R/load-field-lists-data.R

In AdlCruz/rctapi: rctapi: Download Clinical Trial data from ClinicalTrials.gov

# "all_fields"
################################################################################
#function all fields
all_fields <- c("Acronym",
                "AgreementOtherDetails",
                "AgreementPISponsorEmployee",
                "AgreementRestrictionType",
                "AgreementRestrictiveAgreement",
                "ArmGroupDescription",
                "ArmGroupInterventionName",
                "ArmGroupLabel",
                "ArmGroupType",
                "AvailIPDComment",
                "AvailIPDId",
                "AvailIPDType",
                "AvailIPDURL",
                "BaselineCategoryTitle",
                "BaselineClassDenomCountGroupId",
                "BaselineClassDenomCountValue",
                "BaselineClassDenomUnits",
                "BaselineClassTitle",
                "BaselineDenomCountGroupId",
                "BaselineDenomCountValue",
                "BaselineDenomUnits",
                "BaselineGroupDescription",
                "BaselineGroupId",
                "BaselineGroupTitle",
                "BaselineMeasureCalculatePct",
                "BaselineMeasureDenomCountGroupId",
                "BaselineMeasureDenomCountValue",
                "BaselineMeasureDenomUnits",
                "BaselineMeasureDenomUnitsSelected",
                "BaselineMeasureDescription",
                "BaselineMeasureDispersionType",
                "BaselineMeasureParamType",
                "BaselineMeasurePopulationDescription",
                "BaselineMeasureTitle",
                "BaselineMeasureUnitOfMeasure",
                "BaselineMeasurementComment",
                "BaselineMeasurementGroupId",
                "BaselineMeasurementLowerLimit",
                "BaselineMeasurementSpread",
                "BaselineMeasurementUpperLimit",
                "BaselineMeasurementValue",
                "BaselinePopulationDescription",
                "BaselineTypeUnitsAnalyzed",
                "BioSpecDescription",
                "BioSpecRetention",
                "BriefSummary",
                "BriefTitle",
                "CentralContactEMail",
                "CentralContactName",
                "CentralContactPhone",
                "CentralContactPhoneExt",
                "CentralContactRole",
                "CollaboratorClass",
                "CollaboratorName",
                "CompletionDate",
                "CompletionDateType",
                "Condition",
                "ConditionAncestorId",
                "ConditionAncestorTerm",
                "ConditionBrowseBranchAbbrev",
                "ConditionBrowseBranchName",
                "ConditionBrowseLeafAsFound",
                "ConditionBrowseLeafId",
                "ConditionBrowseLeafName",
                "ConditionBrowseLeafRelevance",
                "ConditionMeshId",
                "ConditionMeshTerm",
                "DelayedPosting",
                "DesignAllocation",
                "DesignInterventionModel",
                "DesignInterventionModelDescription",
                "DesignMasking",
                "DesignMaskingDescription",
                "DesignObservationalModel",
                "DesignPrimaryPurpose",
                "DesignTimePerspective",
                "DesignWhoMasked",
                "DetailedDescription",
                "DispFirstPostDate",
                "DispFirstPostDateType",
                "DispFirstSubmitDate",
                "DispFirstSubmitQCDate",
                "EligibilityCriteria",
                "EnrollmentCount",
                "EnrollmentType",
                "EventGroupDeathsNumAffected",
                "EventGroupDeathsNumAtRisk",
                "EventGroupDescription",
                "EventGroupId",
                "EventGroupOtherNumAffected",
                "EventGroupOtherNumAtRisk",
                "EventGroupSeriousNumAffected",
                "EventGroupSeriousNumAtRisk",
                "EventGroupTitle",
                "EventsDescription",
                "EventsFrequencyThreshold",
                "EventsTimeFrame",
                "ExpAccTypeIndividual",
                "ExpAccTypeIntermediate",
                "ExpAccTypeTreatment",
                "ExpandedAccessNCTId",
                "ExpandedAccessStatusForNCTId",
                "FDAAA801Violation",
                "FlowAchievementComment",
                "FlowAchievementGroupId",
                "FlowAchievementNumSubjects",
                "FlowAchievementNumUnits",
                "FlowDropWithdrawComment",
                "FlowDropWithdrawType",
                "FlowGroupDescription",
                "FlowGroupId",
                "FlowGroupTitle",
                "FlowMilestoneComment",
                "FlowMilestoneType",
                "FlowPeriodTitle",
                "FlowPreAssignmentDetails",
                "FlowReasonComment",
                "FlowReasonGroupId",
                "FlowReasonNumSubjects",
                "FlowReasonNumUnits",
                "FlowRecruitmentDetails",
                "FlowTypeUnitsAnalyzed",
                "Gender",
                "GenderBased",
                "GenderDescription",
                "HasExpandedAccess",
                "HealthyVolunteers",
                "IPDSharing",
                "IPDSharingAccessCriteria",
                "IPDSharingDescription",
                "IPDSharingInfoType",
                "IPDSharingTimeFrame",
                "IPDSharingURL",
                "InterventionAncestorId",
                "InterventionAncestorTerm",
                "InterventionArmGroupLabel",
                "InterventionBrowseBranchAbbrev",
                "InterventionBrowseBranchName",
                "InterventionBrowseLeafAsFound",
                "InterventionBrowseLeafId",
                "InterventionBrowseLeafName",
                "InterventionBrowseLeafRelevance",
                "InterventionDescription",
                "InterventionMeshId",
                "InterventionMeshTerm",
                "InterventionName",
                "InterventionOtherName",
                "InterventionType",
                "IsFDARegulatedDevice",
                "IsFDARegulatedDrug",
                "IsPPSD",
                "IsUSExport",
                "IsUnapprovedDevice",
                "Keyword",
                "LargeDocDate",
                "LargeDocFilename",
                "LargeDocHasICF",
                "LargeDocHasProtocol",
                "LargeDocHasSAP",
                "LargeDocLabel",
                "LargeDocTypeAbbrev",
                "LargeDocUploadDate",
                "LastKnownStatus",
                "LastUpdatePostDate",
                "LastUpdatePostDateType",
                "LastUpdateSubmitDate",
                "LeadSponsorClass",
                "LeadSponsorName",
                "LimitationsAndCaveatsDescription",
                "LocationCity",
                "LocationContactEMail",
                "LocationContactName",
                "LocationContactPhone",
                "LocationContactPhoneExt",
                "LocationContactRole",
                "LocationCountry",
                "LocationFacility",
                "LocationState",
                "LocationStatus",
                "LocationZip",
                "MaximumAge",
                "MinimumAge",
                "NCTId",
                "NCTIdAlias",
                "OfficialTitle",
                "OrgClass",
                "OrgFullName",
                "OrgStudyId",
                "OrgStudyIdDomain",
                "OrgStudyIdLink",
                "OrgStudyIdType",
                "OtherEventAssessmentType",
                "OtherEventNotes",
                "OtherEventOrganSystem",
                "OtherEventSourceVocabulary",
                "OtherEventStatsGroupId",
                "OtherEventStatsNumAffected",
                "OtherEventStatsNumAtRisk",
                "OtherEventStatsNumEvents",
                "OtherEventTerm",
                "OtherOutcomeDescription",
                "OtherOutcomeMeasure",
                "OtherOutcomeTimeFrame",
                "OutcomeAnalysisCILowerLimit",
                "OutcomeAnalysisCILowerLimitComment",
                "OutcomeAnalysisCINumSides",
                "OutcomeAnalysisCIPctValue",
                "OutcomeAnalysisCIUpperLimit",
                "OutcomeAnalysisCIUpperLimitComment",
                "OutcomeAnalysisDispersionType",
                "OutcomeAnalysisDispersionValue",
                "OutcomeAnalysisEstimateComment",
                "OutcomeAnalysisGroupDescription",
                "OutcomeAnalysisGroupId",
                "OutcomeAnalysisNonInferiorityComment",
                "OutcomeAnalysisNonInferiorityType",
                "OutcomeAnalysisOtherAnalysisDescription",
                "OutcomeAnalysisPValue",
                "OutcomeAnalysisPValueComment",
                "OutcomeAnalysisParamType",
                "OutcomeAnalysisParamValue",
                "OutcomeAnalysisStatisticalComment",
                "OutcomeAnalysisStatisticalMethod",
                "OutcomeAnalysisTestedNonInferiority",
                "OutcomeCategoryTitle",
                "OutcomeClassDenomCountGroupId",
                "OutcomeClassDenomCountValue",
                "OutcomeClassDenomUnits",
                "OutcomeClassTitle",
                "OutcomeDenomCountGroupId",
                "OutcomeDenomCountValue",
                "OutcomeDenomUnits",
                "OutcomeGroupDescription",
                "OutcomeGroupId",
                "OutcomeGroupTitle",
                "OutcomeMeasureAnticipatedPostingDate",
                "OutcomeMeasureCalculatePct",
                "OutcomeMeasureDenomUnitsSelected",
                "OutcomeMeasureDescription",
                "OutcomeMeasureDispersionType",
                "OutcomeMeasureParamType",
                "OutcomeMeasurePopulationDescription",
                "OutcomeMeasureReportingStatus",
                "OutcomeMeasureTimeFrame",
                "OutcomeMeasureTitle",
                "OutcomeMeasureType",
                "OutcomeMeasureTypeUnitsAnalyzed",
                "OutcomeMeasureUnitOfMeasure",
                "OutcomeMeasurementComment",
                "OutcomeMeasurementGroupId",
                "OutcomeMeasurementLowerLimit",
                "OutcomeMeasurementSpread",
                "OutcomeMeasurementUpperLimit",
                "OutcomeMeasurementValue",
                "OverallOfficialAffiliation",
                "OverallOfficialName",
                "OverallOfficialRole",
                "OverallStatus",
                "OversightHasDMC",
                "PatientRegistry",
                "Phase",
                "PointOfContactEMail",
                "PointOfContactOrganization",
                "PointOfContactPhone",
                "PointOfContactPhoneExt",
                "PointOfContactTitle",
                "PrimaryCompletionDate",
                "PrimaryCompletionDateType",
                "PrimaryOutcomeDescription",
                "PrimaryOutcomeMeasure",
                "PrimaryOutcomeTimeFrame",
                "ReferenceCitation",
                "ReferencePMID",
                "ReferenceType",
                "RemovedCountry",
                "ResponsiblePartyInvestigatorAffiliation",
                "ResponsiblePartyInvestigatorFullName",
                "ResponsiblePartyInvestigatorTitle",
                "ResponsiblePartyOldNameTitle",
                "ResponsiblePartyOldOrganization",
                "ResponsiblePartyType",
                "ResultsFirstPostDate",
                "ResultsFirstPostDateType",
                "ResultsFirstSubmitDate",
                "ResultsFirstSubmitQCDate",
                "RetractionPMID",
                "RetractionSource",
                "SamplingMethod",
                "SecondaryId",
                "SecondaryIdDomain",
                "SecondaryIdLink",
                "SecondaryIdType",
                "SecondaryOutcomeDescription",
                "SecondaryOutcomeMeasure",
                "SecondaryOutcomeTimeFrame",
                "SeeAlsoLinkLabel",
                "SeeAlsoLinkURL",
                "SeriousEventAssessmentType",
                "SeriousEventNotes",
                "SeriousEventOrganSystem",
                "SeriousEventSourceVocabulary",
                "SeriousEventStatsGroupId",
                "SeriousEventStatsNumAffected",
                "SeriousEventStatsNumAtRisk",
                "SeriousEventStatsNumEvents",
                "SeriousEventTerm",
                "StartDate",
                "StartDateType",
                "StatusVerifiedDate",
                "StdAge",
                "StudyFirstPostDate",
                "StudyFirstPostDateType",
                "StudyFirstSubmitDate",
                "StudyFirstSubmitQCDate",
                "StudyPopulation",
                "StudyType",
                "TargetDuration",
                "UnpostedEventDate",
                "UnpostedEventType",
                "UnpostedResponsibleParty",
                "VersionHolder",
                "WhyStopped")

#usethis::use_data(all_fields)
################################################################################
# FROM REGISTRATION DATA ELEMENTS
# "core_info_fields"
################################################################################
# from the registration data elements
core_info_fields <-c("NCTId","OverallStatus","CompletionDate","StudyType",
                     "BriefTitle","BriefSummary","Keyword","EnrollmentCount",
                     "EligibilityCriteria","LocationCountry","Condition","DesignAllocation",
                     "DesignPrimaryPurpose","DesignInterventionModel","ArmGroupLabel",
                     "ArmGroupType","InterventionType","InterventionName",
                     "InterventionDescription","IsFDARegulatedDrug","Phase","PrimaryOutcomeMeasure",
                     "PrimaryOutcomeTimeFrame","ResultsFirstPostDate")
#usethis::use_data(core_info_fields, overwrite = TRUE)
################################################################################
# "extended_info_fields" # curated large list spanning all sections
################################################################################
extended_info_fields <- c( "NCTId","OrgStudyId","BriefTitle","Acronym","OfficialTitle",
                          "StudyType","OverallStatus","WhyStopped","StartDate",
                          "CompletionDate","ResponsiblePartyType","ResponsiblePartyInvestigatorFullName",
                          "LeadSponsorName","IsFDARegulatedDrug","IsFDARegulatedDevice",
                          "IsUnapprovedDevice","OversightHasDMC","BriefSummary",
                          "DetailedDescription","Condition","Keyword","DesignPrimaryPurpose",
                          "Phase","DesignInterventionModel","DesignInterventionModelDescription",
                          "DesignWhoMasked","DesignMasking","DesignMaskingDescription",
                          "DesignAllocation","EnrollmentCount","DesignObservationalModel",
                          "DesignTimePerspective","BioSpecRetention","BioSpecDescription",
                          "TargetDuration","ArmGroupLabel","ArmGroupType",
                          "ArmGroupDescription","InterventionType","InterventionName",
                          "InterventionDescription","PrimaryOutcomeMeasure","PrimaryOutcomeDescription",
                          "PrimaryOutcomeTimeFrame","SecondaryOutcomeMeasure","SecondaryOutcomeDescription",
                          "SecondaryOutcomeTimeFrame","OtherOutcomeMeasure","OtherOutcomeDescription",
                          "OtherOutcomeTimeFrame","Gender","GenderBased","GenderDescription","MinimumAge",
                          "MaximumAge","HealthyVolunteers","EligibilityCriteria",
                          "StudyPopulation","SamplingMethod","CentralContactName",
                          "CentralContactEMail","LocationCountry","LocationContactEMail",
                          "IPDSharing","IPDSharingURL")

#usethis::use_data(extended_info_fields)
################################################################################
# "identification_and_status" # from first 6 sections
################################################################################
identification_and_status_fields <- c("NCTId","OrgStudyId","BriefTitle","Acronym","OfficialTitle",
                                     "StudyType","OverallStatus","WhyStopped","StartDate",
                                     "CompletionDate","ResponsiblePartyType","ResponsiblePartyInvestigatorFullName",
                                     "LeadSponsorName","IsFDARegulatedDrug","IsFDARegulatedDevice",
                                     "IsUnapprovedDevice","OversightHasDMC","BriefSummary",
                                     "DetailedDescription","Condition","Keyword")
# usethis::use_data(identification_and_status_fields)
################################################################################
# "study_design_arms_groups_and_interventions" # from sections 7 and 8
################################################################################
study_design_arms_groups_and_interventions_fields <- c("NCTId","DesignPrimaryPurpose",
                                                        "Phase","DesignInterventionModel","DesignInterventionModelDescription",
                                                        "DesignWhoMasked","DesignMasking","DesignMaskingDescription",
                                                        "DesignAllocation","EnrollmentCount","DesignObservationalModel",
                                                        "DesignTimePerspective","BioSpecRetention","BioSpecDescription",
                                                        "TargetDuration","ArmGroupLabel","ArmGroupType",
                                                        "ArmGroupDescription","InterventionType","InterventionName",
                                                        "InterventionDescription")
#usethis::use_data(study_design_arms_groups_and_interventions_fields)
################################################################################
# "outcome_measures_info_fields" # from section 9
################################################################################
outcome_measures_info_fields <- c("NCTId","PrimaryOutcomeMeasure","PrimaryOutcomeDescription",
                             "PrimaryOutcomeTimeFrame","SecondaryOutcomeMeasure",
                             "SecondaryOutcomeDescription","SecondaryOutcomeTimeFrame",
                             "OtherOutcomeMeasure","OtherOutcomeDescription","OtherOutcomeTimeFrame")
#usethis::use_data(outcome_measures_info_fields)
################################################################################
# "eligibility_fields" # from section 10
################################################################################
eligibility_fields <- c("NCTId","Gender","GenderBased","GenderDescription","MinimumAge",
                        "MaximumAge","HealthyVolunteers","EligibilityCriteria",
                        "StudyPopulation","SamplingMethod")
#usethis::use_data(eligibility_fields)
################################################################################
#FROM RESULTS DATA ELEMENTS

################################################################################
# "participant_flow_fields" # from section 1
################################################################################
participant_flow_fields <- c("NCTId","FlowRecruitmentDetails","FlowPreAssignmentDetails",
                             "FlowGroupTitle","FlowGroupDescription","FlowTypeUnitsAnalyzed",
                             "FlowPeriodTitle","FlowMilestoneComment","FlowMilestoneType",
                             "FlowAchievementNumSubjects","FlowAchievementNumUnits",
                             "FlowDropWithdrawType","FlowReasonNumSubjects","FlowReasonNumUnits",
                             "FlowReasonComment")
#usethis::use_data(participant_flow_fields)
################################################################################
# "baseline_characteristics_fields" # from section 2
################################################################################
baseline_characteristics_fields <-c ("NCTId","BaselineGroupTitle","BaselineGroupDescription",
                                     "BaselineDenomCountValue",
                                      "BaselineDenomUnits","BaselineTypeUnitsAnalyzed","BaselinePopulationDescription",
                                      "BaselineMeasureTitle","BaselineMeasureDescription",
                                      "BaselineMeasureParamType","BaselineMeasureDispersionType",
                                      "BaselineMeasureDenomCountValue","BaselineMeasureDenomUnits",
                                      "BaselineMeasureDenomUnitsSelected","BaselineMeasurePopulationDescription",
                                      "BaselineCategoryTitle","BaselineClassTitle","BaselineMeasurementValue",
                                      "BaselineMeasureUnitOfMeasure")
#usethis::use_data(baseline_characteristics_fields)
################################################################################
#"outcome_measures_results_fields" from section 3
################################################################################
outcome_measures_results_fields <- c( "NCTId","OutcomeMeasureType","OutcomeMeasureTitle","OutcomeMeasureDescription",
                                      "OutcomeMeasureTimeFrame","OutcomeMeasureAnticipatedPostingDate",
                                      "OutcomeGroupTitle","OutcomeGroupDescription","OutcomeDenomCountValue",
                                      "OutcomeMeasureTypeUnitsAnalyzed","OutcomeDenomUnits","OutcomeMeasurePopulationDescription",
                                      "OutcomeMeasureParamType","OutcomeMeasureDispersionType","OutcomeCategoryTitle",
                                      "OutcomeClassTitle","OutcomeClassDenomCountValue","OutcomeClassDenomUnits",
                                      "OutcomeMeasurementValue","OutcomeMeasureUnitOfMeasure",
                                      "OutcomeAnalysisGroupId","OutcomeAnalysisGroupDescription",
                                      "OutcomeAnalysisNonInferiorityType","OutcomeAnalysisTestedNonInferiority",
                                      "OutcomeAnalysisNonInferiorityComment","OutcomeAnalysisPValue",
                                      "OutcomeAnalysisPValueComment","OutcomeAnalysisStatisticalMethod",
                                      "OutcomeAnalysisStatisticalComment","OutcomeAnalysisParamType",
                                      "OutcomeAnalysisParamValue","OutcomeAnalysisCIPctValue","OutcomeAnalysisCINumSides",
                                      "OutcomeAnalysisCILowerLimit","OutcomeAnalysisCIUpperLimit",
                                      "OutcomeAnalysisDispersionType","OutcomeAnalysisDispersionValue",
                                      "OutcomeAnalysisEstimateComment","OutcomeAnalysisOtherAnalysisDescription")
#usethis::use_data(outcome_measures_results_fields)
################################################################################
# missing lists from sections: adverse event info, limitations and caveats, certain
# agreements, results contact
################################################################################



################################################################################
# FIELD LIST COMBINATIONS
# "registration_fields" # large list of registration data elements
################################################################################
registration_fields <- append(identification_and_status_fields,
                              append(study_design_arms_groups_and_interventions_fields,
                              append(outcome_measures_info_fields, eligibility_fields)))
# usethis::use_data(registration_fields)
################################################################################
# "results_fields" # large list of results data elements
################################################################################
results_fields <- append("NCTId",append(participant_flow_fields,append(baseline_characteristics_fields,
                                                        outcome_measures_results_fields)))
 #usethis::use_data(results_fields, overwrite = TRUE)
################################################################################
for_netmeta <-c("NCTId","ArmGroupLabel","ArmGroupType","ArmGroupDescription","ArmGroupInterventionName",
                "InterventionArmGroupLabel","InterventionName","InterventionType","InterventionDescription",
                "InterventionMeshId","InterventionMeshTerm","PrimaryOutcomeMeasure","PrimaryOutcomeTimeFrame",
                "SecondaryOutcomeMeasure","SecondaryOutcomeTimeFrame",
                "OtherOutcomeMeasure","OutcomeMeasureTitle","OutcomeGroupTitle","OutcomeGroupDescription",
                "OutcomeMeasureParamType","OutcomeMeasureDispersionType","OutcomeCategoryTitle",
                "OutcomeClassTitle","OutcomeClassDenomCountValue","OutcomeClassDenomUnits",
                "OutcomeMeasurementValue","OutcomeMeasureUnitOfMeasure",
                "OutcomeAnalysisEstimateComment","OutcomeAnalysisDispersionType","OutcomeAnalysisDispersionValue",
                "OutcomeAnalysisParamValue","OutcomeAnalysisParamType","OutcomeAnalysisDispersionValue",
                "OutcomeAnalysisGroupId","OutcomeAnalysisGroupDescription","ResultsFirstPostDate",
                "EnrollmentCount","IsFDARegulatedDrug","OverallStatus","Phase")
#usethis::use_data(for_netmeta, overwrite = T)
################################################################################
for_explorer <-  c("NCTId","OfficialTitle","BriefTitle","Acronym","StudyType","OverallStatus","StartDate",
                 "CompletionDate","LeadSponsorName","IsFDARegulatedDrug","IsFDARegulatedDevice","IsUnapprovedDevice",
                 "OversightHasDMC","Condition","Keyword","WhyStopped","DesignPrimaryPurpose","Phase",
                 "DesignInterventionModel","DesignMasking","DesignAllocation","EnrollmentCount",
                 "ArmGroupLabel","ArmGroupType","ArmGroupInterventionName","InterventionType","InterventionName","InterventionMeshId",
                 "InterventionMeshTerm","PrimaryOutcomeMeasure","PrimaryOutcomeTimeFrame",
                 "SecondaryOutcomeMeasure","SecondaryOutcomeTimeFrame","Gender",
                 "MinimumAge","MaximumAge","HealthyVolunteers","EligibilityCriteria","ResultsFirstPostDate",
                 "OutcomeAnalysisParamValue","OutcomeAnalysisParamType")
#usethis::use_data(for_explorer, overwrite = T)