, 46272775, 2771217, 37111559, 2771218, 2773444, 35625480, 44791175, 4138868, 2771226, 2771211, 4083672, 44790443, 2771698, 4034665, 4079259, 44783151, 44790803, 2771704, 2771203, 4175642, 2771213, n 4152063, 2773452, 2771699, 4079258, 42538476), ConditionGroupEraMediumTerm = FALSE, DrugExposureMediumTerm = FALSE, DistinctProcedureCountLongTerm = FALSE, DrugEraAnyTimePrior = FALSE, endDays = 0, ConditionOccurrenceShortTerm = FALSE)), studyStartDate = 20060101, washoutPeriod = 365, firstExposureOnly = TRUE, studyEndDate = NULL), compressCohortMethodData = FALSE, cohortMethodDataFolder = “./columbia/ADA/cmOutput/CmData”)
|================================================ | 50%Thread 2 returns error: “numbers of columns of arguments do not match” when using argument(s): list(args = list(connectionDetails = list(dbms = “redshift”, user = “user”, password = “password”, server = “[redacted]”, oracleDriver = “thin”), cdmDatabaseSchema = “full_201903_omop_v5”, oracleTempSchema = NULL, exposureDatabaseSchema = “study_reference”, exposureTable = “arthro”, outcomeDatabaseSchema = “study_reference”, outcomeTable = “arthro”, cdmVersion = 5, outcomeIds = c(885, 26662, 30234, 30753, 31317, 72715, n72737, 73575, 74725, 75860, 76161, 77139, 78162, 78474, 79864, 80824, 81151, 133729, 136057, 136184, 136661, 136773, 137351, 137951, 138384, 138825, 139099, 140641, 141375, 141932, 194686, 195562, 195603, 196456, 197006, 197381, 197607, 197610, 197911, 198101, 198400, 198803, 199866, 200528, 201061, 201072, 201254, 201322, 201418, 201620, 201826, 257004, 261325, 312950, 313459, 316127, 318736, 318800, 321596, 373478, 374375, 375806, 376065, 376382, 377575, 377910, 379805, 381292, 381295, 381877, n432730, 432738, 432798, 432883, 433163, 433316, 433440, 433753, 433811, 434004, 434005, 434610, 434613, 435243, 435510, 435511, 435515, 435796, 436070, 436118, 436246, 436375, 436940, 436962, 437246, 437264, 437833, 437851, 438120, 438409, 439082, 439147, 440129, 441417, 443211, 443597, 443731, 444367, 4033837, 4084229, 4088920, 4098604, 4103703, 4110815, 4168217, 4172432, 4193704, 4209423, 4211231, 4305080, 4308509, 4311591, 40483107, 45768910), targetId = 883, comparatorId = 884, restrictToCommonPeriod = FALSE, n removeDuplicateSubjects = “remove all”, maxCohortSize = 100000, excludeDrugsFromCovariates = FALSE, covariateSettings = list(list(VisitCountMediumTerm = FALSE, ObservationShortTerm = TRUE, shortTermStartDays = -30, MeasurementRangeGroupShortTerm = FALSE, ConditionOccurrenceLongTerm = FALSE, DrugEraStartLongTerm = FALSE, VisitCountShortTerm = FALSE, Chads2Vasc = TRUE, ConditionGroupEraStartLongTerm = FALSE, ConditionEraShortTerm = FALSE, Dcsi = TRUE, DrugGroupEraLongTerm = TRUE, DrugGroupEraShortTerm = TRUE, n ConditionEraStartLongTerm = FALSE, temporal = FALSE, DemographicsIndexMonth = TRUE, ConditionOccurrencePrimaryInpatientLongTerm = FALSE, ConditionEraAnyTimePrior = FALSE, addDescendantsToInclude = FALSE, ConditionGroupEraStartMediumTerm = FALSE, ProcedureOccurrenceLongTerm = TRUE, DrugExposureLongTerm = FALSE, DrugEraStartShortTerm = FALSE, DistinctIngredientCountMediumTerm = FALSE, DistinctMeasurementCountShortTerm = FALSE, MeasurementRangeGroupLongTerm = TRUE, ConditionGroupEraOverlapping = FALSE, n MeasurementRangeGroupMediumTerm = FALSE, DrugGroupEraStartMediumTerm = FALSE, MeasurementAnyTimePrior = FALSE, MeasurementMediumTerm = FALSE, includedCovariateIds = list(), ConditionOccurrenceAnyTimePrior = FALSE, DistinctConditionCountLongTerm = FALSE, MeasurementValueLongTerm = FALSE, DrugEraShortTerm = FALSE, DrugGroupEraAnyTimePrior = FALSE, DrugEraOverlapping = FALSE, ConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE, ConditionEraMediumTerm = FALSE, ConditionEraOverlapping = FALSE, n ConditionEraStartShortTerm = FALSE, ObservationAnyTimePrior = FALSE, VisitConceptCountShortTerm = FALSE, DemographicsEthnicity = TRUE, DistinctIngredientCountLongTerm = FALSE, ConditionOccurrencePrimaryInpatientShortTerm = FALSE, DemographicsAgeGroup = TRUE, DistinctProcedureCountShortTerm = FALSE, DistinctObservationCountMediumTerm = FALSE, includedCovariateConceptIds = list(), DrugGroupEraStartShortTerm = FALSE, addDescendantsToExclude = TRUE, DrugEraLongTerm = FALSE, DistinctConditionCountShortTerm = FALSE, n ConditionGroupEraShortTerm = TRUE, ConditionEraStartMediumTerm = FALSE, VisitCountLongTerm = FALSE, DemographicsRace = TRUE, ProcedureOccurrenceAnyTimePrior = FALSE, DistinctObservationCountLongTerm = FALSE, ProcedureOccurrenceMediumTerm = FALSE, CharlsonIndex = TRUE, DemographicsPriorObservationTime = FALSE, MeasurementShortTerm = TRUE, DistinctProcedureCountMediumTerm = FALSE, ConditionEraLongTerm = FALSE, DrugGroupEraStartLongTerm = FALSE, DemographicsGender = TRUE, DeviceExposureAnyTimePrior = FALSE, n ObservationLongTerm = TRUE, DemographicsIndexYearMonth = FALSE, ConditionOccurrenceMediumTerm = FALSE, longTermStartDays = -365, DemographicsAge = FALSE, DrugGroupEraOverlapping = TRUE, DistinctMeasurementCountLongTerm = FALSE, MeasurementRangeGroupAnyTimePrior = FALSE, DistinctConditionCountMediumTerm = FALSE, DrugGroupEraMediumTerm = FALSE, ProcedureOccurrenceShortTerm = TRUE, ObservationMediumTerm = FALSE, ConditionGroupEraAnyTimePrior = FALSE, Chads2 = TRUE, DrugExposureAnyTimePrior = FALSE, n DeviceExposureLongTerm = TRUE, DemographicsTimeInCohort = FALSE, DistinctMeasurementCountMediumTerm = FALSE, MeasurementValueShortTerm = FALSE, DeviceExposureMediumTerm = FALSE, ConditionGroupEraStartShortTerm = FALSE, ConditionOccurrencePrimaryInpatientMediumTerm = FALSE, MeasurementLongTerm = TRUE, DemographicsIndexYear = TRUE, MeasurementValueMediumTerm = FALSE, DrugEraStartMediumTerm = FALSE, MeasurementValueAnyTimePrior = FALSE, DistinctObservationCountShortTerm = FALSE, DrugEraMediumTerm = FALSE, n ConditionGroupEraLongTerm = TRUE, DrugExposureShortTerm = FALSE, DistinctIngredientCountShortTerm = FALSE, DeviceExposureShortTerm = TRUE, mediumTermStartDays = -180, DemographicsPostObservationTime = FALSE, VisitConceptCountLongTerm = FALSE, VisitConceptCountMediumTerm = FALSE, excludedCovariateConceptIds = c(4001650, 4142923, 2775859, 44790478, 2006200, 44514793, 4079260, 4143687, 4142076, 2104836, 320827, 4150990, 4136345, 4248555, 4203771, 763946, 44515517, 42872820, 2211436, 19058978, n 4001652, 44790486, 4144432, 4149198, 44515513, 4137703, 2104837, 75039, 4035487, 44809076, 2211717, 2211716, 4253808, 199073, 2775846, 35625764, 4140294, 35625794, 4177835, 4152063, 4175642, 4079259, 4079258, 4062247, 200761, 4176868, 4138868, 44791175, 2000025, 44514784, 40756852, 44515510, 44514777, 44515504, 44790443, 4003142, 35625480, 4326255, 46272775, 2105103, 2771224, 2773425, 2773451, 4076882, 2005904, 44514800, 46272777, 2773435, 37115753, 2771205, 37017417, 2773426, 4138870, 4300754, n 35610630, 2771691, 43531648, 2773449, 2771701, 2771684, 44790484, 2773442, 2771220, 2005944, 2771225, 2771697, 2773453, 4205526, 2771705, 4079401, 2771215, 2773424, 4330505, 44514807, 4034666, 2771694, 4078258, 2103716, 4196649, 4077286, 2771703, 2771702, 46272778, 4076609, 4079266, 2771707, 2771223, 2771696, 2771222, 2771221, 2773443, 2771700, 2771706, 2771219, 2771217, 37111559, 2771218, 2773444, 2771226, 2771211, 4083672, 4138872, 2771698, 4034665, 44783151, 44790803, 2771704, 2771203, n 2771213, 2773452, 4076181, 2771699, 42538476), ConditionGroupEraMediumTerm = FALSE, DrugExposureMediumTerm = FALSE, DistinctProcedureCountLongTerm = FALSE, DrugEraAnyTimePrior = FALSE, endDays = 0, ConditionOccurrenceShortTerm = FALSE)), studyStartDate = 20060101, washoutPeriod = 365, firstExposureOnly = TRUE, studyEndDate = NULL), compressCohortMethodData = FALSE, cohortMethodDataFolder = “./columbia/ADA/cmOutput/CmData”)
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Error in ParallelLogger::clusterApply(cluster, objectsToCreate, createCmDataObject) :
Error(s) when calling function ‘fun’, see earlier messages for details
I’m trying to find where rbind exists in the code but it’s a little buried. I know there’s some references in CohortMethod. @schuemie or @msuchard, any suggestions on where you’d go to debug this? I was guessing I may need to adjust rbind to an rbind.fill because I have NAs in some of the data frames. Open to other suggestions on how to deal with the size mismatch.
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