diff --git a/_freeze/data_dictionary/execute-results/html.json b/_freeze/data_dictionary/execute-results/html.json index f049277..d712d19 100644 --- a/_freeze/data_dictionary/execute-results/html.json +++ b/_freeze/data_dictionary/execute-results/html.json @@ -1,7 +1,7 @@ { - "hash": "64f957fef77fe05786dc5c90a3009204", + "hash": "fba44738458e959be4fe8d5966ee4f53", "result": { - "markdown": "# Data Dictionary {.unnumbered}\n\n\n\n::: {.cell}\n\n:::\n\n::: {.cell tbl-colwidths='false'}\n\n:::\n\n\n## Project\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
ProjectIDProject IdentifierSystem-provided Project identifierIntegerSystem-assigned
ProjectNameProject NameUser-given Project nameStringYes
ProjectCrossReferenceIDProject Cross Reference IdentifierThe identifier of the Project under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Project is usedStringNo
ProjectCrossReferenceIDOriginProject Cross Reference Identifier OriginThe location/database/document where other identification \n for the same Project is usedStringNo
ProjectCountryProject CountriesThe countries where the Project takes placeMultiple selectionYes. Provide at least one option
ProjectFunderOrganizationProject Funder OrganizationThe organizations providing the funding to conduct the ProjectMultiple selectionYes. Provide at least one option
ProjectLeadingOrganizationProject Leading OrganizationThe organization/institution leading the Project executionSingle selectionYes. Provide at least one option
ProjectLeaderProject LeaderThe person leading the Project. Usually affiliated to the Leading OrganizationSingle selectionYes
ProjectOtherOrganizationOther OrganizationsOther organizations/partners/institutions involved in the execution of \n the Project (e.g., Laboratories, NGOs, etc.)Multiple selectionNo
ProjectPurposeProject PurposeDescription of the objectives and goals of the ProjectStringYes
ProjectNewSourceDataNew Source DataAnswer to the question: 'Does the Project involve collecting new data from Sources?'\n The answer is 'No' if the Project is using Source or Specimen data already available and generated as \n part of a different Project. The answer is 'Yes' when the Project involves collecting new data\n from Sources exclusively or when the Project involves the collection of new data and also the use of data from previous Projects)BooleanYes
ProjectAnimalSourceSpeciesAnimal Source SpeciesSpecies of the animals of interest for the Project as Animal Sources. It is possible\n to select high taxonomy levels such as 'mammals', 'chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionNo
ProjectObservationSourceObservation Source SpeciesSpecies of the animals of interest for the Project as Observation Sources. \n It is possible to select high taxonomy levels such as 'mammals', 'chordata', 'Insecta' etc. to \n indicate that no particular species is targetedMultiple selectionNo
ProjectEnvironmentalSourceEnvironmental Source TypesThe type(s) of Environmental Source(s) of interest for the ProjectMultiple selectionNo
ProjectInvertebrateSourceInvertebrate Source SpeciesSpecies of invertebrate that cause or transmit diseases collected 'off-host' that\n are of interest for the Project as Invertebrate Sources. It is possible to select high taxonomy\n levels such as 'Diptera', 'Insecta', etc. to indicate that no particular species is targetedMultiple selectionNo
=ProjectBiologicalHazardBiological HazardsThe type(s) of biological health hazard(s) of interest for the Project \n (e.g., 'Virus', 'Bacteria', 'Protozoa', 'Insecta')Multiple selectionNo
=ProjectVirusHazardVirusThe viruses of interest for the Project. It can be as specific as a clade/variant/etc of a species\n or as general as 'Virus' (e.g., 'Virus', 'SARS-CoV-2 Omicron variant', 'H5N1 Highly Pathogenic Avian Influenza clade 2.3.3.4b')Multiple selectionNo
=ProjectBacteriaHazardBacteriaThe bacteria of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Bacteria' (e.g., 'Group-A Streptococcus', 'Mycobacterium bovis')Multiple selectionNo
=ProjectProtozoaHazardProtozoaThe protozoa of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Protozoa' (e.g., 'Plasmodium relictum', 'Toxoplasma gondii')Multiple selectionNo
=ProjectFungiHazardFungiThe fungi of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Fungi' (e.g., 'Pseudogymnoascus destructans', 'Batrachochytrium dendrobatidis')Multiple selectionNo
=ProjectPrionHazardPrionThe prion of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Prion' (e.g., 'Chronic-wasting disease', 'Scrapie', 'Mad cow disease)Multiple selectionNo
=ProjectTransmissibleTumourHazardTransmissible TumourThe transmissible tumour of interest for the Project (e.g., 'Devil facial tumor 1', 'Devil facial tumor 2')Multiple selectionNo
=ProjectNematodaHazardThe nematode of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Nematode' (e.g., 'Toxocara canis', '')Multiple selectionNo
=ProjectPlatyhelminthHazardPlatyhelminthThe platyhelminth of interest for the Project. It can be as specific as a subspecies\n or as general as 'Platyhelminth' (e.g., 'Fasciola gigantica')Multiple selectionNo
=ProjectArthropodHazardArthropodThe arthropod of interest for the Project. It can be as specific as a subspecies\n or as general as 'Arthropod' (e.g., 'Sarcoptes scabiei', 'Rhipicephalus sanguineus')Multiple selectionNo
=ProjectChemicalHazardChemical HazardsThe type(s) of chemical health hazard(s) of interest for the Project \n (e.g., 'Heavy Metal', 'Organochlorine Pesticides', 'Cholinesterase-inhibbiting Pesticide', 'Toxins')Multiple selectionNo
=ProjectHeavyMetalHazardHeavy MetalThe heavy metal of interest for the Project. It can be as specific as a chemical form of the heavy metal \n or as general as the common name of the metal (e.g., 'Lead', 'Methylmercury')Multiple selectionNo
=ProjectOrganochlorinePesticidesHazardOrganochlorine PesticidesThe organochlorine pesticides of interest for the Project. It can be as specific as a type of organochlorine pesticides\n or as general as 'Organochlorine Pesticide' (e.g., 'DDT', 'Lindane')Multiple selectionNo
=ProjectCholinesteraseInhibbitingPesticideHazardCholinesterase-inhibbiting PesticideThe cholinesterase-inhibbiting pesticide of interest for the Project. It can be as specific as a type of \n cholinesterase-inhibbiting pesticide or as general as 'Cholinesterase-inhibbiting Pesticide' \n (e.g., 'Diazinon', 'Malathion')Multiple selectionNo
=ProjectToxinsHazardToxinsThe toxin of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Toxin' (e.g., 'Clostridium botulinum toxin type C', 'Tetanus toxin')Multiple selectionNo
=ProjectPhysicalHazardPhysical HazardsThe type(s) of physical health hazard(s) of interest for the Project \n (e.g., 'Trap', 'Vehicle Collisions', 'Entanglement', 'Burning', 'Electrocution')Multiple selectionNo
=ProjectPhysiologicalHazardPhysiological HazardsThe type(s) of physiological health problems of interest for the Project \n (e.g., 'Hypocalcemia', 'Hyperkalemia', 'Amyloid A amyloidosis')Multiple selectionNo
ProjectStartDateProject Start DateThe starting date of the ProjectDateYes
ProjectEndDateProject End DateThe date when the Project is projected/planned to end or officially endedDateNo
ProjectUrlProject URLsURLs of the Project or of the organizations/institutions involved in the ProjectStringNo
\n
\n```\n:::\n:::\n\n\n## Surveillance Activity \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
Project NameProject NameThe name of the Project containing the Surveillance ActivitySingle selectionYes
WildlifeHealth_SurveillanceActivityIDSurveillance Activity IdentifierSystem-provided Surveillance Activity identifierIntegerSystem-assigned
SurveillanceActivityCodeSurveillance Activity CodeUser-provided Surveillance Activity codeStringYes
SurveillanceActivityCrossIDSurveillance Activity Cross IdentifierThe identifier of the Surveillance Activity under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Surveillance Activity is usedStringNo
SurveillanceActivityCrossIDOriginSurveillance Activity Cross Identifier OriginThe location/database/document where other identification \n for the same Surveillance Activity is usedStringNo
TypeSurveillanceActivityType of Surveillance ActivityThe type of surveillance associated with the Surveillance Activity\n (e.g., Targeted, Scanning, Outbreak Investigation, or Research). If two or more\n surveillance types are involved, then two or more Surveillance Activities are needed\n so each one receives a single type of surveillanceSingle selectionYes
GrantNameGrant NameThe name of the grant funding the Surveillance Activity. If there is not a \n grant involved, type 'N/A'StringYes
GrantNumberGrant NumberThe number of the grant funding the Surveillance ActivityStringNo
SurveillanceActivityLeaderSurveillance Activity LeaderThe person leading the Surveillance ActivitySingle selectionYes
SurveillanceActivityLeaderOrganizationLeader OrganizationThe affiliation of the person leading the Surveillance ActivitySingle selectionYes
SurveillanceActivityLeaderOrganizationRORLeader Organization RORThe ROR of the affiliation of the person leading the Surveillance ActivityStringNo
SurveillanceActivityOrganizationsInvolvedOrganizations InvolvedOrganizations/partners/institutions involved in the execution of \n the Surveillance Activity (e.g., Laboratories, NGOs, etc.)Multiple selectionYes
SurveillanceActivityCountryCountry or Countries Included in the Surveillance ActivityThe countries where the Surveillance Activity takes placeMultiple selectionYes
SurveillanceActivityPurposeSurveillance Activity PurposeDescription of the objectives and goals of the Surveillance ActivityStringYes
SurveillanceActivityDataCuratorSurveillance Activity Data CuratorThe person taking responsibility for the entering and cleaning of the\n Surveillance Activity dataSingle selectionYes
SurveillanceActivityDataOwnerSurveillance Activity Data OwnerThe person or institution that owns the data of the Surveillance ActivityStringYes
SurveillanceActivityOtherIndividualsOther IndividualsOther individuals relevant for the Surveillance Activity, such as laboratory\n point of contacts, local leaders, etc.Multiple selectionNo
SurveillanceActivityNewSourceDataNew Source DataAnswer to the question: 'Does the Surveillance Activity involve collecting new data from Sources?'\n The answer is 'No' if the Surveillance Activity is using Source or Specimen data already available and generated as \n part of a different Surveillance Activity. The answer is 'Yes' when the Surveillance Activity involves collecting new data\n from Sources exclusively or when the Surveillance Activity involves the collection of new data and also the use of data from\n previous Surveillance Activity)BooleanYes
SurveillanceActivityObservationsIncludedSurveillance Activity Includes Observed-only AnimalsAnswer to the question: 'Does the Surveillance Activity include information of observed-only animals'BooleanYes
SurveillanceActivityAnimalSourcesIncludedSurveillance Activity Includes Animal SourcesAnswer to the question: 'Does the Surveillance Activity include information of individual animals?'BooleanYes
SurveillanceActivityEnvironmentalSourcesIncludedSurveillance Activity includes Environmental SourcesAnswer to the question: 'Does the Surveillance Activity include information of Environmental Sources (e.g., water)?'BooleanYes
SurveillanceActivityInvertebrateSourcesIncludedSurveillance Activity Includes Invertebrate SourcesAnswer to the question: 'Does the surveillance objective include information from Invertebrate sources (e.g., CO2 traps)?'BooleanYes
SurveillanceActivityNewObservationRecordsAddedNew Observations RecordsAnswer to the question: 'Does the Surveillance Activity involve the documentation of new \n Observation Records?'BooleanYes
SurveillanceActivityNewAnimalSourceRecordsAddedNew Animal Source RecordsAnswer to the question: 'Does the Surveillance Activity involve the documentation of new \n Animal Source Records?'BooleanYes
SurveillanceActivityNewEnvironmentalSourceRecordsAddedNew Environmental Source RecordsAnswer to the question: 'Does the Surveillance Activity include the documentation of new \n Environmental Source Records (e.g., water)?'BooleanYes
SurveillanceActivityNewInvertebrateSourceRecordsAddedNew Invertebrate Source RecordsAnswer to the question: 'Does the Surveillance Activity include the documentation of new \n Invertebrate Source Records (e.g., new invertebrate collection)?'BooleanYes
SurveillanceActivitySpecimensNew SpecimensAnswer to the question: 'Are new Specimens collected under the Surveillance Activity?BooleanYes
SurveillanceActivityNewDiagnositcProductsNew Diagnostic ProductsAnswer to the question: 'Does the Surveillance Activity creates new diagnostic products?BooleanYes
SurveillanceActivityNewPooledSpecimensNew Pooled SpecimensAnswer to the question: 'Does the Surveillance Activity creates new pooled specimens?BooleanYes
=SurveillanceActivityBiologicalHazardBiological HazardsThe type(s) of biological health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Virus', 'Bacteria', 'Protozoa', 'Insecta')Multiple selectionNo
=SurveillanceActivityVirusHazardVirusThe viruses of interest for the Surveillance Activity. It can be as specific as a clade/variant/etc of a species\n or as general as 'Virus' (e.g., 'Virus', 'SARS-CoV-2 Omicron variant', 'H5N1 Highly Pathogenic Avian Influenza clade 2.3.3.4b')Multiple selectionNo
=SurveillanceActivityBacteriaHazardBacteriaThe bacteria of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Bacteria' (e.g., 'Group-A Streptococcus', 'Mycobacterium bovis')Multiple selectionNo
=SurveillanceActivityProtozoaHazardProtozoaThe protozoa of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Protozoa' (e.g., 'Plasmodium relictum', 'Toxoplasma gondii')Multiple selectionNo
=SurveillanceActivityFungiHazardFungiThe fungi of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Fungi' (e.g., 'Pseudogymnoascus destructans', 'Batrachochytrium dendrobatidis')Multiple selectionNo
=SurveillanceActivityPrionHazardPrionThe prion of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Prion' (e.g., 'Chronic-wasting disease', 'Scrapie', 'Mad cow disease)Multiple selectionNo
=SurveillanceActivityTransmissibleTumourHazardTransmissible TumourThe transmissible tumour of interest for the Surveillance Activity (e.g., 'Devil facial tumor 1', 'Devil facial tumor 2')Multiple selectionNo
=SurveillanceActivityNematodaHazardThe nematode of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Nematode' (e.g., 'Toxocara canis', '')Multiple selectionNo
=SurveillanceActivityPlatyhelminthHazardPlatyhelminthThe platyhelminth of interest for the Surveillance Activity. It can be as specific as a subspecies\n or as general as 'Platyhelminth' (e.g., 'Fasciola gigantica')Multiple selectionNo
=SurveillanceActivityArthropodHazardArthropodThe arthropod of interest for the Surveillance Activity. It can be as specific as a subspecies\n or as general as 'Arthropod' (e.g., 'Sarcoptes scabiei', 'Rhipicephalus sanguineus')Multiple selectionNo
=SurveillanceActivityChemicalHazardChemical HazardsThe type(s) of chemical health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Heavy Metal', 'Organochlorine Pesticides', 'Cholinesterase-inhibbiting Pesticide', 'Toxins')Multiple selectionNo
=SurveillanceActivityHeavyMetalHazardHeavy MetalThe heavy metal of interest for the Surveillance Activity. It can be as specific as a chemical form of the heavy metal \n or as general as the common name of the metal (e.g., 'Lead', 'Methylmercury')Multiple selectionNo
=SurveillanceActivityOrganochlorinePesticidesHazardOrganochlorine PesticidesThe organochlorine pesticides of interest for the Surveillance Activity. It can be as specific as a type of organochlorine pesticides\n or as general as 'Organochlorine Pesticide' (e.g., 'DDT', 'Lindane')Multiple selectionNo
=SurveillanceActivityCholinesteraseInhibbitingPesticideHazardCholinesterase-inhibbiting PesticideThe cholinesterase-inhibbiting pesticide of interest for the Surveillance Activity. It can be as specific as a type of \n cholinesterase-inhibbiting pesticide or as general as 'Cholinesterase-inhibbiting Pesticide' \n (e.g., 'Diazinon', 'Malathion')Multiple selectionNo
=SurveillanceActivityToxinsHazardToxinsThe toxin of interest for the Surveillance Activity. It can be as specific as the protein subtype\n or as general as 'Toxin' (e.g., 'Clostridium botulinum toxin type C', 'Tetanus toxin')Multiple selectionNo
=SurveillanceActivityPhysicalHazardPhysical HazardsThe type(s) of physical health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Trap', 'Vehicle Collisions', 'Entanglement', 'Burning', 'Electrocution')Multiple selectionNo
=SurveillanceActivityPhysiologicalHazardPhysiological HazardsThe type(s) of physiological health problems of interest for the Surveillance Activity \n (e.g., 'Hypocalcemia', 'Hyperkalemia', 'Amyloid A amyloidosis')Multiple selectionNo
SurveillanceActivityIACUCNeededIACUC NeededAnswer to the question: 'Is an IACUC needed to conduct the Surveillance Activity?'BooleanYes
SurveillanceActivityOrganizationProvidingIACUCOrganization providing IACUCThe organization providing the IACUC approving the methodology of the Surveillance ActivityStringYes
SurveillanceActivityIACUCCodeIACUC CodeThe code of the IACUC approving the methodology of the Surveillance ActivityStringYes
SurveillanceActivityLocationPolygonUnitOfInterestLocation Polygon Is a Unit of InterestAnswer to the question: 'Is the Location a Polygon that represents a unit of interest for the Surveillance Activity\n (e.g., a parcel or a house)?'BooleanYes
SurveillanceActivityLocationPolygonRepresentsLocation Polygon DescriptionA description of what each polygon Location represents in the Surveillance Activity (e.g., a parcel or a house)StringYes
SurveillanceActivityLocationSpatialFileProvidedSpatial File with Location Polygons Provided'Answer to the question: 'Are the Location polygons included in the \n Surveillance Activity provided as a spatial file (.shp, .geojson, other)?'BooleanYes
SurveillanceActivityLocationPolygonProjectionSpatial Projection Of Location Polygons In Spatial FileAnswer to the question: 'Is the spatial projection of the Location Polygons file provided as a spatial file?'StringYes
SurveillanceActivityEventUnitOfInterestThe Event Is a Unit of InterestAnswer to the question: 'Is the Event (and its associated longitude, latitude, and time) \n a unit of interest for the Surveillance Activity?'BooleanYes
SurveillanceActivityEventRepresentsEvent DescriptionA description of what each Event represents in the Surveillance Activity \n (e.g., a trap, a stall, the location of a health event, etc.)StringYes
SurveillanceActivityEventGroupingEvents Are GroupedAnswer to the question: 'Are Events associated with the current \n Surveillance Activity clustered in units smaller than 'Location'?'BooleanYes
SurveillanceActivityEventGroupingStructureGrouping of EventsExplain the grouping structure of the Events below 'location'\n (e.g., The location is a market. The events are stalls of each vendor in the market. \n The Events are grouped by vendor in each market. So stalls [events], \n within vendors [group], within markets [location])StringYes
SurveillanceActivityEventGroupsSpatialFileProvidedEvent Groups File Provided'Answer to the question: 'Are the Event groups provided as a spatial file (.shp, .geojson, other)?'BooleanYes
SurveillanceActivityEventGroupsProjectionSpatial Projection of Event Groups Spatial FileThe spatial projection of Event groups file provided as a spatial fileStringYes
SurveillanceActivitySourceRecordGroupingSource Records Are GroupedAnswer to the question: 'Are Source Records associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
SurveillanceActivitySourceRecordGroupingStructureGrouping of Source RecordsExplain the grouping structure of the Source Records below 'Event' \n (e.g., Events represent a stall in a market. Source records (animals in the stall) \n are grouped by cage in each stall)StringYes
SurveillanceActivityLabParticipating LaboratoriesThe laboratories associated with the Surveillance ActivityMultiple selectionYes
SurveillanceActivityOtherSurveillanceActivityAssociatedOther Surveillance Activities or Datasets AssociatedAnswer to the question: 'Are there other Surveillance Activities\n associated with the current Surveillance Activity or other datasets?' \n (e.g., if the current Surveillance Activity uses Specimens collected as part of \n other associated Surveillance Objective, or if the full set of events of a ranger\n patrol (beyond health events) belong to the patrol XXXX of the protected\n area Y')BooleanYes
SurveillanceActivityOtherSurveillanceActivityAssociatedCodeAssociated Surveillance Activities CodesDescribe why other Surveillance Activities are associated with the\n current Surveillance Activity (e.g., the current Surveillance Activity uses \n Specimens collected as part of Surveillance Objective ZZZZ, or the health Events\n are part of patrols conducted in protected YYY'. The patrol ID including \n the Events of the current Surveillance Activity are given in the Field Visit\n Cross Reference Identifier)Multiple selectionYes
SurveillanceActivityReasonOtherSurveillanceActivityAssociatedReason other Surveillance Activities or Datasets Are AssociatedDescribe why other Surveillance Activities are associated with the\n current Surveillance Activity (e.g., the current Surveillance Activity uses \n Specimens collected as part of Surveillance Objective ZZZZ, or the health Events\n are part of patrols conducted in protected YYY'. The patrol ID including \n the Events of the current Surveillance Activity are given in the Field Visit\n Cross Reference Identifier)StringYes
SurveillanceActivityRelevantUrlSurveillance Activity URLsURLs of the Surveillance Activity, associated with the Surveillance\n Activity, or organizations leading the Surveillance ActivityStringNo
SurveillanceActivityPublicationSurveillance Activity PublicationsPublication references associated with the Surveillance ActivityStringNo
SurveillanceActivityStartDateSurveillance Activity Start DateThe date the Surveillance Objective officially startedDateYes
SurveillanceActivityEndDateSurveillance Activity End DateThe date the Surveillance Activity is projected to end or officially endedDateNo
\n
\n```\n:::\n:::\n\n\n## Field Visit\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
FieldVisitIDField Visit IdentifierSystem-provided Field Visit identifierIntegerSystem-assigned
FieldVisitCodeField Visit CodeUser-provided Field Visit codeStringYes
FieldVisitCrossIDField Visit Cross IdentifierThe identifier of the Field Visit under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Field Visit is usedStringNo
FieldVisitCrossIDOriginField Visit Cross Identifier OriginThe location/database/document where other identification \n for the same Field Visit is usedStringNo
FieldVisitLeaderField Visit LeaderThe name of the leader of the Field VisitSingle selectionYes
FieldVisitTypeField Visit TypeThe type of Field Visit (e.g., 'Market', 'Free-ranging', 'Ranger patrolling').\n More than one Field Visit type can be selectedMultiple selectionYes
FieldVisitDescriptionField Visit DescriptionThe background for the Field Visit (e.g., why, who, how, where, what for)StringYes
FieldVisitStartDateField Visit Start DateThe date the Field Visit startedDateYes
FieldVisitEndDateField Visit End DateThe date the Field Visit ended or the anticipated ending dateDateYes
\n
\n```\n:::\n:::\n\n\n## Location\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
LocationIDLocation IdentifierSystem-provided Location identifierIntegerSystem-assigned
Location Polygon IDLocation Polygon IdentifierIf a spatial file with the different Locations has been entered in the database.\n then provide the ID of the polygon representing the Location in such file. This attribute is\n available only when the spatial file has been entered in the database as reported in the \n Surveillance Activity metadataStringYes
LocationNameLocation CodeUser-provided Location codeStringYes
LocationCrossID Location Cross IdentifierThe identifier of the Location under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Location is usedStringNo
LocationCrossIDOriginLocation Cross Identifier OriginThe database/document/other where other identification \n for the same Location is usedStringNo
LocationTypeLocation TypeThe type of Location containing Events \n (e.g., 'market', 'zone in Protected area', 'grid cell', 'parcel', etc')Single selectionYes
LocationTargetedRecordsLocation Targeted RecordsIndicate what type of Records (Group, Animal, Environmental,\n or from Arthropod Sources) are targeted in the EventMultiple selectionYes
LocationStartDateStart DateThe date the activities in the Location startedDateYes
LocationEndDateEnd DateThe date the activities in the Location ended or the anticipated ending dateDateNo
LocationCommentsCommentsProvided any other relevant information regarding the LocationStringNo
\n
\n```\n:::\n:::\n\n\n\n## Event\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
EventIDEvent IdentifierSystem-provided Event identifierIntegerSystem-assigned
EventCodeEvent CodeUser-provided Event codeStringYes
EventCrossIDEvent Cross IdentifierThe identifier of an Event in another system (e.g., database/document/other)StringNo
EventCrossIDOriginEvent Cross Identifier OriginThe database/document/other where other identification \n for the same Event is usedStringNo
EventLongitudeLongitudeLongitude coordinate. Non decimal degree coordinates are automatically converted. \n If coordinates are provided in UTM, then the UTM zone must be provided (see below)FloatYes
EventLatitudeLatitudeLatitude coordinate. Non decimal degree coordinates are automatically converted. \n If coordinates are provided in UTM, then the UTM zone must be provided (see below)FloatYes
EventUTMZoneEvent UTM ZoneUTM Zone where the Event occurs. It applies if the longitude an latitude odf\n the Event are provided in UTM coordinate reference system. \n See https://www.dmap.co.uk/utmworld.htmFloatYes
EventCoordinatesExactOrEstimatedEvent Coordinates Exact Or EstimatedIndicate weather the longitude and latitude coordinates are exact (GPS device)\n or estimated based on another method (e.g., by pointinf the location in the map above)Single selectionYes
EventCountryCountryCountry where the Event happensSingle selectionYes
EventStateStateState where the Event happensSingle selectionNo
EventProvinceProvinceProvince where the Event happensSingle selectionNo
EventUnitEvent unitExplanation of what the Event represents (e.g., a field finding, \n a market, a vendor, a cage, a grid cell, a point in a transect, a mist net, \n a point in a parcel, a point in a protected area, etc.)Single selectionYes
EventFeaturesEvent FeaturesSpecific set of findings at the Event that are dynamic over time\n (e.g., fire, smoke, etc)Multiple selectionYes
EventByEvent reported byThe person that reported the EventSingle selectionYes
EventBySectorSector of the reporterThe sector of the person that reported the EventSingle selectionNo
EventTargetedRecordsEvent Targeted RecordsIndicate what type of Records (Group, Animal, Environmental,\n or from Arthropod Sources) are targeted in the EventMultiple selectionYes
EventSmartSourceEvent from SMARTAnswer to the question: 'Was the Event recorded using SMART?'Single selectionNo
EventSiteCodeSite codeThe site the Events are grouped by siteSingle selectionNo
EventZoneCodeZone codeThe zone the Events are grouped by zoneSingle selectionNo
EventMarketCodeMarket codeThe market the Events are grouped by marketSingle selectionNo
EventGridCodeGrid codeThe grid code the when Events are grouped by gridSingle selectionNo
EventGridCellCodeGrid cell codeThe grid cell code when Events are grouped by grid cellSingle selectionNo
EventStationCodeStation codeThe station code when Events are grouped by stationSingle selectionNo
EventTransectCodeTransect codeThe transect code when Events are grouped by transectSingle selectionNo
EventVendorCodeVendor codeThe vendor code when Events are grouped by vendorSingle selectionNo
EventTrapCodeTrap codeThe vendor code when Events are grouped by trapSingle selectionNo
EventMistNetCodeMist net codeThe mist net code when Events are grouped by mist net codeSingle selectionNo
EventOtherSpatialUnitCodeOther spatial unit codeThe spatial unit code when Events are grouped by another spatial unitSingle selectionNo
EventStudyYearThe study yearThe temporal unit code when Events are grouped by year unitSingle selectionNo
EventStudySeasonThe study seasonThe temporal unit code when Events are grouped by study seasonSingle selectionNo
EventStudyMonthThe study monthThe temporal unit code when Events are grouped by monthSingle selectionNo
EventStudyWeekThe study weekThe temporal unit code when Events are grouped by weekSingle selectionNo
EventStudyDayPeriodThe study day periodThe temporal unit code when Events are grouped by study daySingle selectionNo
EventStudyHourThe study hourThe temporal unit code when Events are grouped by study hourSingle selectionNo
EventOtherTemporalUnitOther spatial temporal unit codeThe temporal unit code when Events are grouped by another temporal unitSingle selectionNo
EventDateEvent DateThe date and time of the Event. If the Event is a period of time (e.g, \n mist-nets to capture bats) then the end time and date can be obtained from the effort\n associated fields (see below)StringYes
EventTimeAssembledTime assembledThe time a trap or similar representing an Event is set upDatetimeNo
EventTimeDisassembledTime disassembledThe time a trap or similar representing an Event is dissamsembledDatetimeNo
\n
\n```\n:::\n:::\n\n\n## Group Source \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
GroupSourceCodeStructureGroup Source Code StructureExplain the nomenclature of the Group Source Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, and then the number is \n the sequential number of the Group Source in the Surveillance InitiativeStringYes
GroupSourceSpeciesGroup Source SpeciesSpecies of the Group Sources of interest for the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Mammalia', 'Chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
GroupSourceSpeciesIdentificationMethodGroup Source Species IdentificationExplain the methodology used to identify the species of the Group SourcesMultiple selectionYes
GroupSourceSpeciesIdentificationMethodReferencesGroup Source Species Identification Method ReferencesProvide references associated with the identification method of the species of Group SourcesStringNo
GroupSourceInclusionCriteriaGroup Source Inclusion CriteriaProvide specific inclusion criteria for the Group Sources of the species of interest \n considered for the Surveillance Activity, if anyStringYes
GroupSourceExclusionCriteriaGroup Source Exclusion CriteriaExplain the reason to exclude certain Group Sources \n of the species of interest for the Surveillance Activity, if anyStringNo
GroupSourceHowObtainedObtaining Group SourcesExplain how Group Sources were obtained for the Surveillance ActivityStringYes
GroupSourceIdentificationGroup Sources Are Identified IndividuallyAnswer to the question: 'Are Group Sources (herds, etc.) individually identified?'\n (e.g. herd, farm, etc.)BooleanYes
GroupSourceIdentificationMethodGroup Source Identification MethodExplain how Group Sources are individually identified\n (e.g. herd, farm, etc.)StringYes
GroupSourceIdentificationMethodReferencesGroup Source Identification Method ReferencesProvide references associated with identification method of Group SourcesStringNo
GroupSourceRecordsOverTimeGroup Source Records Over TimeAnswer to the question: 'Is it aimed to obtained records of the same Group Source during the \n Surveillance Activity?'BooleanYes
GroupSourceGroupingGroup Source Are GroupedAnswer to the question: 'Are Group Sources associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
GroupSourceGroupingStructureGrouping of Group SourcesExplain the grouping structure of the Group Sources below 'Event' \n (e.g., Events represent a market vendor. Group Sources (animals of the same species) \n are grouped by each cage of the vendor (so a cage of a unique vendor can have only-observed \n animals of multiple species)StringYes
GroupSourceDiagnosticsUsedDiagnostics Are Applied in the Group SourceAnswer to the question: 'Are diagnostics conducted in the Group Source?' \n This question refers to Diagnostics that the full Group\n as the tested Specimen. For example, herd body condition. Information on Diagnostics applied in \n a Specimen sourced by an Group (e.g., feces from a herd) are requested below at the Group\n Source Specimen levelBooleanYes
GroupSourceDiagnosticsUsedProtocolGroup Source Diagnostic ProtocolsName and describe the protocols of the Diagnostics applied in Group SourcesStringYes
GroupSourceDiagnosticsUsedProtocolReferencesGroup Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in Group SourcesStringYes
GroupSourceSpecimenUsedGroup Specimen UsedAnswer to the question: 'Are Specimens from Group Sources\n (e.g., feces, etc.) collected under a different Surveillance Activity\n used in the current Surveillance Activity?'BooleanYes
GroupSourceSpecimenCollectionGroup Specimen CollectionAnswer to the question: 'Are Specimens collected from the Group Sources\n (e.g., feces, etc.) while in the field under the current Surveillance Activity?'BooleanYes
GroupSourceSpecimenTypeGroup Source Specimen TypeSelect the Specimen Types used or collected from Group SourcesMultiple selectionYes
GroupSourceSpecimenCollectionMethodGroup Source Specimen Collection MethodExplain how the Specimens were collected from the surroundings of Group Sources \n (e.g., feces in a cage, urine under a bat roost)StringYes
GroupSourceSpecimenCollectionMethodReferencesGroup Source Specimen Collection Method ReferencesProvide references associated with the collection method of the Group Source SpecimensStringNo
GroupSourceSpecimenCollectionParasitesVectorsGroup Specimen Collection Includes Parasites or VectorsAnswer to the question: 'Are parasites or vectors collected from the Group Sources surroundings \n (e.g., when collecting a bat species-specific lice below a roost of the corresponding bat host species.\n Otherwise the parasite or vector is an 'Arthropod Source')BooleanYes
GroupSourceSpecimenFieldStorageGroup Specimen Field StorageMethod to preserve the Group Specimens collected in the fieldMutiple selectionYes
GroupSourceSpecimenLabStorageGroup Specimen Laboratory StorageMethod to preserve the Group Specimens collected in the laboratoryMutiple selectionYes
GroupSourceSpecimenPoolingGroup Source Specimen PoolingAnswer to the question: 'Are the Group Source Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' in the database see the online database manual)BooleanYes
GroupSourceSpecimenPoolingStrategyGroup Source Specimen Pooling StrategyExplain the pooling method of the Group Source Specimens \n (for a definition of 'pooling' in the database see the online database manual)StringYes
GroupSourceSpecimenCodeStructureGroup Source Specimen Code StructureExplain the nomenclature of the Group Source Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, the following letters\n are the type of Specimen, then the numbers are the Group Source, and the last number is \n the sequential Specimen from the Group SourceStringYes
GroupSourceSpecimenDiagnosticsUsedDiagnostics Are Applied in the Group SpecimensAnswer to the question: 'Are diagnostics applied to Group Source Specimens?'.\n Diagnostics applied in a full Group Source are requested aboveBooleanYes
GroupSourceSpecimenDiagnosticsUsedProtocolGroup Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conducted with in the Group Source SpecimensStringYes
GroupSourceSpecimenDiagnosticsUsedProtocolReferencesGroup Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in the Group Source SpecimensStringNo
GroupSourceSpecimenCriteriaPositiveTestGroup Specimen Criteria Positive TestExplain the criteria to establish that each diagnostic test method applied to an Group\n Source Specimen is positive. The criteria for positive Group Source and Group Source Specimens are requested belowStringYes
GroupSourceSpecimenCriteriaPositiveTestReferencesGroup Specimen Criteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test method applied to an Group\n Source Specimen is positiveStringNo
GroupSourceSpecimenCriteriaPositiveCaseGroup Source Specimen Criteria Positive CaseExplain the criteria to establish that an Group\n Source Specimen is positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for positive Group Source Records are requested belowStringYes
GroupSourceSpecimenCriteriaPositiveCaseReferencesGroup Source Specimen Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Group\n Source Specimen is positive for each specific hazard targeted in the Surveillance ActivityStringNo
GroupSourceRecordCriteriaPositiveCaseGroup Source Record Criteria Positive CaseExplain the criteria to establish that an Group\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
GroupSourceRecordCriteriaPositiveCaseReferencesGroup Source Record Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Group\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Animal Source \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
AnimalSourceCodeStructureAnimal Source Code StructureExplain the nomenclature of the Animal Source Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, and then the number is \n the sequential number of the Animal Source in the Surveillance InitiativeStringYes
AnimalSourceSpeciesAnimal Source SpeciesSpecies of the Animal Sources of interest for the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Mammalia', 'Chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
AnimalSourceSpeciesIdentificationMethodAnimal Source Species IdentificationExplain the methodology used to identify the species of the Animal SourcesMultiple selectionYes
AnimalSourceSpeciesIdentificationMethodReferencesBAnimal Source Species Identification Method ReferencesProvide references associated with the identification method of the species of Animal SourceStringNo
AnimalSourceInclusionCriteriaAnimal Source Inclusion CriteriaProvide specific inclusion criteria for the Animal Sources of the species of interest \n considered for the Surveillance Activity, if anyStringYes
AnimalSourceExclusionCriteriaAnimal Source Exclusion CriteriaExplain the reason to exclude certain Animal Sources \n of the species of interest for the Surveillance Activity, if anyStringNo
AnimalSourceHowObtainedObtaining Animal SourcesExplain how Animal Sources are obtained for the Surveillance ActivityStringYes
AnimalSourceCapturedAnimal Source CapturedAnswer to the question: 'Are Animal Sources associated with the current \n Surveillance Activity captured?'BooleanYes
AnimalSourceCaptureProtocolAnimal Source Capture ProtocolExplain how Animal Sources are capturedStringYes
AnimalSourceCaptureProtocolReferencesAnimal Source Capture Protocol ReferencesProvide references associated with the capture method of the Animal SourcesStringNo
AnimalSourceIdentificationAnimal Sources Are Identified IndividuallyAnswer to the question: 'Are Animal Sources individually identified?'\n (e.g. rings, line pattern, chip, etc.)BooleanYes
AnimalSourceIdentificationMethodAnimal Source Identification MethodExplain how Animal Sources are individually identified\n (e.g. rings, line pattern, chip, etc.)StringYes
AnimalSourceIdentificationMethodReferencesAnimal Source Identification Method ReferencesProvide references associated with identification method of Animal SourcesStringNo
AnimalSourceRecordsOverTimeAnimal Source Records Over TimeAnswer to the question: 'Is it aimed to obtained records of the same Animal Source during the \n Surveillance Activity?'BooleanYes
AnimalSourceRecaptureAnimal Source RecaptureAnswer to the question: 'Are Animal Sources recaptured during the Surveillance Activity?'BooleanYes
AnimalSourceFateAfterRecaptureAnimal Source Fate After Capture RecaptureExplain what happens with the Animal Sources identified individually after recaptureStringNo
AnimalSourceEuthanasiaAnimal Sources EuthanasiaAnswer to the question: 'Are Animal Sources euthanized?'BooleanYes
AnimalSourceEuthanasiaMethodAnimal Source Euthanasia MethodExplain how Animal Sources are euthanized'StringYes
AnimalSourceEuthanasiaMethodReferencesAnimal Source Euthanasia Method ReferencesProvide references associated with the euthanasia method usedStringNo
AnimalSourceCarcassCollectedAnimal Source Carcass CollectedAnswer to the question: 'Are Animal Source carcasses collected as part the Surveillance Activity?'BooleanYes
AnimalSourceCarcassFieldStorageCarcass Field StorageThe methods used to preserve carcasses collected while in the fieldMutiple selectionYes
AnimalSourceCarcassLabStorageCarcass Laboratory StorageThe methods to preserve carcasses collected while in the laboratoryMutiple selectionYes
AnimalSourceCarcassNecropsyAnimal Source Carcass For NecropsyAnswer to the question: 'Are Animal Source carcasses collected as part the Surveillance Activity necropsied?'BooleanYes
AnimalSourceCarcassNecropsyProtocolAnimal Source Necropsy ProtocolDescribe the protocol used to conduct the necropsiesStringNo
AnimalSourceCarcassNecropsyProtocolReferencesAnimal Source Necropsy Protocol ReferencesProvide references associated with the protocol to conduct the necropsiesStringNo
AnimalSourceGroupingAnimal Source Are GroupedAnswer to the question: 'Are Animal Sources associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
AnimalSourceGroupingStructureGrouping of Animal SourcesExplain the grouping structure of the Animal Sources below 'Event' \n (e.g., Events represent a stall in a market. Animal Sources are grouped by cage in each stall)StringYes
AnimalSourceDiagnosticsUsedDiagnostics Are Applied in the Animal SourceAnswer to the question: 'Are diagnostics conducted in Animal Source?' \n This question refers to Diagnostics that use either the carcass or the full animal\n as the tested Specimen. For example, ultrasound or X-rays. Information on Diagnostics applied in \n a Specimen sourced by an animal are requested below at the Animal Source Specimen levelBooleanYes
AnimalSourceDiagnosticsUsedProtocolAnimal Source Diagnostic ProtocolsName and describe the protocols of the Diagnostics applied in Animal SourcesStringYes
AnimalSourceDiagnosticsUsedProtocolReferencesAnimal Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in Animal SourcesStringYes
AnimalSourceSpecimenUsedAnimal Specimen UsedAnswer to the question: 'Are Specimens from Animal Sources\n (e.g., live animal, carcass) collected under a different Surveillance Activity\n used in the current Surveillance Activity?'BooleanYes
AnimalSourceSpecimenCollectionAnimal Specimen CollectionAnswer to the question: 'Are Specimens collected from the Animal Sources\n (e.g., live animal, carcass) while in the field or during a necropsy under the current \n Surveillance Activity?'BooleanYes
AnimalSourceSpecimenTypeAnimal Source Specimen TypeSelect the Specimen Types used or collected from Animal SourcesMultiple selectionYes
AnimalSourceSpecimenCollectionMethodAnimal Source Specimen Collection MethodExplain how the Specimens are collected from the Animal SourcesStringYes
AnimalSourceSpecimenCollectionMethodReferencesAnimal Source Specimen Collection Method ReferencesProvide references associated with the collection method of the Animal Source SpecimensStringNo
AnimalSourceSpecimenCollectionAtRecaptureAnimal Specimen Collection at RecaptureAnswer to the question: 'Are Specimens collected from Animal Sources when they are recaptured?'BooleanYes
AnimalSourceSpecimenCollectionParasitesVectorsAnimal Specimen Collection Includes Parasites or VectorsAnswer to the question: 'Are parasites or vectors collected directly from the Animal Sources or\n are they collected from a known Animal Source?' (in the first, case the parasites or vectors are collected \n directly from the Animal Source. In the second case, they can be associated to an Animal Source, \n for example, when collecting a tick right below a carcass. Otherwise the parasite or vector is an 'Arthropod \n Source')BooleanYes
AnimalSourceSpecimenFieldStorageAnimal Specimen Field StorageMethod to preserve the Animal Specimens collected in the fieldMutiple selectionYes
AnimalSourceSpecimenLabStorageAnimal Specimen Laboratory StorageMethod to preserve the Animal Specimens collected in the laboratoryMutiple selectionYes
AnimalSourceSpecimenPoolingAnimal Source Specimen PoolingAnswer to the question: 'Are the Animal Source Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' in the database see the online database manual)BooleanYes
AnimalSourceSpecimenPoolingStrategyAnimal Source Specimen Pooling StrategyExplain the pooling method of the Animal Source Specimens \n (for a definition of 'pooling' in the database see the online database manual)StringYes
AnimalSourceSpecimenCodeStructureAnimal Source Specimen Code StructureExplain the nomenclature of the Animal Source Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, the following letters\n are the type of Specimen, then the numbers are the Animal Source, and the last number is \n the sequential Specimen from the Animal SourceStringYes
AnimalSourceSpecimenDiagnosticsUsedDiagnostics Are Applied in the Animal SpecimensAnswer to the question: 'Are diagnostics applied to Animal Source Specimens?'.\n Diagnostics applied in a full Animal Source are requested aboveBooleanYes
AnimalSourceSpecimenDiagnosticsUsedProtocolAnimal Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conducted with in the Animal Source SpecimensStringYes
AnimalSourceSpecimenDiagnosticsUsedProtocolReferencesAnimal Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in the Animal Source SpecimensStringNo
AnimalSourceSpecimenCriteriaPositiveTestAnimal Specimen Criteria Positive TestExplain the criteria to establish that each diagnostic test method applied to an Animal\n Source Specimen is positive. The criteria for positive Animal Source and Animal Source Specimens are requested belowStringYes
AnimalSourceSpecimenCriteriaPositiveTestReferencesAnimal Specimen Criteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test method applied to an Animal\n Source Specimen is positiveStringNo
AnimalSourceSpecimenCriteriaPositiveCaseAnimal Source Specimen Criteria Positive CaseExplain the criteria to establish that an Animal\n Source Specimen is positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for positive Animal Source Records are requested belowStringYes
AnimalSourceSpecimenCriteriaPositiveCaseReferencesAnimal Source Specimen Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Animal\n Source Specimen is positive for each specific hazard targeted in the Surveillance ActivityStringNo
AnimalSourceRecordCriteriaPositiveCaseAnimal Source Record Criteria Positive CaseExplain the criteria to establish that an Animal\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
AnimalSourceRecordCriteriaPositiveCaseReferencesAnimal Source Record Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Animal\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Environmental Source\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
EnvironmentalSourceOriginEnvironmental Sources OriginSelect the appropriate origing of the Environmental Sources used in the current \n Surveillance Activity (e.g., generated during the current Surveillance Activity or \n already available and collected during a previous Surveillance Activity)Multiple selectionYes
EnvironmentalSourceOriginIdentifierSurveillance Activity Identifier Environmental Source OriginThe identifier of the Surveillance Activity under which the Environmental Sources used\n in the current Surveillance Activity were collectedStringYes
EnvironmentalSourcePolygonOrPointPolygon or Trap is of InterestEstablish if a polygon (e.g., parcel, grid cell, protected area zone, hunting range) \n where the collection of Environmental Specimens takes place or the exact position of each Environmental Source Record\n (e.g., longitude, latitude, time) of interest for the Surveillance Activity?Multiple selectionYes
EnvironmentalSourceSpeciesEnvironmental SpeciesSpecies of the Environmental Sources that are the target of the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
EnvironmentalSourceSpeciesIdentificationMethodEnvironmental Species IdentificationExplain the methodology used to identify the Environmental species collectedMultiple selectionYes
EnvironmentalSourceSpeciesIdentificationMethodReferencesEnvironmental Species Identification ReferencesProvide references associated with the identification method of the Environmental species collectedStringNo
EnvironmentalSourceHowObtainedEnvironmental Source SelectionExplain how Environmental Sources are selectedStringYes
EnvironmentalSourceInclusionCriteriaInclusion Criteria of Environmental Sources Collection SitesProvide specific inclusion criteria of Environmental Sources (collection areas or points) \n in the Surveillance Activity, if anyStringYes
EnvironmentalSourceExclusionCriteriaExclusion Criteria of Environmental Sources Collection SitesExplain the reason to exclude certain Environmental Sources (collection areas or points) from the Surveillance Activity, if anyStringNo
EnvironmentalSourceIdentificationEnvironmental Sources Are Identified IndividuallyAnswer to the question: 'Are Environmental Sources (polygon, traps, water container) individually identified?'\n (e.g. code, color, type, other)BooleanYes
EnvironmentalSourceIdentificationMethodEnvironmental Sources Identification MethodExplain how Environmental Sources are individually identified (e.g. grid cell code, other)StringYes
EnvironmentalSourceGroupingEnvironmental Sources Are GroupedAnswer to the question: 'Are Environmental collections clustered in units smaller\n than 'Event'?'. Grouping can be physical (e.g., parcel) or temporal (e.g., month)BooleanYes
EnvironmentalSourceGroupingStructureGrouping of Environmental SourcesExplain the grouping structure of the Environmental Sources below 'Event' \n (e.g., Events represent a area of a lake. Environmental Sources are grouped by the north or south borders)StringYes
EnvironmentalSourceRecordCodeStructureEnvironmental Source Record Code StructureExplain the nomenclature of the Environmental Source Record Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the Environmental taxonomic group, and then the number is \n the sequential number of the Environmental Source Record from Environmental Source X)StringYes
EnvironmentalSourceRecordsOverTimeEnvironmental Source Records Over TimeAnswer to the question: 'Is it aimed to obtain Environmental Sources Records from the same Environmental Source\n during the Surveillance Activity?' (e.g., several Records from the Environmental Source)BooleanYes
EnvironmentalSourceRecordHowObtainedEnvironmental Source Records Collection ProcessExplain how Environmental Source Records are collected in the field (e.g., how water is collected from a spceific site of a river)StringYes
EnvironmentalSourceRecordInclusionCriteriaInclusion Criteria of Environmental Sources CollectionsProvide specific inclusion criteria of Environmental collections in the Surveillance Activity, if anyStringYes
EnvironmentalSourceRecordExclusionCriteriaExclusion Criteria of Environmental CollectionsExplain the reason to exclude certain Environmental collections from the Surveillance Activity, if anyStringNo
EnvironmentalSourceRecordFieldStorageEnvironmental Collection Field StorageMethod to preserve the Environmental Sources collected while in the fieldMultiple selectionYes
EnvironmentalSourceRecordLabStorageEnvironmental Collection Lab StorageMethod to preserve the Environmental Sources collected in the laboratoryMultiple selectionYes
EnvironmentalSourceSpecimenCollectionEnvironmental Specimen CreationAnswer to the question: 'Are Environmental Specimens created from the collections (Environmental Source Records)?'BooleanYes
EnvironmentalSourceSpecimenCollectionMethodEnvironmental Specimen Creation MethodExplain how the Environmental Specimens are created from the collections (Environmental Source Records)StringYes
EnvironmentalSourceSpecimenCollectionMethodReferencesEnvironmental Specimen Creation Method ReferencesProvide references associated with the creation method of the Environmental Specimens from \n the collections (Environmental Sources Records)StringNo
EnvironmentalSourceSpecimenCodeStructureEnvironmental Specimen Code StructureExplain the nomenclature of the Environmental Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the Environmental group, the following letters\n are the type of Specimen, then the numbers are the collection site, and the last number is \n the sequential Specimen from each collectionStringYes
EnvironmentalSourceSpecimenFieldStorageEnvironmental Specimen Field StorageMethod to preserve the Environmental Specimens in the fieldMutiple selectionYes
EnvironmentalSourceSpecimenLabStorageEnvironmental Specimen Laboratory StorageMethod to preserve the Environmental Specimens in the laboratoryMutiple selectionYes
EnvironmentalSourceSpecimenPoolingEnvironmental Specimen PoolingAnswer to the question: 'Are Environmental Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' for the database see the online database manual)BooleanYes
EnvironmentalSourceSpecimenPoolingStrategyEnvironmental Specimen Pooling StrategyExplain the pooling method of the Environmental Specimens \n (for a definition of 'pooling' for the database see the online database manual)StringYes
EnvironmentalSourceSpecimenDiagnosticsUsedDiagnostics Are Conducted in the Environmental SpecimensAnswer to the question: 'Are diagnostics conducted in the Environmental Specimens?'BooleanYes
EnvironmentalSourceSpecimenDiagnosticsUsedProtocolEnvironmental Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conductedStringYes
EnvironmentalSourceSpecimenDiagnosticsUsedProtocolReferencesEnvironmental Specimen Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conductedStringNo
EnvironmentalSourceSpecimenCriteriaPositiveTestCriteria Positive TestExplain the criteria to establish that each diagnostic test method conducted in an\n Environmental Specimen is positive. The criteria for positive Environmental Source and Environmental Source Specimens are requested belowStringYes
EnvironmentalSourceSpecimenCriteriaPositiveTestReferencesCriteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test conducted in\n in an Environmental Specimen is positiveStringNo
EnvironmentalSourceSpecimenCriteriaPositiveCaseCriteria Environmental Specimen Positive CaseExplain the criteria to establish that an Environmental Specimen is \n positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for a positive Environmental Source Record is requested belowStringYes
EnvironmentalSourceSpecimenCriteriaPositiveCaseReferencesCriteria Environmental Specimen Positive Case ReferencesProvide references associated with the criteria to establish that an \n Environmental Specimen is positive for each specific hazard targeted in the Surveillance\n ActivityStringNo
EnvironmentalSourceRecordCriteriaPositiveCaseCriteria Environmental Source Record (Collection) Positive CaseExplain the criteria to establish that an Environmental\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
EnvironmentalSourceRecordCriteriaPositiveCaseReferencesCriteria Environmental Source Record (Collection) Positive Case ReferencesProvide references associated with the criteria to establish that an Environmental\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Arthropod Source\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
ArthropodSourceOriginArthropod Sources OriginSelect the appropriate origing of the arthropods used in the current \n Surveillance Activity (e.g., generated during the current Surveillance Activity or \n already available and collected during a previous Surveillance Activity)Multiple selectionYes
ArthropodSourceOriginIdentifierSurveillance Activity Identifier Arthropod Source OriginThe identifier of the Surveillance Activity under which the arthropods used\n in the current Surveillance Activity were collectedStringYes
ArthropodSourcePolygonOrPointPolygon or Trap is of InterestEstablish if a polygon (e.g., parcel, grid cell, protected area zone, hunting range) \n where the arthropod collection takes place or the exact position of each arthropod collection\n (e.g., longitude, latitude, time) of interest for the Surveillance Activity?Multiple selectionYes
ArthropodSourceSpeciesArthropod SpeciesSpecies of the arthropods that are the target of the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
ArthropodSourceSpeciesIdentificationMethodArthropod Species IdentificationExplain the methodology used to identify the arthropod species collectedMultiple selectionYes
ArthropodSourceSpeciesIdentificationMethodReferencesArthropod Species Identification ReferencesProvide references associated with the identification method of the arthropod species collectedStringNo
ArthropodSourceLifeStageTargetedLife Stage TargetedIndication of the life stages of the arthropods collectedMultiple selectionYes
ArthropodSourcePassiveOrActiveCollectionActive or Passive CollectionDescribe if the arthropods are collected actively (e.g., trap or lure) \n or passively (e.g., larvae from water container)Multiple selectionYes
ArthropodSourcePassivePassive Source of ArthropodsDescribe how arthropods are collected passivelyStringYes
ArthropodSourceTrapTypeTrap Type EmployedDescribe the type of traps used to collect arthropodsMultiple selectionYes
ArthropodSourceTrapModelTrap ModelProvide the specific characterristics of traps used in the collections \n (e.g., brand, model, name, identifier, url, etc)StringYes
ArthropodSourceLureLure EmployedDescribe the lure used to collect arthropodsMultiple selectionYes
ArthropodSourceHowObtainedCollection Site SelectionExplain how arthropod collection sites are selectedStringYes
ArthropodSourceInclusionCriteriaInclusion Criteria of Arthropods Collection SitesProvide specific inclusion criteria of arthropod collections sites (collection areas or points) \n in the Surveillance Activity, if anyStringYes
ArthropodSourceExclusionCriteriaExclusion Criteria of Arthropod Collection SitesExplain the reason to exclude certain arthropod collections sites (collection areas or points) \n or specific arthropod collections from the Surveillance Activity, if anyStringNo
ArthropodSourceIdentificationCollection Sites Are Identified IndividuallyAnswer to the question: 'Are arthropod collections sites (polygon, traps, water container) individually identified?'\n (e.g. code, color, type, other)BooleanYes
ArthropodSourceIdentificationMethodCollection Sites Identification MethodExplain how arthropod collections are individually identified (e.g. color, other)StringYes
ArthropodSourceGroupingArthropod Collections Are GroupedAnswer to the question: 'Are arthropod collections clustered in units smaller\n than 'Event'?'. Grouping can be physical (e.g., parcel) or temporal (e.g., month)BooleanYes
ArthropodSourceGroupingStructureGrouping of Arthropod CollectionsExplain the grouping structure of the arthropod collections below 'Event' \n (e.g., Events represent a cell of a grid cell. Arthropod Sources are grouped by green plots in the cell)StringYes
ArthropodSourceRecordCodeStructureArthropod Source Record Code StructureExplain the nomenclature of the Arthropod Source Record Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the arthropod taxonomic group, and then the number is \n the sequential number of the Arthropod Source Records from trap X)StringYes
ArthropodSourceRecordsOverTimeCollection Records Over TimeAnswer to the question: 'Is it aimed to obtain arthropods from the same collection sites\n (polygon, trap, etc.) during the Surveillance Activity?' (e.g., several collections or Records from the same site)BooleanYes
ArthropodSourceRecordHowObtainedArthropod collection ProcessExplain how arthropods are collected in the field (e.g., how are they collected from a trap)StringYes
ArthropodSourceRecordInclusionCriteriaInclusion Criteria of Arthropods CollectionsProvide specific inclusion criteria of arthropod collections in the Surveillance Activity, if anyStringYes
ArthropodSourceRecordExclusionCriteriaExclusion Criteria of Arthropod CollectionsExplain the reason to exclude certain arthropod collections from the Surveillance Activity, if anyStringNo
ArthropodSourceRecordFieldStorageArthropod Collection Field StorageMethod to preserve the arthropods collected while in the fieldMultiple selectionYes
ArthropodSourceRecordLabStorageArthropod Collection Lab StorageMethod to preserve the arthropods collected in the laboratoryMultiple selectionYes
ArthropodSourceSpecimenCollectionArthropod Specimen CreationAnswer to the question: 'Are Arthropod Specimens created from the collections (Arthropod Source Records)?'BooleanYes
ArthropodSourceSpecimenCollectionMethodArthropod Specimen Creation MethodExplain how the Arthropod Specimens are created from the collections (Arthropod Source Records)StringYes
ArthropodSourceSpecimenCollectionMethodReferencesArthropod Specimen Creation Method ReferencesProvide references associated with the creation method of the Arthropod Specimens from \n the collections (Arthropod Sources Records)StringNo
ArthropodSourceSpecimenCodeStructureArthropod Specimen Code StructureExplain the nomenclature of the Arthropod Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the arthropod group, the following letters\n are the type of Specimen, then the numbers are the collection site, and the last number is \n the sequential Specimen from each collectionStringYes
ArthropodSourceSpecimenFieldStorageArthropod Specimen Field StorageMethod to preserve the Arthropod Specimens in the fieldMutiple selectionYes
ArthropodSourceSpecimenLabStorageArthropod Specimen Laboratory StorageMethod to preserve the Arthropod Specimens in the laboratoryMutiple selectionYes
ArthropodSourceSpecimenPoolingArthropod Specimen PoolingAnswer to the question: 'Are Arthropod Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' for the database see the online database manual)BooleanYes
ArthropodSourceSpecimenPoolingStrategyArthropod Specimen Pooling StrategyExplain the pooling method of the Arthropod Specimens \n (for a definition of 'pooling' for the database see the online database manual)StringYes
ArthropodSourceSpecimenDiagnosticsUsedDiagnostics Are Conducted in the Arthropod SpecimensAnswer to the question: 'Are diagnostics conducted in the Arthropod Specimens?'BooleanYes
ArthropodSourceSpecimenDiagnosticsUsedProtocolArthropod Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conductedStringYes
ArthropodSourceSpecimenDiagnosticsUsedProtocolReferencesArthropod Specimen Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conductedStringNo
ArthropodSourceSpecimenCriteriaPositiveTestCriteria Positive TestExplain the criteria to establish that each diagnostic test method conducted in an\n Arthropod Specimen is positive. The criteria for positive Arthropod Source and Arthropod Source Specimens are requested belowStringYes
ArthropodSourceSpecimenCriteriaPositiveTestReferencesCriteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test conducted in\n in an Arthropod Specimen is positiveStringNo
ArthropodSourceSpecimenCriteriaPositiveCaseCriteria Arthropod Specimen Positive CaseExplain the criteria to establish that an Arthropod Specimen is \n positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for a positive Arthropod Source Record is requested belowStringYes
ArthropodSourceSpecimenCriteriaPositiveCaseReferencesCriteria Arthropod Specimen Positive Case ReferencesProvide references associated with the criteria to establish that an \n Arthropod Specimen is positive for each specific hazard targeted in the Surveillance\n ActivityStringNo
ArthropodSourceRecordCriteriaPositiveCaseCriteria Arthropod Source Record (Collection) Positive CaseExplain the criteria to establish that an Arthropod\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
ArthropodSourceRecordCriteriaPositiveCaseReferencesCriteria Arthropod Source Record (Collection) Positive Case ReferencesProvide references associated with the criteria to establish that an Arthropod\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n\n\n\n::: {.cell}\n\n:::\n", + "markdown": "# Data Dictionary {.unnumbered}\n\n\n\n::: {.cell}\n\n:::\n\n::: {.cell tbl-colwidths='false'}\n\n:::\n\n\n## Project\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
ProjectIDProject IdentifierSystem-provided Project identifierIntegerSystem-assigned
ProjectNameProject NameUser-given Project nameStringYes
ProjectCrossReferenceIDProject Cross Reference IdentifierThe identifier of the Project under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Project is usedStringNo
ProjectCrossReferenceIDOriginProject Cross Reference Identifier OriginThe location/database/document where other identification \n for the same Project is usedStringNo
ProjectCountryProject CountriesThe countries where the Project takes placeMultiple selectionYes. Provide at least one option
ProjectFunderOrganizationProject Funder OrganizationThe organizations providing the funding to conduct the ProjectMultiple selectionYes. Provide at least one option
ProjectLeadingOrganizationProject Leading OrganizationThe organization/institution leading the Project executionSingle selectionYes. Provide at least one option
ProjectLeaderProject LeaderThe person leading the Project. Usually affiliated to the Leading OrganizationSingle selectionYes
ProjectOtherOrganizationOther OrganizationsOther organizations/partners/institutions involved in the execution of \n the Project (e.g., Laboratories, NGOs, etc.)Multiple selectionNo
ProjectPurposeProject PurposeDescription of the objectives and goals of the ProjectStringYes
ProjectNewSourceDataNew Source DataAnswer to the question: 'Does the Project involve collecting new data from Sources?'\n The answer is 'No' if the Project is using Source or Specimen data already available and generated as \n part of a different Project. The answer is 'Yes' when the Project involves collecting new data\n from Sources exclusively or when the Project involves the collection of new data and also the use of data from previous Projects)BooleanYes
ProjectAnimalSourceSpeciesAnimal Source SpeciesSpecies of the animals of interest for the Project as Animal Sources. It is possible\n to select high taxonomy levels such as 'mammals', 'chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionNo
ProjectObservationSourceObservation Source SpeciesSpecies of the animals of interest for the Project as Observation Sources. \n It is possible to select high taxonomy levels such as 'mammals', 'chordata', 'Insecta' etc. to \n indicate that no particular species is targetedMultiple selectionNo
ProjectEnvironmentalSourceEnvironmental Source TypesThe type(s) of Environmental Source(s) of interest for the ProjectMultiple selectionNo
ProjectInvertebrateSourceInvertebrate Source SpeciesSpecies of invertebrate that cause or transmit diseases collected 'off-host' that\n are of interest for the Project as Invertebrate Sources. It is possible to select high taxonomy\n levels such as 'Diptera', 'Insecta', etc. to indicate that no particular species is targetedMultiple selectionNo
=ProjectBiologicalHazardBiological HazardsThe type(s) of biological health hazard(s) of interest for the Project \n (e.g., 'Virus', 'Bacteria', 'Protozoa', 'Insecta')Multiple selectionNo
=ProjectVirusHazardVirusThe viruses of interest for the Project. It can be as specific as a clade/variant/etc of a species\n or as general as 'Virus' (e.g., 'Virus', 'SARS-CoV-2 Omicron variant', 'H5N1 Highly Pathogenic Avian Influenza clade 2.3.3.4b')Multiple selectionNo
=ProjectBacteriaHazardBacteriaThe bacteria of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Bacteria' (e.g., 'Group-A Streptococcus', 'Mycobacterium bovis')Multiple selectionNo
=ProjectProtozoaHazardProtozoaThe protozoa of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Protozoa' (e.g., 'Plasmodium relictum', 'Toxoplasma gondii')Multiple selectionNo
=ProjectFungiHazardFungiThe fungi of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Fungi' (e.g., 'Pseudogymnoascus destructans', 'Batrachochytrium dendrobatidis')Multiple selectionNo
=ProjectPrionHazardPrionThe prion of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Prion' (e.g., 'Chronic-wasting disease', 'Scrapie', 'Mad cow disease)Multiple selectionNo
=ProjectTransmissibleTumourHazardTransmissible TumourThe transmissible tumour of interest for the Project (e.g., 'Devil facial tumor 1', 'Devil facial tumor 2')Multiple selectionNo
=ProjectNematodaHazardThe nematode of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Nematode' (e.g., 'Toxocara canis', '')Multiple selectionNo
=ProjectPlatyhelminthHazardPlatyhelminthThe platyhelminth of interest for the Project. It can be as specific as a subspecies\n or as general as 'Platyhelminth' (e.g., 'Fasciola gigantica')Multiple selectionNo
=ProjectArthropodHazardArthropodThe arthropod of interest for the Project. It can be as specific as a subspecies\n or as general as 'Arthropod' (e.g., 'Sarcoptes scabiei', 'Rhipicephalus sanguineus')Multiple selectionNo
=ProjectChemicalHazardChemical HazardsThe type(s) of chemical health hazard(s) of interest for the Project \n (e.g., 'Heavy Metal', 'Organochlorine Pesticides', 'Cholinesterase-inhibbiting Pesticide', 'Toxins')Multiple selectionNo
=ProjectHeavyMetalHazardHeavy MetalThe heavy metal of interest for the Project. It can be as specific as a chemical form of the heavy metal \n or as general as the common name of the metal (e.g., 'Lead', 'Methylmercury')Multiple selectionNo
=ProjectOrganochlorinePesticidesHazardOrganochlorine PesticidesThe organochlorine pesticides of interest for the Project. It can be as specific as a type of organochlorine pesticides\n or as general as 'Organochlorine Pesticide' (e.g., 'DDT', 'Lindane')Multiple selectionNo
=ProjectCholinesteraseInhibbitingPesticideHazardCholinesterase-inhibbiting PesticideThe cholinesterase-inhibbiting pesticide of interest for the Project. It can be as specific as a type of \n cholinesterase-inhibbiting pesticide or as general as 'Cholinesterase-inhibbiting Pesticide' \n (e.g., 'Diazinon', 'Malathion')Multiple selectionNo
=ProjectToxinsHazardToxinsThe toxin of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Toxin' (e.g., 'Clostridium botulinum toxin type C', 'Tetanus toxin')Multiple selectionNo
=ProjectPhysicalHazardPhysical HazardsThe type(s) of physical health hazard(s) of interest for the Project \n (e.g., 'Trap', 'Vehicle Collisions', 'Entanglement', 'Burning', 'Electrocution')Multiple selectionNo
=ProjectPhysiologicalHazardPhysiological HazardsThe type(s) of physiological health problems of interest for the Project \n (e.g., 'Hypocalcemia', 'Hyperkalemia', 'Amyloid A amyloidosis')Multiple selectionNo
ProjectStartDateProject Start DateThe starting date of the ProjectDateYes
ProjectEndDateProject End DateThe date when the Project is projected/planned to end or officially endedDateNo
ProjectUrlProject URLsURLs of the Project or of the organizations/institutions involved in the ProjectStringNo
\n
\n```\n:::\n:::\n\n\n## Surveillance Activity \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
Project NameProject NameThe name of the Project containing the Surveillance ActivitySingle selectionYes
WildlifeHealth_SurveillanceActivityIDSurveillance Activity IdentifierSystem-provided Surveillance Activity identifierIntegerSystem-assigned
SurveillanceActivityCodeSurveillance Activity CodeUser-provided Surveillance Activity codeStringYes
SurveillanceActivityCrossIDSurveillance Activity Cross IdentifierThe identifier of the Surveillance Activity under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Surveillance Activity is usedStringNo
SurveillanceActivityCrossIDOriginSurveillance Activity Cross Identifier OriginThe location/database/document where other identification \n for the same Surveillance Activity is usedStringNo
TypeSurveillanceActivityType of Surveillance ActivityThe type of surveillance associated with the Surveillance Activity\n (e.g., Targeted, Scanning, Outbreak Investigation, or Research). If two or more\n surveillance types are involved, then two or more Surveillance Activities are needed\n so each one receives a single type of surveillanceSingle selectionYes
GrantNameGrant NameThe name of the grant funding the Surveillance Activity. If there is not a \n grant involved, type 'N/A'StringYes
GrantNumberGrant NumberThe number of the grant funding the Surveillance ActivityStringNo
SurveillanceActivityLeaderSurveillance Activity LeaderThe person leading the Surveillance ActivitySingle selectionYes
SurveillanceActivityLeaderOrganizationLeader OrganizationThe affiliation of the person leading the Surveillance ActivitySingle selectionYes
SurveillanceActivityLeaderOrganizationRORLeader Organization RORThe ROR of the affiliation of the person leading the Surveillance ActivityStringNo
SurveillanceActivityOrganizationsInvolvedOrganizations InvolvedOrganizations/partners/institutions involved in the execution of \n the Surveillance Activity (e.g., Laboratories, NGOs, etc.)Multiple selectionYes
SurveillanceActivityCountryCountry or Countries Included in the Surveillance ActivityThe countries where the Surveillance Activity takes placeMultiple selectionYes
SurveillanceActivityPurposeSurveillance Activity PurposeDescription of the objectives and goals of the Surveillance ActivityStringYes
SurveillanceActivityDataCuratorSurveillance Activity Data CuratorThe person taking responsibility for the entering and cleaning of the\n Surveillance Activity dataSingle selectionYes
SurveillanceActivityDataOwnerSurveillance Activity Data OwnerThe person or institution that owns the data of the Surveillance ActivityStringYes
SurveillanceActivityOtherIndividualsOther IndividualsOther individuals relevant for the Surveillance Activity, such as laboratory\n point of contacts, local leaders, etc.Multiple selectionNo
SurveillanceActivityNewSourceDataNew Source DataAnswer to the question: 'Does the Surveillance Activity involve collecting new data from Sources?'\n The answer is 'No' if the Surveillance Activity is using Source or Specimen data already available and generated as \n part of a different Surveillance Activity. The answer is 'Yes' when the Surveillance Activity involves collecting new data\n from Sources exclusively or when the Surveillance Activity involves the collection of new data and also the use of data from\n previous Surveillance Activity)BooleanYes
SurveillanceActivityObservationsIncludedSurveillance Activity Includes Observed-only AnimalsAnswer to the question: 'Does the Surveillance Activity include information of observed-only animals'BooleanYes
SurveillanceActivityAnimalSourcesIncludedSurveillance Activity Includes Animal SourcesAnswer to the question: 'Does the Surveillance Activity include information of individual animals?'BooleanYes
SurveillanceActivityEnvironmentalSourcesIncludedSurveillance Activity includes Environmental SourcesAnswer to the question: 'Does the Surveillance Activity include information of Environmental Sources (e.g., water)?'BooleanYes
SurveillanceActivityInvertebrateSourcesIncludedSurveillance Activity Includes Invertebrate SourcesAnswer to the question: 'Does the surveillance objective include information from Invertebrate sources (e.g., CO2 traps)?'BooleanYes
SurveillanceActivityNewObservationRecordsAddedNew Observations RecordsAnswer to the question: 'Does the Surveillance Activity involve the documentation of new \n Observation Records?'BooleanYes
SurveillanceActivityNewAnimalSourceRecordsAddedNew Animal Source RecordsAnswer to the question: 'Does the Surveillance Activity involve the documentation of new \n Animal Source Records?'BooleanYes
SurveillanceActivityNewEnvironmentalSourceRecordsAddedNew Environmental Source RecordsAnswer to the question: 'Does the Surveillance Activity include the documentation of new \n Environmental Source Records (e.g., water)?'BooleanYes
SurveillanceActivityNewInvertebrateSourceRecordsAddedNew Invertebrate Source RecordsAnswer to the question: 'Does the Surveillance Activity include the documentation of new \n Invertebrate Source Records (e.g., new invertebrate collection)?'BooleanYes
SurveillanceActivitySpecimensNew SpecimensAnswer to the question: 'Are new Specimens collected under the Surveillance Activity?BooleanYes
SurveillanceActivityNewDiagnositcProductsNew Diagnostic ProductsAnswer to the question: 'Does the Surveillance Activity creates new diagnostic products?BooleanYes
SurveillanceActivityNewPooledSpecimensNew Pooled SpecimensAnswer to the question: 'Does the Surveillance Activity creates new pooled specimens?BooleanYes
=SurveillanceActivityBiologicalHazardBiological HazardsThe type(s) of biological health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Virus', 'Bacteria', 'Protozoa', 'Insecta')Multiple selectionNo
=SurveillanceActivityVirusHazardVirusThe viruses of interest for the Surveillance Activity. It can be as specific as a clade/variant/etc of a species\n or as general as 'Virus' (e.g., 'Virus', 'SARS-CoV-2 Omicron variant', 'H5N1 Highly Pathogenic Avian Influenza clade 2.3.3.4b')Multiple selectionNo
=SurveillanceActivityBacteriaHazardBacteriaThe bacteria of interest for the Project. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Bacteria' (e.g., 'Group-A Streptococcus', 'Mycobacterium bovis')Multiple selectionNo
=SurveillanceActivityProtozoaHazardProtozoaThe protozoa of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Protozoa' (e.g., 'Plasmodium relictum', 'Toxoplasma gondii')Multiple selectionNo
=SurveillanceActivityFungiHazardFungiThe fungi of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Fungi' (e.g., 'Pseudogymnoascus destructans', 'Batrachochytrium dendrobatidis')Multiple selectionNo
=SurveillanceActivityPrionHazardPrionThe prion of interest for the Project. It can be as specific as the protein subtype\n or as general as 'Prion' (e.g., 'Chronic-wasting disease', 'Scrapie', 'Mad cow disease)Multiple selectionNo
=SurveillanceActivityTransmissibleTumourHazardTransmissible TumourThe transmissible tumour of interest for the Surveillance Activity (e.g., 'Devil facial tumor 1', 'Devil facial tumor 2')Multiple selectionNo
=SurveillanceActivityNematodaHazardThe nematode of interest for the Surveillance Activity. It can be as specific as a strain/serovar/etc of a species\n or as general as 'Nematode' (e.g., 'Toxocara canis', '')Multiple selectionNo
=SurveillanceActivityPlatyhelminthHazardPlatyhelminthThe platyhelminth of interest for the Surveillance Activity. It can be as specific as a subspecies\n or as general as 'Platyhelminth' (e.g., 'Fasciola gigantica')Multiple selectionNo
=SurveillanceActivityArthropodHazardArthropodThe arthropod of interest for the Surveillance Activity. It can be as specific as a subspecies\n or as general as 'Arthropod' (e.g., 'Sarcoptes scabiei', 'Rhipicephalus sanguineus')Multiple selectionNo
=SurveillanceActivityChemicalHazardChemical HazardsThe type(s) of chemical health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Heavy Metal', 'Organochlorine Pesticides', 'Cholinesterase-inhibbiting Pesticide', 'Toxins')Multiple selectionNo
=SurveillanceActivityHeavyMetalHazardHeavy MetalThe heavy metal of interest for the Surveillance Activity. It can be as specific as a chemical form of the heavy metal \n or as general as the common name of the metal (e.g., 'Lead', 'Methylmercury')Multiple selectionNo
=SurveillanceActivityOrganochlorinePesticidesHazardOrganochlorine PesticidesThe organochlorine pesticides of interest for the Surveillance Activity. It can be as specific as a type of organochlorine pesticides\n or as general as 'Organochlorine Pesticide' (e.g., 'DDT', 'Lindane')Multiple selectionNo
=SurveillanceActivityCholinesteraseInhibbitingPesticideHazardCholinesterase-inhibbiting PesticideThe cholinesterase-inhibbiting pesticide of interest for the Surveillance Activity. It can be as specific as a type of \n cholinesterase-inhibbiting pesticide or as general as 'Cholinesterase-inhibbiting Pesticide' \n (e.g., 'Diazinon', 'Malathion')Multiple selectionNo
=SurveillanceActivityToxinsHazardToxinsThe toxin of interest for the Surveillance Activity. It can be as specific as the protein subtype\n or as general as 'Toxin' (e.g., 'Clostridium botulinum toxin type C', 'Tetanus toxin')Multiple selectionNo
=SurveillanceActivityPhysicalHazardPhysical HazardsThe type(s) of physical health hazard(s) of interest for the Surveillance Activity \n (e.g., 'Trap', 'Vehicle Collisions', 'Entanglement', 'Burning', 'Electrocution')Multiple selectionNo
=SurveillanceActivityPhysiologicalHazardPhysiological HazardsThe type(s) of physiological health problems of interest for the Surveillance Activity \n (e.g., 'Hypocalcemia', 'Hyperkalemia', 'Amyloid A amyloidosis')Multiple selectionNo
SurveillanceActivityIACUCNeededIACUC NeededAnswer to the question: 'Is an IACUC needed to conduct the Surveillance Activity?'BooleanYes
SurveillanceActivityOrganizationProvidingIACUCOrganization providing IACUCThe organization providing the IACUC approving the methodology of the Surveillance ActivityStringYes
SurveillanceActivityIACUCCodeIACUC CodeThe code of the IACUC approving the methodology of the Surveillance ActivityStringYes
SurveillanceActivityLocationPolygonUnitOfInterestLocation Polygon Is a Unit of InterestAnswer to the question: 'Is the Location a Polygon that represents a unit of interest for the Surveillance Activity\n (e.g., a parcel or a house)?'BooleanYes
SurveillanceActivityLocationPolygonRepresentsLocation Polygon DescriptionA description of what each polygon Location represents in the Surveillance Activity (e.g., a parcel or a house)StringYes
SurveillanceActivityLocationSpatialFileProvidedSpatial File with Location Polygons Provided'Answer to the question: 'Are the Location polygons included in the \n Surveillance Activity provided as a spatial file (.shp, .geojson, other)?'BooleanYes
SurveillanceActivityLocationPolygonProjectionSpatial Projection Of Location Polygons In Spatial FileAnswer to the question: 'Is the spatial projection of the Location Polygons file provided as a spatial file?'StringYes
SurveillanceActivityEventUnitOfInterestThe Event Is a Unit of InterestAnswer to the question: 'Is the Event (and its associated longitude, latitude, and time) \n a unit of interest for the Surveillance Activity?'BooleanYes
SurveillanceActivityEventRepresentsEvent DescriptionA description of what each Event represents in the Surveillance Activity \n (e.g., a trap, a stall, the location of a health event, etc.)StringYes
SurveillanceActivityEventGroupingEvents Are GroupedAnswer to the question: 'Are Events associated with the current \n Surveillance Activity clustered in units smaller than 'Location'?'BooleanYes
SurveillanceActivityEventGroupingStructureGrouping of EventsExplain the grouping structure of the Events below 'location'\n (e.g., The location is a market. The events are stalls of each vendor in the market. \n The Events are grouped by vendor in each market. So stalls [events], \n within vendors [group], within markets [location])StringYes
SurveillanceActivityEventGroupsSpatialFileProvidedEvent Groups File Provided'Answer to the question: 'Are the Event groups provided as a spatial file (.shp, .geojson, other)?'BooleanYes
SurveillanceActivityEventGroupsProjectionSpatial Projection of Event Groups Spatial FileThe spatial projection of Event groups file provided as a spatial fileStringYes
SurveillanceActivitySourceRecordGroupingSource Records Are GroupedAnswer to the question: 'Are Source Records associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
SurveillanceActivitySourceRecordGroupingStructureGrouping of Source RecordsExplain the grouping structure of the Source Records below 'Event' \n (e.g., Events represent a stall in a market. Source records (animals in the stall) \n are grouped by cage in each stall)StringYes
SurveillanceActivityLabParticipating LaboratoriesThe laboratories associated with the Surveillance ActivityMultiple selectionYes
SurveillanceActivityOtherSurveillanceActivityAssociatedOther Surveillance Activities or Datasets AssociatedAnswer to the question: 'Are there other Surveillance Activities\n associated with the current Surveillance Activity or other datasets?' \n (e.g., if the current Surveillance Activity uses Specimens collected as part of \n other associated Surveillance Objective, or if the full set of events of a ranger\n patrol (beyond health events) belong to the patrol XXXX of the protected\n area Y')BooleanYes
SurveillanceActivityOtherSurveillanceActivityAssociatedCodeAssociated Surveillance Activities CodesDescribe why other Surveillance Activities are associated with the\n current Surveillance Activity (e.g., the current Surveillance Activity uses \n Specimens collected as part of Surveillance Objective ZZZZ, or the health Events\n are part of patrols conducted in protected YYY'. The patrol ID including \n the Events of the current Surveillance Activity are given in the Field Visit\n Cross Reference Identifier)Multiple selectionYes
SurveillanceActivityReasonOtherSurveillanceActivityAssociatedReason other Surveillance Activities or Datasets Are AssociatedDescribe why other Surveillance Activities are associated with the\n current Surveillance Activity (e.g., the current Surveillance Activity uses \n Specimens collected as part of Surveillance Objective ZZZZ, or the health Events\n are part of patrols conducted in protected YYY'. The patrol ID including \n the Events of the current Surveillance Activity are given in the Field Visit\n Cross Reference Identifier)StringYes
SurveillanceActivityRelevantUrlSurveillance Activity URLsURLs of the Surveillance Activity, associated with the Surveillance\n Activity, or organizations leading the Surveillance ActivityStringNo
SurveillanceActivityPublicationSurveillance Activity PublicationsPublication references associated with the Surveillance ActivityStringNo
SurveillanceActivityStartDateSurveillance Activity Start DateThe date the Surveillance Objective officially startedDateYes
SurveillanceActivityEndDateSurveillance Activity End DateThe date the Surveillance Activity is projected to end or officially endedDateNo
\n
\n```\n:::\n:::\n\n\n## Outbreak\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
OutbreakNameOutbreak NameThe name provided to the outbreakStringYes
OutbreakDiagnosisOutbreak DiagnosisThe diagnosis provided to the outbreakStringNo
\n
\n```\n:::\n:::\n\n\n## Field Visit\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
FieldVisitIDField Visit IdentifierSystem-provided Field Visit identifierIntegerSystem-assigned
FieldVisitCodeField Visit CodeUser-provided Field Visit codeStringYes
FieldVisitCrossIDField Visit Cross IdentifierThe identifier of the Field Visit under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Field Visit is usedStringNo
FieldVisitCrossIDOriginField Visit Cross Identifier OriginThe location/database/document where other identification \n for the same Field Visit is usedStringNo
FieldVisitLeaderField Visit LeaderThe name of the leader of the Field VisitSingle selectionYes
FieldVisitTypeField Visit TypeThe type of Field Visit (e.g., 'Market', 'Free-ranging', 'Ranger patrolling').\n More than one Field Visit type can be selectedMultiple selectionYes
FieldVisitDescriptionField Visit DescriptionThe background for the Field Visit (e.g., why, who, how, where, what for)StringYes
FieldVisitStartDateField Visit Start DateThe date the Field Visit startedDateYes
FieldVisitEndDateField Visit End DateThe date the Field Visit ended or the anticipated ending dateDateYes
\n
\n```\n:::\n:::\n\n\n## Location\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
LocationIDLocation IdentifierSystem-provided Location identifierIntegerSystem-assigned
Location Polygon IDLocation Polygon IdentifierIf a spatial file with the different Locations has been entered in the database.\n then provide the ID of the polygon representing the Location in such file. This attribute is\n available only when the spatial file has been entered in the database as reported in the \n Surveillance Activity metadataStringYes
LocationNameLocation CodeUser-provided Location codeStringYes
LocationCrossID Location Cross IdentifierThe identifier of the Location under another nomenclature system. \n For example, in a different database or document where other identification \n for the same Location is usedStringNo
LocationCrossIDOriginLocation Cross Identifier OriginThe database/document/other where other identification \n for the same Location is usedStringNo
LocationTypeLocation TypeThe type of Location containing Events \n (e.g., 'market', 'zone in Protected area', 'grid cell', 'parcel', etc')Single selectionYes
LocationTargetedRecordsLocation Targeted RecordsIndicate what type of Records (Group, Animal, Environmental,\n or from Arthropod Sources) are targeted in the EventMultiple selectionYes
LocationStartDateStart DateThe date the activities in the Location startedDateYes
LocationEndDateEnd DateThe date the activities in the Location ended or the anticipated ending dateDateNo
LocationCommentsCommentsProvided any other relevant information regarding the LocationStringNo
\n
\n```\n:::\n:::\n\n\n\n## Event\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
EventIDEvent IdentifierSystem-provided Event identifierIntegerSystem-assigned
EventCodeEvent CodeUser-provided Event codeStringYes
EventCrossIDEvent Cross IdentifierThe identifier of an Event in another system (e.g., database/document/other)StringNo
EventCrossIDOriginEvent Cross Identifier OriginThe database/document/other where other identification \n for the same Event is usedStringNo
EventLongitudeLongitudeLongitude coordinate. Non decimal degree coordinates are automatically converted. \n If coordinates are provided in UTM, then the UTM zone must be provided (see below)FloatYes
EventLatitudeLatitudeLatitude coordinate. Non decimal degree coordinates are automatically converted. \n If coordinates are provided in UTM, then the UTM zone must be provided (see below)FloatYes
EventUTMZoneEvent UTM ZoneUTM Zone where the Event occurs. It applies if the longitude an latitude odf\n the Event are provided in UTM coordinate reference system. \n See https://www.dmap.co.uk/utmworld.htmFloatYes
EventCoordinatesExactOrEstimatedEvent Coordinates Exact Or EstimatedIndicate weather the longitude and latitude coordinates are exact (GPS device)\n or estimated based on another method (e.g., by pointinf the location in the map above)Single selectionYes
EventCountryCountryCountry where the Event happensSingle selectionYes
EventStateStateState where the Event happensSingle selectionNo
EventProvinceProvinceProvince where the Event happensSingle selectionNo
EventUnitEvent unitExplanation of what the Event represents (e.g., a field finding, \n a market, a vendor, a cage, a grid cell, a point in a transect, a mist net, \n a point in a parcel, a point in a protected area, etc.)Single selectionYes
EventFeaturesEvent FeaturesSpecific set of findings at the Event that are dynamic over time\n (e.g., fire, smoke, etc)Multiple selectionYes
EventByEvent reported byThe person that reported the EventSingle selectionYes
EventBySectorSector of the reporterThe sector of the person that reported the EventSingle selectionNo
EventTargetedRecordsEvent Targeted RecordsIndicate what type of Records (Group, Animal, Environmental,\n or from Arthropod Sources) are targeted in the EventMultiple selectionYes
EventSmartSourceEvent from SMARTAnswer to the question: 'Was the Event recorded using SMART?'Single selectionNo
EventSiteCodeSite codeThe site the Events are grouped by siteSingle selectionNo
EventZoneCodeZone codeThe zone the Events are grouped by zoneSingle selectionNo
EventMarketCodeMarket codeThe market the Events are grouped by marketSingle selectionNo
EventGridCodeGrid codeThe grid code the when Events are grouped by gridSingle selectionNo
EventGridCellCodeGrid cell codeThe grid cell code when Events are grouped by grid cellSingle selectionNo
EventStationCodeStation codeThe station code when Events are grouped by stationSingle selectionNo
EventTransectCodeTransect codeThe transect code when Events are grouped by transectSingle selectionNo
EventVendorCodeVendor codeThe vendor code when Events are grouped by vendorSingle selectionNo
EventTrapCodeTrap codeThe vendor code when Events are grouped by trapSingle selectionNo
EventMistNetCodeMist net codeThe mist net code when Events are grouped by mist net codeSingle selectionNo
EventOtherSpatialUnitCodeOther spatial unit codeThe spatial unit code when Events are grouped by another spatial unitSingle selectionNo
EventStudyYearThe study yearThe temporal unit code when Events are grouped by year unitSingle selectionNo
EventStudySeasonThe study seasonThe temporal unit code when Events are grouped by study seasonSingle selectionNo
EventStudyMonthThe study monthThe temporal unit code when Events are grouped by monthSingle selectionNo
EventStudyWeekThe study weekThe temporal unit code when Events are grouped by weekSingle selectionNo
EventStudyDayPeriodThe study day periodThe temporal unit code when Events are grouped by study daySingle selectionNo
EventStudyHourThe study hourThe temporal unit code when Events are grouped by study hourSingle selectionNo
EventOtherTemporalUnitOther spatial temporal unit codeThe temporal unit code when Events are grouped by another temporal unitSingle selectionNo
EventDateEvent DateThe date and time of the Event. If the Event is a period of time (e.g, \n mist-nets to capture bats) then the end time and date can be obtained from the effort\n associated fields (see below)StringYes
EventTimeAssembledTime assembledThe time a trap or similar representing an Event is set upDatetimeNo
EventTimeDisassembledTime disassembledThe time a trap or similar representing an Event is dissamsembledDatetimeNo
\n
\n```\n:::\n:::\n\n\n## Group Source \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
GroupSourceCodeStructureGroup Source Code StructureExplain the nomenclature of the Group Source Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, and then the number is \n the sequential number of the Group Source in the Surveillance InitiativeStringYes
GroupSourceSpeciesGroup Source SpeciesSpecies of the Group Sources of interest for the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Mammalia', 'Chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
GroupSourceSpeciesIdentificationMethodGroup Source Species IdentificationExplain the methodology used to identify the species of the Group SourcesMultiple selectionYes
GroupSourceSpeciesIdentificationMethodReferencesGroup Source Species Identification Method ReferencesProvide references associated with the identification method of the species of Group SourcesStringNo
GroupSourceInclusionCriteriaGroup Source Inclusion CriteriaProvide specific inclusion criteria for the Group Sources of the species of interest \n considered for the Surveillance Activity, if anyStringYes
GroupSourceExclusionCriteriaGroup Source Exclusion CriteriaExplain the reason to exclude certain Group Sources \n of the species of interest for the Surveillance Activity, if anyStringNo
GroupSourceHowObtainedObtaining Group SourcesExplain how Group Sources were obtained for the Surveillance ActivityStringYes
GroupSourceIdentificationGroup Sources Are Identified IndividuallyAnswer to the question: 'Are Group Sources (herds, etc.) individually identified?'\n (e.g. herd, farm, etc.)BooleanYes
GroupSourceIdentificationMethodGroup Source Identification MethodExplain how Group Sources are individually identified\n (e.g. herd, farm, etc.)StringYes
GroupSourceIdentificationMethodReferencesGroup Source Identification Method ReferencesProvide references associated with identification method of Group SourcesStringNo
GroupSourceRecordsOverTimeGroup Source Records Over TimeAnswer to the question: 'Is it aimed to obtained records of the same Group Source during the \n Surveillance Activity?'BooleanYes
GroupSourceGroupingGroup Source Are GroupedAnswer to the question: 'Are Group Sources associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
GroupSourceGroupingStructureGrouping of Group SourcesExplain the grouping structure of the Group Sources below 'Event' \n (e.g., Events represent a market vendor. Group Sources (animals of the same species) \n are grouped by each cage of the vendor (so a cage of a unique vendor can have only-observed \n animals of multiple species)StringYes
GroupSourceDiagnosticsUsedDiagnostics Are Applied in the Group SourceAnswer to the question: 'Are diagnostics conducted in the Group Source?' \n This question refers to Diagnostics that the full Group\n as the tested Specimen. For example, herd body condition. Information on Diagnostics applied in \n a Specimen sourced by an Group (e.g., feces from a herd) are requested below at the Group\n Source Specimen levelBooleanYes
GroupSourceDiagnosticsUsedProtocolGroup Source Diagnostic ProtocolsName and describe the protocols of the Diagnostics applied in Group SourcesStringYes
GroupSourceDiagnosticsUsedProtocolReferencesGroup Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in Group SourcesStringYes
GroupSourceSpecimenUsedGroup Specimen UsedAnswer to the question: 'Are Specimens from Group Sources\n (e.g., feces, etc.) collected under a different Surveillance Activity\n used in the current Surveillance Activity?'BooleanYes
GroupSourceSpecimenCollectionGroup Specimen CollectionAnswer to the question: 'Are Specimens collected from the Group Sources\n (e.g., feces, etc.) while in the field under the current Surveillance Activity?'BooleanYes
GroupSourceSpecimenTypeGroup Source Specimen TypeSelect the Specimen Types used or collected from Group SourcesMultiple selectionYes
GroupSourceSpecimenCollectionMethodGroup Source Specimen Collection MethodExplain how the Specimens were collected from the surroundings of Group Sources \n (e.g., feces in a cage, urine under a bat roost)StringYes
GroupSourceSpecimenCollectionMethodReferencesGroup Source Specimen Collection Method ReferencesProvide references associated with the collection method of the Group Source SpecimensStringNo
GroupSourceSpecimenCollectionParasitesVectorsGroup Specimen Collection Includes Parasites or VectorsAnswer to the question: 'Are parasites or vectors collected from the Group Sources surroundings \n (e.g., when collecting a bat species-specific lice below a roost of the corresponding bat host species.\n Otherwise the parasite or vector is an 'Arthropod Source')BooleanYes
GroupSourceSpecimenFieldStorageGroup Specimen Field StorageMethod to preserve the Group Specimens collected in the fieldMutiple selectionYes
GroupSourceSpecimenLabStorageGroup Specimen Laboratory StorageMethod to preserve the Group Specimens collected in the laboratoryMutiple selectionYes
GroupSourceSpecimenPoolingGroup Source Specimen PoolingAnswer to the question: 'Are the Group Source Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' in the database see the online database manual)BooleanYes
GroupSourceSpecimenPoolingStrategyGroup Source Specimen Pooling StrategyExplain the pooling method of the Group Source Specimens \n (for a definition of 'pooling' in the database see the online database manual)StringYes
GroupSourceSpecimenCodeStructureGroup Source Specimen Code StructureExplain the nomenclature of the Group Source Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, the following letters\n are the type of Specimen, then the numbers are the Group Source, and the last number is \n the sequential Specimen from the Group SourceStringYes
GroupSourceSpecimenDiagnosticsUsedDiagnostics Are Applied in the Group SpecimensAnswer to the question: 'Are diagnostics applied to Group Source Specimens?'.\n Diagnostics applied in a full Group Source are requested aboveBooleanYes
GroupSourceSpecimenDiagnosticsUsedProtocolGroup Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conducted with in the Group Source SpecimensStringYes
GroupSourceSpecimenDiagnosticsUsedProtocolReferencesGroup Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in the Group Source SpecimensStringNo
GroupSourceSpecimenCriteriaPositiveTestGroup Specimen Criteria Positive TestExplain the criteria to establish that each diagnostic test method applied to an Group\n Source Specimen is positive. The criteria for positive Group Source and Group Source Specimens are requested belowStringYes
GroupSourceSpecimenCriteriaPositiveTestReferencesGroup Specimen Criteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test method applied to an Group\n Source Specimen is positiveStringNo
GroupSourceSpecimenCriteriaPositiveCaseGroup Source Specimen Criteria Positive CaseExplain the criteria to establish that an Group\n Source Specimen is positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for positive Group Source Records are requested belowStringYes
GroupSourceSpecimenCriteriaPositiveCaseReferencesGroup Source Specimen Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Group\n Source Specimen is positive for each specific hazard targeted in the Surveillance ActivityStringNo
GroupSourceRecordCriteriaPositiveCaseGroup Source Record Criteria Positive CaseExplain the criteria to establish that an Group\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
GroupSourceRecordCriteriaPositiveCaseReferencesGroup Source Record Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Group\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Animal Source \n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
AnimalSourceCodeStructureAnimal Source Code StructureExplain the nomenclature of the Animal Source Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, and then the number is \n the sequential number of the Animal Source in the Surveillance InitiativeStringYes
AnimalSourceSpeciesAnimal Source SpeciesSpecies of the Animal Sources of interest for the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Mammalia', 'Chordata', 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
AnimalSourceSpeciesIdentificationMethodAnimal Source Species IdentificationExplain the methodology used to identify the species of the Animal SourcesMultiple selectionYes
AnimalSourceSpeciesIdentificationMethodReferencesBAnimal Source Species Identification Method ReferencesProvide references associated with the identification method of the species of Animal SourceStringNo
AnimalSourceInclusionCriteriaAnimal Source Inclusion CriteriaProvide specific inclusion criteria for the Animal Sources of the species of interest \n considered for the Surveillance Activity, if anyStringYes
AnimalSourceExclusionCriteriaAnimal Source Exclusion CriteriaExplain the reason to exclude certain Animal Sources \n of the species of interest for the Surveillance Activity, if anyStringNo
AnimalSourceHowObtainedObtaining Animal SourcesExplain how Animal Sources are obtained for the Surveillance ActivityStringYes
AnimalSourceCapturedAnimal Source CapturedAnswer to the question: 'Are Animal Sources associated with the current \n Surveillance Activity captured?'BooleanYes
AnimalSourceCaptureProtocolAnimal Source Capture ProtocolExplain how Animal Sources are capturedStringYes
AnimalSourceCaptureProtocolReferencesAnimal Source Capture Protocol ReferencesProvide references associated with the capture method of the Animal SourcesStringNo
AnimalSourceIdentificationAnimal Sources Are Identified IndividuallyAnswer to the question: 'Are Animal Sources individually identified?'\n (e.g. rings, line pattern, chip, etc.)BooleanYes
AnimalSourceIdentificationMethodAnimal Source Identification MethodExplain how Animal Sources are individually identified\n (e.g. rings, line pattern, chip, etc.)StringYes
AnimalSourceIdentificationMethodReferencesAnimal Source Identification Method ReferencesProvide references associated with identification method of Animal SourcesStringNo
AnimalSourceRecordsOverTimeAnimal Source Records Over TimeAnswer to the question: 'Is it aimed to obtained records of the same Animal Source during the \n Surveillance Activity?'BooleanYes
AnimalSourceRecaptureAnimal Source RecaptureAnswer to the question: 'Are Animal Sources recaptured during the Surveillance Activity?'BooleanYes
AnimalSourceFateAfterRecaptureAnimal Source Fate After Capture RecaptureExplain what happens with the Animal Sources identified individually after recaptureStringNo
AnimalSourceEuthanasiaAnimal Sources EuthanasiaAnswer to the question: 'Are Animal Sources euthanized?'BooleanYes
AnimalSourceEuthanasiaMethodAnimal Source Euthanasia MethodExplain how Animal Sources are euthanized'StringYes
AnimalSourceEuthanasiaMethodReferencesAnimal Source Euthanasia Method ReferencesProvide references associated with the euthanasia method usedStringNo
AnimalSourceCarcassCollectedAnimal Source Carcass CollectedAnswer to the question: 'Are Animal Source carcasses collected as part the Surveillance Activity?'BooleanYes
AnimalSourceCarcassFieldStorageCarcass Field StorageThe methods used to preserve carcasses collected while in the fieldMutiple selectionYes
AnimalSourceCarcassLabStorageCarcass Laboratory StorageThe methods to preserve carcasses collected while in the laboratoryMutiple selectionYes
AnimalSourceCarcassNecropsyAnimal Source Carcass For NecropsyAnswer to the question: 'Are Animal Source carcasses collected as part the Surveillance Activity necropsied?'BooleanYes
AnimalSourceCarcassNecropsyProtocolAnimal Source Necropsy ProtocolDescribe the protocol used to conduct the necropsiesStringNo
AnimalSourceCarcassNecropsyProtocolReferencesAnimal Source Necropsy Protocol ReferencesProvide references associated with the protocol to conduct the necropsiesStringNo
AnimalSourceGroupingAnimal Source Are GroupedAnswer to the question: 'Are Animal Sources associated with the current \n Surveillance Activity clustered in units smaller than 'Event'?'BooleanYes
AnimalSourceGroupingStructureGrouping of Animal SourcesExplain the grouping structure of the Animal Sources below 'Event' \n (e.g., Events represent a stall in a market. Animal Sources are grouped by cage in each stall)StringYes
AnimalSourceDiagnosticsUsedDiagnostics Are Applied in the Animal SourceAnswer to the question: 'Are diagnostics conducted in Animal Source?' \n This question refers to Diagnostics that use either the carcass or the full animal\n as the tested Specimen. For example, ultrasound or X-rays. Information on Diagnostics applied in \n a Specimen sourced by an animal are requested below at the Animal Source Specimen levelBooleanYes
AnimalSourceDiagnosticsUsedProtocolAnimal Source Diagnostic ProtocolsName and describe the protocols of the Diagnostics applied in Animal SourcesStringYes
AnimalSourceDiagnosticsUsedProtocolReferencesAnimal Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in Animal SourcesStringYes
AnimalSourceSpecimenUsedAnimal Specimen UsedAnswer to the question: 'Are Specimens from Animal Sources\n (e.g., live animal, carcass) collected under a different Surveillance Activity\n used in the current Surveillance Activity?'BooleanYes
AnimalSourceSpecimenCollectionAnimal Specimen CollectionAnswer to the question: 'Are Specimens collected from the Animal Sources\n (e.g., live animal, carcass) while in the field or during a necropsy under the current \n Surveillance Activity?'BooleanYes
AnimalSourceSpecimenTypeAnimal Source Specimen TypeSelect the Specimen Types used or collected from Animal SourcesMultiple selectionYes
AnimalSourceSpecimenCollectionMethodAnimal Source Specimen Collection MethodExplain how the Specimens are collected from the Animal SourcesStringYes
AnimalSourceSpecimenCollectionMethodReferencesAnimal Source Specimen Collection Method ReferencesProvide references associated with the collection method of the Animal Source SpecimensStringNo
AnimalSourceSpecimenCollectionAtRecaptureAnimal Specimen Collection at RecaptureAnswer to the question: 'Are Specimens collected from Animal Sources when they are recaptured?'BooleanYes
AnimalSourceSpecimenCollectionParasitesVectorsAnimal Specimen Collection Includes Parasites or VectorsAnswer to the question: 'Are parasites or vectors collected directly from the Animal Sources or\n are they collected from a known Animal Source?' (in the first, case the parasites or vectors are collected \n directly from the Animal Source. In the second case, they can be associated to an Animal Source, \n for example, when collecting a tick right below a carcass. Otherwise the parasite or vector is an 'Arthropod \n Source')BooleanYes
AnimalSourceSpecimenFieldStorageAnimal Specimen Field StorageMethod to preserve the Animal Specimens collected in the fieldMutiple selectionYes
AnimalSourceSpecimenLabStorageAnimal Specimen Laboratory StorageMethod to preserve the Animal Specimens collected in the laboratoryMutiple selectionYes
AnimalSourceSpecimenPoolingAnimal Source Specimen PoolingAnswer to the question: 'Are the Animal Source Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' in the database see the online database manual)BooleanYes
AnimalSourceSpecimenPoolingStrategyAnimal Source Specimen Pooling StrategyExplain the pooling method of the Animal Source Specimens \n (for a definition of 'pooling' in the database see the online database manual)StringYes
AnimalSourceSpecimenCodeStructureAnimal Source Specimen Code StructureExplain the nomenclature of the Animal Source Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the taxonomic group, the following letters\n are the type of Specimen, then the numbers are the Animal Source, and the last number is \n the sequential Specimen from the Animal SourceStringYes
AnimalSourceSpecimenDiagnosticsUsedDiagnostics Are Applied in the Animal SpecimensAnswer to the question: 'Are diagnostics applied to Animal Source Specimens?'.\n Diagnostics applied in a full Animal Source are requested aboveBooleanYes
AnimalSourceSpecimenDiagnosticsUsedProtocolAnimal Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conducted with in the Animal Source SpecimensStringYes
AnimalSourceSpecimenDiagnosticsUsedProtocolReferencesAnimal Source Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conducted in the Animal Source SpecimensStringNo
AnimalSourceSpecimenCriteriaPositiveTestAnimal Specimen Criteria Positive TestExplain the criteria to establish that each diagnostic test method applied to an Animal\n Source Specimen is positive. The criteria for positive Animal Source and Animal Source Specimens are requested belowStringYes
AnimalSourceSpecimenCriteriaPositiveTestReferencesAnimal Specimen Criteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test method applied to an Animal\n Source Specimen is positiveStringNo
AnimalSourceSpecimenCriteriaPositiveCaseAnimal Source Specimen Criteria Positive CaseExplain the criteria to establish that an Animal\n Source Specimen is positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for positive Animal Source Records are requested belowStringYes
AnimalSourceSpecimenCriteriaPositiveCaseReferencesAnimal Source Specimen Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Animal\n Source Specimen is positive for each specific hazard targeted in the Surveillance ActivityStringNo
AnimalSourceRecordCriteriaPositiveCaseAnimal Source Record Criteria Positive CaseExplain the criteria to establish that an Animal\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
AnimalSourceRecordCriteriaPositiveCaseReferencesAnimal Source Record Criteria Positive Case ReferencesProvide references associated with the criteria to establish that an Animal\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Environmental Source\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
EnvironmentalSourceOriginEnvironmental Sources OriginSelect the appropriate origing of the Environmental Sources used in the current \n Surveillance Activity (e.g., generated during the current Surveillance Activity or \n already available and collected during a previous Surveillance Activity)Multiple selectionYes
EnvironmentalSourceOriginIdentifierSurveillance Activity Identifier Environmental Source OriginThe identifier of the Surveillance Activity under which the Environmental Sources used\n in the current Surveillance Activity were collectedStringYes
EnvironmentalSourcePolygonOrPointPolygon or Trap is of InterestEstablish if a polygon (e.g., parcel, grid cell, protected area zone, hunting range) \n where the collection of Environmental Specimens takes place or the exact position of each Environmental Source Record\n (e.g., longitude, latitude, time) of interest for the Surveillance Activity?Multiple selectionYes
EnvironmentalSourceSpeciesEnvironmental SpeciesSpecies of the Environmental Sources that are the target of the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
EnvironmentalSourceSpeciesIdentificationMethodEnvironmental Species IdentificationExplain the methodology used to identify the Environmental species collectedMultiple selectionYes
EnvironmentalSourceSpeciesIdentificationMethodReferencesEnvironmental Species Identification ReferencesProvide references associated with the identification method of the Environmental species collectedStringNo
EnvironmentalSourceHowObtainedEnvironmental Source SelectionExplain how Environmental Sources are selectedStringYes
EnvironmentalSourceInclusionCriteriaInclusion Criteria of Environmental Sources Collection SitesProvide specific inclusion criteria of Environmental Sources (collection areas or points) \n in the Surveillance Activity, if anyStringYes
EnvironmentalSourceExclusionCriteriaExclusion Criteria of Environmental Sources Collection SitesExplain the reason to exclude certain Environmental Sources (collection areas or points) from the Surveillance Activity, if anyStringNo
EnvironmentalSourceIdentificationEnvironmental Sources Are Identified IndividuallyAnswer to the question: 'Are Environmental Sources (polygon, traps, water container) individually identified?'\n (e.g. code, color, type, other)BooleanYes
EnvironmentalSourceIdentificationMethodEnvironmental Sources Identification MethodExplain how Environmental Sources are individually identified (e.g. grid cell code, other)StringYes
EnvironmentalSourceGroupingEnvironmental Sources Are GroupedAnswer to the question: 'Are Environmental collections clustered in units smaller\n than 'Event'?'. Grouping can be physical (e.g., parcel) or temporal (e.g., month)BooleanYes
EnvironmentalSourceGroupingStructureGrouping of Environmental SourcesExplain the grouping structure of the Environmental Sources below 'Event' \n (e.g., Events represent a area of a lake. Environmental Sources are grouped by the north or south borders)StringYes
EnvironmentalSourceRecordCodeStructureEnvironmental Source Record Code StructureExplain the nomenclature of the Environmental Source Record Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the Environmental taxonomic group, and then the number is \n the sequential number of the Environmental Source Record from Environmental Source X)StringYes
EnvironmentalSourceRecordsOverTimeEnvironmental Source Records Over TimeAnswer to the question: 'Is it aimed to obtain Environmental Sources Records from the same Environmental Source\n during the Surveillance Activity?' (e.g., several Records from the Environmental Source)BooleanYes
EnvironmentalSourceRecordHowObtainedEnvironmental Source Records Collection ProcessExplain how Environmental Source Records are collected in the field (e.g., how water is collected from a spceific site of a river)StringYes
EnvironmentalSourceRecordInclusionCriteriaInclusion Criteria of Environmental Sources CollectionsProvide specific inclusion criteria of Environmental collections in the Surveillance Activity, if anyStringYes
EnvironmentalSourceRecordExclusionCriteriaExclusion Criteria of Environmental CollectionsExplain the reason to exclude certain Environmental collections from the Surveillance Activity, if anyStringNo
EnvironmentalSourceRecordFieldStorageEnvironmental Collection Field StorageMethod to preserve the Environmental Sources collected while in the fieldMultiple selectionYes
EnvironmentalSourceRecordLabStorageEnvironmental Collection Lab StorageMethod to preserve the Environmental Sources collected in the laboratoryMultiple selectionYes
EnvironmentalSourceSpecimenCollectionEnvironmental Specimen CreationAnswer to the question: 'Are Environmental Specimens created from the collections (Environmental Source Records)?'BooleanYes
EnvironmentalSourceSpecimenCollectionMethodEnvironmental Specimen Creation MethodExplain how the Environmental Specimens are created from the collections (Environmental Source Records)StringYes
EnvironmentalSourceSpecimenCollectionMethodReferencesEnvironmental Specimen Creation Method ReferencesProvide references associated with the creation method of the Environmental Specimens from \n the collections (Environmental Sources Records)StringNo
EnvironmentalSourceSpecimenCodeStructureEnvironmental Specimen Code StructureExplain the nomenclature of the Environmental Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the Environmental group, the following letters\n are the type of Specimen, then the numbers are the collection site, and the last number is \n the sequential Specimen from each collectionStringYes
EnvironmentalSourceSpecimenFieldStorageEnvironmental Specimen Field StorageMethod to preserve the Environmental Specimens in the fieldMutiple selectionYes
EnvironmentalSourceSpecimenLabStorageEnvironmental Specimen Laboratory StorageMethod to preserve the Environmental Specimens in the laboratoryMutiple selectionYes
EnvironmentalSourceSpecimenPoolingEnvironmental Specimen PoolingAnswer to the question: 'Are Environmental Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' for the database see the online database manual)BooleanYes
EnvironmentalSourceSpecimenPoolingStrategyEnvironmental Specimen Pooling StrategyExplain the pooling method of the Environmental Specimens \n (for a definition of 'pooling' for the database see the online database manual)StringYes
EnvironmentalSourceSpecimenDiagnosticsUsedDiagnostics Are Conducted in the Environmental SpecimensAnswer to the question: 'Are diagnostics conducted in the Environmental Specimens?'BooleanYes
EnvironmentalSourceSpecimenDiagnosticsUsedProtocolEnvironmental Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conductedStringYes
EnvironmentalSourceSpecimenDiagnosticsUsedProtocolReferencesEnvironmental Specimen Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conductedStringNo
EnvironmentalSourceSpecimenCriteriaPositiveTestCriteria Positive TestExplain the criteria to establish that each diagnostic test method conducted in an\n Environmental Specimen is positive. The criteria for positive Environmental Source and Environmental Source Specimens are requested belowStringYes
EnvironmentalSourceSpecimenCriteriaPositiveTestReferencesCriteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test conducted in\n in an Environmental Specimen is positiveStringNo
EnvironmentalSourceSpecimenCriteriaPositiveCaseCriteria Environmental Specimen Positive CaseExplain the criteria to establish that an Environmental Specimen is \n positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for a positive Environmental Source Record is requested belowStringYes
EnvironmentalSourceSpecimenCriteriaPositiveCaseReferencesCriteria Environmental Specimen Positive Case ReferencesProvide references associated with the criteria to establish that an \n Environmental Specimen is positive for each specific hazard targeted in the Surveillance\n ActivityStringNo
EnvironmentalSourceRecordCriteriaPositiveCaseCriteria Environmental Source Record (Collection) Positive CaseExplain the criteria to establish that an Environmental\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
EnvironmentalSourceRecordCriteriaPositiveCaseReferencesCriteria Environmental Source Record (Collection) Positive Case ReferencesProvide references associated with the criteria to establish that an Environmental\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n## Arthropod Source\n\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
VariableLabelDefinitionTypeMandatory
ArthropodSourceOriginArthropod Sources OriginSelect the appropriate origing of the arthropods used in the current \n Surveillance Activity (e.g., generated during the current Surveillance Activity or \n already available and collected during a previous Surveillance Activity)Multiple selectionYes
ArthropodSourceOriginIdentifierSurveillance Activity Identifier Arthropod Source OriginThe identifier of the Surveillance Activity under which the arthropods used\n in the current Surveillance Activity were collectedStringYes
ArthropodSourcePolygonOrPointPolygon or Trap is of InterestEstablish if a polygon (e.g., parcel, grid cell, protected area zone, hunting range) \n where the arthropod collection takes place or the exact position of each arthropod collection\n (e.g., longitude, latitude, time) of interest for the Surveillance Activity?Multiple selectionYes
ArthropodSourceSpeciesArthropod SpeciesSpecies of the arthropods that are the target of the Surveillance Activity. It is possible\n to select high taxonomy levels such as 'Insecta', etc. to indicate that\n no particular species is targetedMultiple selectionYes
ArthropodSourceSpeciesIdentificationMethodArthropod Species IdentificationExplain the methodology used to identify the arthropod species collectedMultiple selectionYes
ArthropodSourceSpeciesIdentificationMethodReferencesArthropod Species Identification ReferencesProvide references associated with the identification method of the arthropod species collectedStringNo
ArthropodSourceLifeStageTargetedLife Stage TargetedIndication of the life stages of the arthropods collectedMultiple selectionYes
ArthropodSourcePassiveOrActiveCollectionActive or Passive CollectionDescribe if the arthropods are collected actively (e.g., trap or lure) \n or passively (e.g., larvae from water container)Multiple selectionYes
ArthropodSourcePassivePassive Source of ArthropodsDescribe how arthropods are collected passivelyStringYes
ArthropodSourceTrapTypeTrap Type EmployedDescribe the type of traps used to collect arthropodsMultiple selectionYes
ArthropodSourceTrapModelTrap ModelProvide the specific characterristics of traps used in the collections \n (e.g., brand, model, name, identifier, url, etc)StringYes
ArthropodSourceLureLure EmployedDescribe the lure used to collect arthropodsMultiple selectionYes
ArthropodSourceHowObtainedCollection Site SelectionExplain how arthropod collection sites are selectedStringYes
ArthropodSourceInclusionCriteriaInclusion Criteria of Arthropods Collection SitesProvide specific inclusion criteria of arthropod collections sites (collection areas or points) \n in the Surveillance Activity, if anyStringYes
ArthropodSourceExclusionCriteriaExclusion Criteria of Arthropod Collection SitesExplain the reason to exclude certain arthropod collections sites (collection areas or points) \n or specific arthropod collections from the Surveillance Activity, if anyStringNo
ArthropodSourceIdentificationCollection Sites Are Identified IndividuallyAnswer to the question: 'Are arthropod collections sites (polygon, traps, water container) individually identified?'\n (e.g. code, color, type, other)BooleanYes
ArthropodSourceIdentificationMethodCollection Sites Identification MethodExplain how arthropod collections are individually identified (e.g. color, other)StringYes
ArthropodSourceGroupingArthropod Collections Are GroupedAnswer to the question: 'Are arthropod collections clustered in units smaller\n than 'Event'?'. Grouping can be physical (e.g., parcel) or temporal (e.g., month)BooleanYes
ArthropodSourceGroupingStructureGrouping of Arthropod CollectionsExplain the grouping structure of the arthropod collections below 'Event' \n (e.g., Events represent a cell of a grid cell. Arthropod Sources are grouped by green plots in the cell)StringYes
ArthropodSourceRecordCodeStructureArthropod Source Record Code StructureExplain the nomenclature of the Arthropod Source Record Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the arthropod taxonomic group, and then the number is \n the sequential number of the Arthropod Source Records from trap X)StringYes
ArthropodSourceRecordsOverTimeCollection Records Over TimeAnswer to the question: 'Is it aimed to obtain arthropods from the same collection sites\n (polygon, trap, etc.) during the Surveillance Activity?' (e.g., several collections or Records from the same site)BooleanYes
ArthropodSourceRecordHowObtainedArthropod collection ProcessExplain how arthropods are collected in the field (e.g., how are they collected from a trap)StringYes
ArthropodSourceRecordInclusionCriteriaInclusion Criteria of Arthropods CollectionsProvide specific inclusion criteria of arthropod collections in the Surveillance Activity, if anyStringYes
ArthropodSourceRecordExclusionCriteriaExclusion Criteria of Arthropod CollectionsExplain the reason to exclude certain arthropod collections from the Surveillance Activity, if anyStringNo
ArthropodSourceRecordFieldStorageArthropod Collection Field StorageMethod to preserve the arthropods collected while in the fieldMultiple selectionYes
ArthropodSourceRecordLabStorageArthropod Collection Lab StorageMethod to preserve the arthropods collected in the laboratoryMultiple selectionYes
ArthropodSourceSpecimenCollectionArthropod Specimen CreationAnswer to the question: 'Are Arthropod Specimens created from the collections (Arthropod Source Records)?'BooleanYes
ArthropodSourceSpecimenCollectionMethodArthropod Specimen Creation MethodExplain how the Arthropod Specimens are created from the collections (Arthropod Source Records)StringYes
ArthropodSourceSpecimenCollectionMethodReferencesArthropod Specimen Creation Method ReferencesProvide references associated with the creation method of the Arthropod Specimens from \n the collections (Arthropod Sources Records)StringNo
ArthropodSourceSpecimenCodeStructureArthropod Specimen Code StructureExplain the nomenclature of the Arthropod Specimen Codes used \n (e.g., first letter refers to the pathogen, the next two letters refer to the \n country, the next letter refers to the arthropod group, the following letters\n are the type of Specimen, then the numbers are the collection site, and the last number is \n the sequential Specimen from each collectionStringYes
ArthropodSourceSpecimenFieldStorageArthropod Specimen Field StorageMethod to preserve the Arthropod Specimens in the fieldMutiple selectionYes
ArthropodSourceSpecimenLabStorageArthropod Specimen Laboratory StorageMethod to preserve the Arthropod Specimens in the laboratoryMutiple selectionYes
ArthropodSourceSpecimenPoolingArthropod Specimen PoolingAnswer to the question: 'Are Arthropod Specimens used in the Surveillance Activity\n pooled?' (for a definition of 'pooling' for the database see the online database manual)BooleanYes
ArthropodSourceSpecimenPoolingStrategyArthropod Specimen Pooling StrategyExplain the pooling method of the Arthropod Specimens \n (for a definition of 'pooling' for the database see the online database manual)StringYes
ArthropodSourceSpecimenDiagnosticsUsedDiagnostics Are Conducted in the Arthropod SpecimensAnswer to the question: 'Are diagnostics conducted in the Arthropod Specimens?'BooleanYes
ArthropodSourceSpecimenDiagnosticsUsedProtocolArthropod Specimen Diagnostic ProtocolsName and describe the protocols of the Diagnostics conductedStringYes
ArthropodSourceSpecimenDiagnosticsUsedProtocolReferencesArthropod Specimen Diagnostic Protocols ReferencesProvide references associated with the Diagnostic protocols conductedStringNo
ArthropodSourceSpecimenCriteriaPositiveTestCriteria Positive TestExplain the criteria to establish that each diagnostic test method conducted in an\n Arthropod Specimen is positive. The criteria for positive Arthropod Source and Arthropod Source Specimens are requested belowStringYes
ArthropodSourceSpecimenCriteriaPositiveTestReferencesCriteria Positive Test ReferencesProvide references associated with the criteria to establish that each diagnostic test conducted in\n in an Arthropod Specimen is positiveStringNo
ArthropodSourceSpecimenCriteriaPositiveCaseCriteria Arthropod Specimen Positive CaseExplain the criteria to establish that an Arthropod Specimen is \n positive for each specific hazard targeted in the Surveillance Activity. \n The criteria for a positive Arthropod Source Record is requested belowStringYes
ArthropodSourceSpecimenCriteriaPositiveCaseReferencesCriteria Arthropod Specimen Positive Case ReferencesProvide references associated with the criteria to establish that an \n Arthropod Specimen is positive for each specific hazard targeted in the Surveillance\n ActivityStringNo
ArthropodSourceRecordCriteriaPositiveCaseCriteria Arthropod Source Record (Collection) Positive CaseExplain the criteria to establish that an Arthropod\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringYes
ArthropodSourceRecordCriteriaPositiveCaseReferencesCriteria Arthropod Source Record (Collection) Positive Case ReferencesProvide references associated with the criteria to establish that an Arthropod\n Source Record is positive for each specific hazard targeted in the Surveillance ActivityStringNo
\n
\n```\n:::\n:::\n\n\n\n\n\n::: {.cell}\n\n:::\n", "supporting": [], "filters": [ "rmarkdown/pagebreak.lua" diff --git a/_freeze/data_model/execute-results/html.json b/_freeze/data_model/execute-results/html.json new file mode 100644 index 0000000..ad38d35 --- /dev/null +++ b/_freeze/data_model/execute-results/html.json @@ -0,0 +1,14 @@ +{ + "hash": "4bb54132a3b603ec13962dfcb243c515", + "result": { + "markdown": "# Data Model {.unnumbered}\n\nData in the WildHealthDB is organized in units that are generally hierarchical, starting from the highest level of \"**Projects**\" down to \"**Surveillance Activities**\", \"**Field Visits**\", \"**Locations**\", \"**Events**\", \"**Sources**\", \"**Source Records**\", \"**Specimens**\", and \"**Diagnostics**\". Briefly, **Projects** are a set of **Surveillance Activities** with a common leader and organizer (e.g., a national veterinary services agency). **Surveillance Activity** is a surveillance task that have a specific methodology and objectives. **Field Visit** represents a period of time when surveillance activities are conducted in the field. The **Location** is a specific area where surveillance activities are conducted. An **Event** is a site where wildlife health surveillance data is collected from. Sources are the units that can provide Specimens for hazard detection. **Specimens** are tissue taken from the **Sources** at time *t* (**Source Records**). **Diagnostics** are the tests conducted in lived animals (\"Animal Source\"), **Carcasses**, or **Specimens** collected to assess hazards. **Diagnosis** are the final status assigned to a Diagnostic, a Specimen, or a Source at time *t* with respect to the hazards surveyed, based on well-documented case definitions. Exceptions to the \"hierarchical\" rule are given in the sections for each unit below. To learn more about these units, please scan the menu on the top right corner of this website and click on the corresponding unit. A diagram shoing the relationship among the units is shown at the bottom of this website.\n\n## Project\n\n\n\n\n\nA Project in the data model is a surveillance initiative supported by specific entities. For example, the PREDICT Project funded by USAID, an isolated cross-sectional study with a single field visit to a single location (sample collection in a market), or a national or local wildlife health surveillance network led by a government agency. Projects are the highest hierarchical unit in the database and they contain at least one Surveillance Activity. Projects can involve a single date or they can extend for as long as wanted.\n\n\n## Surveillance Activity \n\n\n\n\n\nA Surveillance Activity in the data model refers to a set of activities to collect data with the aim of detecting, proving freedom of disease, measure incidence or prevalence, or assessing trends of specific health hazards within specific populations, using a standardized methodology. For example, the [longitudinal assessment of coronavirus shedding in two *Eidolon helvum* bat roosts in Africa](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0274490).\n\nSurveillance Activities can encompass targeted surveillance, scanning surveillance, citizen science monitoring, freedom of disease assessments, ranger patrols, and others. An example is a capture-mark-recapture study targeting lead accumulation in a specific vulture population involving the collection of blood samples and conducting tests using the same capture, marking, and diagnostic methods. **Surveillance Activities include detailed metadata that describe their objectives and methods, including information on the targeted species, populations, hazards, type of Sources and Specimens, collection methods, Diagnostics, and case definitions for Diagnostics, Specimens, and Sources**. \n\nField Visits, Locations, Events, Sources, Source Records, and Diagnostics usually belong to a single Surveillance Activity. The Surveillance Activity that commanded the Field Visits at different Locations to document Events, collect Sources and Specimens, perform Diagnostics for a specific hazard, and provide Diagnosis for Diagnostics, Specimens, and Sources. However, there are exceptions to this rule. For example, rodents trapped in the same Event may be sampled using the same methodology but tested for coronaviruses and Rickettsia *sp*. In this scenario, two Surveillance Activities should be assigned to the Field Visits, Locations, Events, Source Records, and Specimens. Diagnostics for either group of pathogens and the corresponding Diagnosis should only get a single Surveillance Activity. \n\nAnother exception to this rule is the collection of Specimens from Sources that belonged to other Surveillance Activities. For example, marked rodents that were released, and later captured and tested for a specific hazard under Surveillance Activity A that were captured and sampled during Surveillance Activity B months later. In this case, these rodents will be part of two Surveillance Activities (A and B).\n\nAnother exception occurs when Specimens were collected during past surveillance efforts but are included in new surveillance initiatives. For instance, using pangolin Specimens collected by veterinarians in 2017 and tested for Salmonella sps. which are then tested in 2023 for SARS-CoV-2. In this case, the latter Surveillance Activity is assigned to the Specimens being tested (as a second Surveillance Activity) and to the SARS-CoV-2 Diagnostics and Diagnosis. Therefore, these Specimens should have two Surveillance Objectives. The first one corresponds to the original Surveillance Activity that lead to their collection and the second one corresponds to the Surveillance Activity testing them for SARS-CoV-2. The Source (pangolin) and the corresponding Record should keep a single Surveillance Activity.\n\nMoreover, Necropsies might be conducted as part of a secondary Surveillance Activity (on a Carcass that was collected under other Surveillance Activity) or new Specimens could be created from a previously unused Carcass as part of a new Surveillance Activity. In this case, the new data (Necropsy and Specimens) should receive the second Surveillance Activity only. Diagnostics using the new Specimens should receive the second Surveillance Activity only. The Carcass should receive the Surveillance Activity that lead to its collection only.\n\nTherefore, Surveillance Activities can be interconnected through the reuse of Specimens or expanding the data generated by previous Surveillance Activities. These connections will be evident in the exported data, where each component with multiple Surveillance Activities (e.g., Specimen) will be represented by one row per Surveillance Activity. \n\n## Outbreak Investigation\n\nAll outbreak investigations are considered Surveillance Activities. Outbreak Surveillance Activities can encompass the Field Visit that lead to the Outbreak detection and the following Field Visits associated with Outbreak investigation and control. The detection could have been made during a Field Activity conducted by rangers during their patrols. This initial Field Visit and its components should be assigned to a the ranger patrol Surveillance Activity and to the Outbreak Surveillance Activity. The following Field Activities that could be completed by veterinarians or public health officers receive the outbreak Surveillance Activity only. \n\n\n## Field Visit\n\n\n\n\n\nA Field Activity in the data model represents a visit to the field within a specific time period, including a start and end date, to find Events, Sources, and Specimens (see below) and document data from them. A Field Visit can include visits to various types of Locations, such as markets, natural areas, rehabilitation centers, caves, etc that are completed within the same trip and common start and end date.\n\n\n## Location\n\n\n\n\n\nA Location in the data model refers to a general place where Events, Source Records, Carcasses, and Specimens can be collected from. During a single Field Visit, data may be collected from various Locations, such as two rehabilitation centers, a cave within a protected area, or three different zones within another protected area. In this case, there would be a total of six Locations. Therefore, a Location serves as a way to group data in a more generalized manner compared to the exact latitude and longitude coordinates where data is collected ('Event'; see below), but it provides more specificity than the overall 'Field Activity'. \n\nWhat a 'Location' represents will inevitably vary depending on the Surveillance Activity methodology. For example, for the collection of arthropods, a Location can represent a parcel where traps are set. In a structured research, the Location could represent a grid cell. In ranger patrols, the Location can correspond to either the full protected area, or a specific zone within the protected area. **It is up to the user to define what unit the Location represents and report it in the Surveillance Activity metadata**. \n\nProperties of Location include the start and end date, a unique identifier, the cross referential identifier, the type of location, environmental characteristics, among others (see Data Dictionary).\n\nLocations can be clustered in units smaller than Field Visit if needed. For a detail explanation, see \"Grouping of Locations, Events, and Source Records\" section below.\n\n\n## Event\n\n\n\n\n\nAn Event in the data model refers to a distinct wildlife health event that occurs at a specific longitude and latitude on a particular date. A single Location can include between zero to a indefinite number of Events. \n\nThe definition of a wildlife health event, and thus what an 'Event' represents, will inevitably vary depending on the Surveillance Activity and the particular definition of Event. For example, in active surveillance efforts, an Event can refer to the site and time where and when animals are captured to obtain Specimens. The site where a dead dead animal is found during a ranger patrol can be an Event. Furthermore, an 'Event' can be defined as the site where water is collected from a pond. In the case of surveillance for vector-borne diseases, an Event can represent a specific point in time and space where one or several traps for vectors are deployed. In the case of beached fish, an Event can represent each individual dead fish at one extreme, or the total count of dead fish across the beach as a single point in time and space at the other extreme. In the context of a wet market, the definition of Event can be applied to the market, or to the vendor, or to the stall, or to the cage. Structured studies can have multiple levels of hierarchy (zone, grid, area, trap, etc.) that represent can Event. For study A it could the grid cell whilst for study B it could each trap. \n\nMoreover, the presence of at least one Source could be needed to establish an Event. For example, a dead animal found during a ranger patrol. In Active Surveillance, an Event can occur without the presence of any Source, for example, when a capturing effort ended in the absence of animals captured. Additionally, the definition of an Event can include healthy animals found nearby a dead animal or animals not captured nearby animals captured, or not, depending on the Event definition.\n\nConsequently, an Event in wildlife health surveillance can represent different spatio-temporal units depending on the objectives and the methodology used to collect wildlife health data. **It is up to the user to define what unit the Event represents and report it in the Surveillance Activity metadata and it should be unique for a specific Surveillance Activity**. \n\nProperties of Event include the start and end date, a unique identifier, the cross referential identifier, longitude, latitude, the coordinate system reference used, the accuracy of the latitude and longitude valies, date-time, among others (see Data Dictionary).\n\nEvents can be clustered in units smaller than Location if needed. For a detailed explanation, see “Clustering of Locations, Events, and Source Records” section below.\n\n\n\n\n## Source and Source Records\n\n\n\n\n\n### Generalities\n\nA Source in the data model is a unit that can be observed and provide Specimens, including carcasses, organic tissue, abiotic tissue, or arthropods. The data model manages four types of Sources: i) a co-specific group of animals (Group Source), ii) individual animals (Animal Source), iii) sites that can provide abiotic tissue of interest or biotic material of animal origin whose individual or group animal of origin is unknown (Environmental Source), and iv) sites where active or passive collection arthropods at any life stage is completed (Arthropod Source). A Group Source could correspond to a specific bat roost of species X sourcing guano, an Animal Source could be a collared animal, an Environmental Source could be a pond where water is collected from, and an Arthropod Source could be a site where mosquito larvae are collected from. Sources contain time-independent data only, such as the species of an animal in the case of a Group Source or an Animal Source (more below).\n\nAll Sources can be individually identified and followed over time. **Animal Sources and Group Sources might not be individually identified preventing following them over time**. \n**All Sources belong to at least one Surveillance Activity** but they can be defined prior to any Event or after. For example, a set of animals can all be individually identified and released before any Field Visit starts. Then, capturing, recapturing, and sampling are conducted in following Field Visits. In that case, these animals are initially Animal Sources in the data model linked to the corresponding Surveillance Activity only. Once the Field Visits begin, all, none, or some of the Sources (rodents) will be part of Events. The Sources that are not part any Event by the end of the Surveillance Activity will still be part of it, but they will not have any data associated with Events, Specimens, Diagnostics, etc. Therefore, **Sources might not be part of any Event**.\n\nSources that are individually identified during an Event will certainly belong to at least that Event when they were identified and potentially others. For example, a bat (Source) caught in a mist net (Event), identified individually, and recaptured in a following Event. This bat is linked to the capture Event and the recapture Event. \n\n**Sources that are not individually identified will belong to the Event when they were observed or captured only**. For example, a bat (Source) that is captured and sampled during an Event but not marked or a dead animal found by a ranger during a patrol. The bat and the animal found are linked only to the Event they were capture and observed, respectively.\n\nSources observed, collected, or captured at time *t* are linked to Events through a **Source Record** (the Source at time *t*). Source Records contain time-dependent data only, such as health status at time *t*. **Sources individually identified can be followed longitudinally and have multiple Source Records that link them to multiple Events over time**.\n\n**An Event can contain any number of Source Records associated with Sources of any type**. For example, an Event can contain Group Source Records, Animal Source Records, Environmental Source Records, and Invertebrate Source Records, two of them, one of them, or three of them. Also remember that **an Event might not contain any Source Record** (e.g., a set up mist net without birds captured).\n\n\n### Group Source\n\n**A Group Source is a unit of co-specific individuals (animals of the same species) associated to a herd, an area, a site, a farm, a cage, a stall, an enclosure, or another that makes the individuals part a single epidemiological unit**. Group Sources can be observed, captured, and provide Specimens at time *t*. Data of a Group Source include the species, the identifier, the cross identifier, and the date of extinction (see Data Dictionary). \n\nThe purpose of Group Source is to record individuals at health events at the species level instead of individual by individual. This can occur when herds are the unit of interest, when protected area rangers find animals of the same species in a health event, or animals in a unit such as a cage, stall, or vendor of a market. For example, animals of two species in a single cage. If the animals are not meant to be tracked individually, the animals of each species in the cage represent a Group Source. \n\n#### Group Source Record\n\n**A Group Source Record consists of a count of the animals in the Group Source at time *t*, stratified by sex, age, and health status (e.g., healthy, injured, sick, or dead)**. Other properties of the Group Source Record are observed anomalies, potential causes of disease or death if they apply at time *t* among others (see Data Dictionary). Properties of a Group Source Record are documented at the group level and each property can receive multiple options. For example, a Group Source with three dead animals can receive several potential causes of death. Therefore, **is not possible to know the distribution of several properties across individuals of the Group Source Record**, but only that it was present in at least one individual (the exception is the \"species\" property and other properties when a Group Source has a single individual). \n\n**Group Source Records can include a mix of dead, diseased, poisoned, infected, injured, and healthy individuals of the same species or animals of the same species that belong to just one of these categories exclusively (all animals are dead for example)**. A Group Source Record of only healthy animals can also be part of a Health Event depending on the definition of Health Event (e.g., animals of species X with all of them observed healthy next to dead animals of species Y and Z). **Group Source Records can have a single individual**. For example, rangers patrolling a protected area might find a dead animal of species X and two dead animals of species Y at the same site (Event) and rangers record their animal data as Group Sources. If this is the case, the animal of species X belong to a Group Source Record and the animals of species Y correspond to another Source Group Record. Moreover, if only a single animal of a known herd is observed at time *t*, then that individual is the representation of the herd for the Source Group Record. Finally, **an Event can have more than one Group Source Record of the same species**. For example, animals of the same species in two cages hold by a vendor in market where each vendor is considered an Event. Then each cage with the corresponding animals could be considered a unit, and therefore, a Group Source Record belonging to the same vendor (same Event).\n\nAn Group Source can be used directly for a Diagnostic (e.g., assessment of fat in carcasses of animals belonging to a specific herd). The data model can accommodate Diagnostics applied to the \"group\" itself rather than Specimens taken from that Group Source. The diagnostic information is part of the set of Diagnostics conducted in the corresponding Group Source (see Diagnostics). \n\n**An animal of species X documented as part of a Group Source Record must not be included as an Animal Source Record and vice-versa**. If an Event contains a Group Source Record and an Animal Source Record of species X, then the total number of animals of species X at the Event is the sum of number of animals of species X in the Group Source Record and the single individual of species X recorded as an Animal Source Records. An example is a herd of cows illegally raised in a protected area whose health is assessed at time *t*. The herd of this example contains 20 cows. Two of them are sampled and the rest are part of a single unit. In this case, the sampled cows can be added as Animal Source Records (one per sampled cow) and the remaining 18 animals can be added as a single Group Source Record that distributes the animals per sex, age, and health status. The total number of cows are the individuals in the Group Source Record (18) and the two cows recorded as Animal Records (2). The \"herd\" identity of the 20 cows can be kept using a \"Tag\" (see below) so the three Source Records receive the same unit (another option is to add the 20 cows as a Group Source but the data of the specific animals sampled will be lost. See next section). If the Group Source Record contains the original 20 cows and also two Animal Source Records, then the total number of cows will be 22.\n\n### Animal Source\n\n**An Animal Source represents an individual animal whose specific individual-level data is of interest**. Animal Sources can be observed, captured, tested, and provide Specimens at time *t*, including the full carcass to have a Necropsy completed. Animal Source data includes the species, the identifier, the cross identifier, the sex, and the date of death (see Data Dictionary). Past marking codes (if any have been used) are considered immutable and entered as data of an the Animal Source.\n\nAn example of Animal Sources are animals of different or the same species in a cage located in a live market. If the data of the animals is to be collected at the individual-level, then each individual represents an Animal Group Source in the cage. \n\n#### Animal Source Record\n\n**An Animal Source Record consists of an Animal Source at time *t* **. Properties of an Animal Source Record are its age, health status, observed anomalies, and potential cause of disease or death if they apply at time *t*, among others (see Data Dictionary). The marking of an individual animal at time *t* is considered mutable and a property of the corresponding Animal Source Record. Properties of an Animal Source Record can receive single or multiple choices. For example, the observed health status in only one (live healthy, live sick) but an Animal Source Record can receive several observed anomalies if they apply at time *t* (wounded, hair loss, diarrhea, etc. See Data Dictionary).\n\nAn Animal Source can be either dead, diseased, poisoned, infected, injured, or healthy at time *t*. **An Animal Source Record with an observed health status \"live healthy\" can be part of an Event if they are of interest** (e.g., a healthy animal of species X next to dead animals of species X, Y, and Z; healthy animals captured for Specimen collection). \n\nAn Animal Source can be used directly for a Diagnostic (e.g., X-rays in a live animal). The data model can accommodate Diagnostics applied to the \"animal\" itself rather than a Specimen taken from that Animal Source. The diagnostic information is part of the set of Diagnostics conducted in the corresponding Animal Source (see Diagnostics). \n\n**An animal of species X documented as part of a Group Source Record cannot be included as an Animal Source Record and vice versa**. If an Event contains a Group Source Record and an Animal Source Record of species X, then the total number of animals of species X at the Event is the sum of number of animals of species X in the Group Source Record and the single individual of species X recorded as an Animal Source Record. An example is a herd of cows illegally raised in a protected area whose health is assessed at time *t*. The herd of this example contains 20 cows. Two of them are sampled and the rest are part of a single unit. In this case, the sampled cows can be added as Animal Source Records (one per sampled cow) and the remaining 18 animals can be added as a single Group Source Record that distributes the animals per sex, age, and health status. The total number of cows are the individuals in the Group Source Record (18) and the two cows recorded as Animal Records (2). The \"herd\" identity of the 20 cows can be kept using a \"Tag\" (see below) so the three Source Records receive the same unit (another option is to add the 20 cows as a Group Source but the data of the specific animals sampled will be lost. See next section). If the Group Source Record contains the original 20 cows and also two Animal Source Records, then the total number of cows will be 22.\n\n#### Carcass\n\nThe carcass of a dead Animal Source can be used as a source for Specimens and Diagnosis. A Carcass entered to the database comes from a specific Animal Source and they are collected at a single specific time *t*. Therefore, each Carcass is associated with one and only one Animal Source Record (when the Carcass was collected). Properties of a Carcass include its decomposition condition, storage during transport, storage in a facility, and its location (building, room, refrigerator, etc.), among others (see Data Dictionary). The data regarding changes in the storage of the carcass can have many units for the same carcass if it changes over time. \n\nAn carcass can be used directly for a Diagnostic (e.g., X-rays in a dead animal). The data model can accommodate Diagnostics applied to the Carcass itself rather than a Specimen taken from that Carcass (see Diagnostics). The diagnostic information is part of the set of Diagnostics conducted in the corresponding Animal Source. \n\n##### Necropsy\n\nA Necropsy is associated with a specific Animal Source Record that can occur any date after the corresponding Animal is found dead. However, **a Necropsy is tied to the Carcass**, which is tied to the Animal Source Record when it was collected. **The earliest date a Necropsy can occur is when the dead animal was found and a Field Necropsy was conducted (no Carcass collection) or when the Carcass was collected and used for Necropsy**. Necropsy data includes the identifier, the cross identifier, the date of the necropsy, findings per system, among others (see Data Dictionary).\n\nNecropsies can be primary or secondary. A primary necropsy usually starts with an intact carcass (not previously used in a necropsy). A secondary necropsy is usually conducted by a veterinarian pathologist using pictures of the primary necropsy or using a carcass already necropsied. \n\n### Environmental Source\n\n**An Environmental Source is a unit in space where Specimens that cannot be associated with a Group Source, an Animal Source, or Arthropod Source can be collected from** (e.g., feces found in the field but unknown individual dropping them or unknown group of animals with the individual that could have dropped them). Properties of an Environmental Source include the type (e.g., water, soil, sediment, air , feces), the species (only for biotic types if it is known), the identifier, and the cross identifier (see Data Dictionary). The species can be either NA (abiotic type such as water, sediment, or soil), \"unknown\" (e.g., \"unknown\" for feces found by themselves), or the most accurate taxonomy level that can be given to a biotic Environmental Source if barcoding or another species determination method is not used (e.g., \"mammalia\" for feces found by themselves). \n\n#### Environmental Source Record\n\n**An Environmental Source Record is the collected biotic or abiotic tissue from the Environmental Source at time *t* using the same method**. For example, the water obtained from a pond at time *t* across devices targeting water collection. This mean that air collected by any number of devices \"X\" deployed at the Environmental Source at time *t* to collect air is an Environmental Source Record and air collected by any number of devices \"Y\" deployed at the Environmental Source at time *t* to collect air is another Environmental Source Record. **A key difference between the Environmental Source and the Group and Animal Sources is that an Event can contain multiple Environmental Source Records of the same Environmental Source (one per collection method) compared with Group and Animal Sources Records types that only have a single Source Record per Source per Event**. The properties of an Environmental Source Record include the identifier, the cross identifier, the volume collected, the unit of the volume collected, among others (see Data Dictionary).\n\n### Arthropod Source\n\n**An Arthropod Source is a unit in space where collection of arthropods can be completed** (e.g., a household in the forest where traps are set). Properties of an Arthropod Source include the identifier, the cross identifier, the area covered, among others (see Data Dictionary).\n\n**If the interest of the Surveillance Activity is at the arthropod individual level (e.g., butterflies with problems in their wings or with parasites), then the user should consider these arthropods as Animal Sources. Arthropods from Animals Sources (attached ticks, lice, fleas, mites) are Specimens from an Animal Source and not Arthropod Sources**.\n\n#### Arthropod Source Record\n\n**An Arthropod Source Record is the collected arthropods from the Arthropod Source at time *t* using the same method**. For example, the number of mosquitoes obtained at the household in the forest at time *t* per species and age-sex-condition across the traps targeting the same group of arthropods. This mean that adult mosquitoes of *n* species collected by any number of CO2 traps deployed at the Arthropod Source at time *t* is an Arthropod Source Record and that adult mosquitoes of *n* species collected by any number of BG traps deployed at the Arthropod Source at time *t* is another Arthropod Source Record. **A key difference between the Arthropod Source and the Group and Animal Sources is that an Event can contain multiple Arthropod Source Records of the same Arthropod Source (one per collection method) compared with Group and Animal Sources Records types that only have a single Source Record per Source per Event**. The properties of an Arthropod Source Record include the identifier, the cross identifier, the species, the age, sex, condition of the females, the corresponding number, among others (see Data Dictionary).\n\nSources can be clustered in units smaller than Event if needed. For a detailed explanation, see “Clustering of Locations, Events, and Source Records” section below.\n\n\n## Clustering of Locations, Events, and Source Records\n\n\n\n\n\nFollowing the standard units in the data model, the simplest data of a Field Visit is an Source Record found in a single Event in a single Location. However, depending on the methodology of a specific Surveillance Activity, Sources Records could be clustered in units that are clustered by Events. In the same manner, Events can be clustered by units that are clustered by Locations, and Locations can be clustered by units that are clustered by Field Visits: \n\n- Field Activityw\n - **Cluster unit**𝛼\n - **Cluster unit**𝛽\n - Locationx\n - **Cluster unit**γ\n - **Cluster unit**𝛿\n - Eventy\n - **Cluster unit**𝜂\n - Source Recordz\n\nA second layer of complexity is the addition of clustered units that are not nested. For example, the same structure shown before plus the cluster of Source Records per season of the year: \n\n- Field Activityw\n - **Spatial Cluster unit**𝛼\n - **Spatial Cluster unit**𝛽\n - Locationx\n - **Spatial Cluster unit**γ\n - **Spatial Cluster unit**𝛿\n - Eventy\n - **Spatial Cluster unit**𝜂\n - **Temporal Cluster unit**д\n - Source Recordz\n\nThe data model considers the possibility to include clustering levels between the Source Record and Event, Event and Location, and Location and Field Visit. The data model also allows the inclusion of non-nested clustering units. Unavoidably, how many clustering levels are considered, what each of these clustering units represent, what are they clustering, and the data to be collected from each of these extra units will vary among Surveillance Activities. Therefore, clustering levels and their meaning must be reported in the Surveillance Activity metadata and the only properties for each level are the identifier, the cross identifier, the origin of the cross identifier, and a description.\n\nFor example, the units Location, Event, and Source Record could be enough to record the data structure of a specific Surveillance Activity gathering information from Protected Areas (Locations) at points (Events) where dead animals (Source Records) are found any given time. However, another Surveillance Activity could have the following structure: protected area, zones within protected area (Location), grid cells within each zone, capture site with a pair of mist nests within each grid cell (Event), mist nets of the capture site, and bats captured (Source Records) per season.\n\n\n\nIn another example, a Surveillance Activity involved sampling animals and cages in a market. One of the potential options to structure these data is to set the market as the Location and set each vendor within the market as an Event. Animals are in cages and cages are clustered in stalls. In one of the Events (a vendor), a sample of feces is collected from the bottom of a cage, the cage has three animals of the same species X, and only one of these three animals is sampled (Animal Source).\n\nIn this scenario, the Sources (a Group Source Record with two animals of species X and a Animal Source Record), are clustered by cage (clustering unit 1), by stall (clustering group 2), Event (vendor), Location (market), and Field Activity.\n\n\n\n## Specimen\n\n\n\n\n\n#### Generalities\n\nSpecimens are tissue or material collected from Sources, other Specimens, and Diagnostic products (See Diagnostics) to conduct Diagnostics and identify hazards or other potential health threats. **Specimens can originate from Sources at time *t*, but also from other Specimens, or Diagnostic Products**.\n\nIn the data model, a single Specimen can be composed of feces of a specific animal collected in the field mixed with water from a pond next to that Animal. Therefore, **Specimens can be created using tissue collected from many Sources of different types**. \n\nIn the data model, a new Specimen can be created by mixing Specimens of any origin and Diagnostic Products. Therefore, **Specimens can originate by mixing Specimens, or by mixing Diagnostic Products, or by mixing Specimens and Diagnostic Products. These are \"Pooled Specimens\"**. \n\nSpecimens are characterized by an identifier, the type of material (water, hair, kidney, animal), the original amount collected (e.g., 'full animal' or 0.35 mm), the current amount, their origin (Source Record, other Specimen, or Diagnostic Product), among others. Additionally, the data model can hold data on the storage location of Specimens (building, laboratory name, refrigerator name, etc.), their availability, ownership, current amount, and exportation processes (See Data Dictionary). \n\nSpecimens without any amount of tissue left can be kept in the data model so the last storage, exportation processes, and its use in Diagnostic procedures can be tracked.\n\n#### Specimens from Source Records \n\nSpecimens can be tissue collected from Sources at time **t** (from Source Records). These Specimens can range from the entire body of a living animal to conduct an ultrasound to a minimal amount of fluid (e.g., blood) to perform advanced assays. An example of Group Source Specimen is feces collected from the bottom of a cage with animals of the same species but it is unknown which of the animals dropped the feces. An example of Animal Source Specimen is 2 ml of blood taken from a lion. An example of Environmental Source Specimen is 10 grams of soil collected from a specific site. An example of Arthropod Source Specimen is a set mosquitoes of the same species coming from the same trap type collection. In vector-borne disease surveillance, this last type of Specimen are usually called \"pools\". \n\nThe data model does not accommodate Specimens that were collected after the last date a Source was observed. For example, it is possible to collect feces from an empty cage that a Group Source providing feces longitudinally was using until two days ago. In this case, the Specimen origin changes from the Group Source followed longitudinally to an Environmental Source (the cage). Using a clustering variable, it is possible to track that the Specimens are coming from the same cage, in one case with animals and in the last one without animals (clustering the Sources coming from the same cage). \n\n**An Group Source used directly for a Diagnostic (e.g., assessment of fat in carcasses of animals belonging to a specific herd) is not a Specimen**.\n\nIn the case of Animal Sources, new Specimens can be generated during a Necropsy (e.g., Specimens from the Carcass). In this case, the date of Specimen collection is not necessarily the date when the Animal Source was found, when the Carcass was collected, or when the animal died, but the date of the Necropsy (primary or secondary). It is possible to track if a Specimen was collected during the primary or secondary Necropsy based on the information entered for Specimens. **An Animal Source used directly for a Diagnostic (e.g., X-rays in a live animal) is not a Specimen**\n\nIn the case of Environmental Sources, its type determines the Specimen type. For example, a pond of water can only yield Specimens of type \"water\".\n\n#### Specimens from Diagnostic Products\n\nProducts generated by Diagnostic methods applied to a regular Specimen can be stored and used as Specimen in further Diagnostics (e.g., use cDNA created to complete Diagnostic A in a new RT-PCR Diagnostic B). The data model can accommodate Diagnostic Products to be use in future Diagnostics. In this case, the origin of these new \"Specimens\" is a specific Diagnostic and not a Source Record,m and its type is \"Diagnostic Product\". The remaining properties of the new Specimen from a Diagnostic Product are the same (see Data Dictionary).\n\n#### Pooled Specimens \n\nSpecimens can be created by mixing other Specimens of any origin. For example, mixing a Specimen from a Diagnostic Product, a Specimen from an Arthropod Source, a Specimen from an Animal Source, and a Specimen from an Environmental Source. The origin of Pooled Specimens is tracked in the data model. In the example, the origin will be associated with four Specimens. The remaining properties are the same (see Data Dictionary). \n\n#### Specimens in Containers\n\nIn situations where space or materials are limited, it is possible that multiple Specimens are stored in a unique container. This approach is clearly not ideal because it can lead to cross-contamination and make actual Specimen tracing more complex. To address the tracing of these Specimens, a unique container identifier, such as a jar identifier, can be provided to the Specimen (see Data Dictionary). Specific properties for each individual Specimen within the container, such as type, quantity, etc, should allow their visual identification within the container.\n\n\n## Relationships\n\nA summary of the relationships in the data model is provided in the following figures:\n\n### For Animal Group Source\n\n![](Pictures_and_diagrams/Relationships_Animal_Source.png){width=\"680\"}\n\n", + "supporting": [], + "filters": [ + "rmarkdown/pagebreak.lua" + ], + "includes": {}, + "engineDependencies": {}, + "preserve": {}, + "postProcess": true + } +} \ No newline at end of file diff --git a/_freeze/data_model/libs/bootstrap/bootstrap-icons.css b/_freeze/data_model/libs/bootstrap/bootstrap-icons.css new file mode 100644 index 0000000..94f1940 --- /dev/null +++ b/_freeze/data_model/libs/bootstrap/bootstrap-icons.css @@ -0,0 +1,2018 @@ +@font-face { + font-display: block; + font-family: "bootstrap-icons"; + src: +url("./bootstrap-icons.woff?2ab2cbbe07fcebb53bdaa7313bb290f2") format("woff"); +} + 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i=`click.dismiss${t.EVENT_KEY}`,s=t.NAME;j.on(document,i,`[data-bs-dismiss="${s}"]`,(function(i){if(["A","AREA"].includes(this.tagName)&&i.preventDefault(),c(this))return;const o=n(this)||this.closest(`.${s}`);t.getOrCreateInstance(o)[e]()}))};class W extends B{static get NAME(){return"alert"}close(){if(j.trigger(this._element,"close.bs.alert").defaultPrevented)return;this._element.classList.remove("show");const t=this._element.classList.contains("fade");this._queueCallback((()=>this._destroyElement()),this._element,t)}_destroyElement(){this._element.remove(),j.trigger(this._element,"closed.bs.alert"),this.dispose()}static jQueryInterface(t){return this.each((function(){const e=W.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}R(W,"close"),g(W);const $='[data-bs-toggle="button"]';class z extends B{static get NAME(){return"button"}toggle(){this._element.setAttribute("aria-pressed",this._element.classList.toggle("active"))}static jQueryInterface(t){return this.each((function(){const e=z.getOrCreateInstance(this);"toggle"===t&&e[t]()}))}}function q(t){return"true"===t||"false"!==t&&(t===Number(t).toString()?Number(t):""===t||"null"===t?null:t)}function F(t){return t.replace(/[A-Z]/g,(t=>`-${t.toLowerCase()}`))}j.on(document,"click.bs.button.data-api",$,(t=>{t.preventDefault();const e=t.target.closest($);z.getOrCreateInstance(e).toggle()})),g(z);const U={setDataAttribute(t,e,i){t.setAttribute(`data-bs-${F(e)}`,i)},removeDataAttribute(t,e){t.removeAttribute(`data-bs-${F(e)}`)},getDataAttributes(t){if(!t)return{};const e={};return Object.keys(t.dataset).filter((t=>t.startsWith("bs"))).forEach((i=>{let n=i.replace(/^bs/,"");n=n.charAt(0).toLowerCase()+n.slice(1,n.length),e[n]=q(t.dataset[i])})),e},getDataAttribute:(t,e)=>q(t.getAttribute(`data-bs-${F(e)}`)),offset(t){const 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t=t=>this._pointerEvent&&("pen"===t.pointerType||"touch"===t.pointerType),e=e=>{t(e)?this.touchStartX=e.clientX:this._pointerEvent||(this.touchStartX=e.touches[0].clientX)},i=t=>{this.touchDeltaX=t.touches&&t.touches.length>1?0:t.touches[0].clientX-this.touchStartX},n=e=>{t(e)&&(this.touchDeltaX=e.clientX-this.touchStartX),this._handleSwipe(),"hover"===this._config.pause&&(this.pause(),this.touchTimeout&&clearTimeout(this.touchTimeout),this.touchTimeout=setTimeout((t=>this.cycle(t)),500+this._config.interval))};V.find(".carousel-item 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n=this._getDimension();this._element.classList.remove(ct),this._element.classList.add(ht),this._element.style[n]=0,this._addAriaAndCollapsedClass(this._triggerArray,!0),this._isTransitioning=!0;const s=`scroll${n[0].toUpperCase()+n.slice(1)}`;this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct,lt),this._element.style[n]="",j.trigger(this._element,"shown.bs.collapse")}),this._element,!0),this._element.style[n]=`${this._element[s]}px`}hide(){if(this._isTransitioning||!this._isShown())return;if(j.trigger(this._element,"hide.bs.collapse").defaultPrevented)return;const t=this._getDimension();this._element.style[t]=`${this._element.getBoundingClientRect()[t]}px`,u(this._element),this._element.classList.add(ht),this._element.classList.remove(ct,lt);const e=this._triggerArray.length;for(let t=0;t{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct),j.trigger(this._element,"hidden.bs.collapse")}),this._element,!0)}_isShown(t=this._element){return t.classList.contains(lt)}_getConfig(t){return(t={...rt,...U.getDataAttributes(this._element),...t}).toggle=Boolean(t.toggle),t.parent=r(t.parent),a(ot,t,at),t}_getDimension(){return this._element.classList.contains("collapse-horizontal")?"width":"height"}_initializeChildren(){if(!this._config.parent)return;const t=V.find(ut,this._config.parent);V.find(ft,this._config.parent).filter((e=>!t.includes(e))).forEach((t=>{const e=n(t);e&&this._addAriaAndCollapsedClass([t],this._isShown(e))}))}_addAriaAndCollapsedClass(t,e){t.length&&t.forEach((t=>{e?t.classList.remove(dt):t.classList.add(dt),t.setAttribute("aria-expanded",e)}))}static jQueryInterface(t){return this.each((function(){const e={};"string"==typeof t&&/show|hide/.test(t)&&(e.toggle=!1);const 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e=t.ownerDocument;return e&&e.defaultView||window}return t}function $t(t){return t instanceof Wt(t).Element||t instanceof Element}function zt(t){return t instanceof Wt(t).HTMLElement||t instanceof HTMLElement}function qt(t){return"undefined"!=typeof ShadowRoot&&(t instanceof Wt(t).ShadowRoot||t instanceof ShadowRoot)}const Ft={name:"applyStyles",enabled:!0,phase:"write",fn:function(t){var e=t.state;Object.keys(e.elements).forEach((function(t){var i=e.styles[t]||{},n=e.attributes[t]||{},s=e.elements[t];zt(s)&&Rt(s)&&(Object.assign(s.style,i),Object.keys(n).forEach((function(t){var e=n[t];!1===e?s.removeAttribute(t):s.setAttribute(t,!0===e?"":e)})))}))},effect:function(t){var e=t.state,i={popper:{position:e.options.strategy,left:"0",top:"0",margin:"0"},arrow:{position:"absolute"},reference:{}};return Object.assign(e.elements.popper.style,i.popper),e.styles=i,e.elements.arrow&&Object.assign(e.elements.arrow.style,i.arrow),function(){Object.keys(e.elements).forEach((function(t){var 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Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;ij.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in 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t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:''},pn={...un.DefaultType,content:"(string|element|function)"},mn={HIDE:"hide.bs.popover",HIDDEN:"hidden.bs.popover",SHOW:"show.bs.popover",SHOWN:"shown.bs.popover",INSERTED:"inserted.bs.popover",CLICK:"click.bs.popover",FOCUSIN:"focusin.bs.popover",FOCUSOUT:"focusout.bs.popover",MOUSEENTER:"mouseenter.bs.popover",MOUSELEAVE:"mouseleave.bs.popover"};class gn extends un{static get Default(){return fn}static get NAME(){return"popover"}static get Event(){return mn}static get DefaultType(){return pn}isWithContent(){return this.getTitle()||this._getContent()}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),".popover-header"),this._sanitizeAndSetContent(t,this._getContent(),".popover-body")}_getContent(){return this._resolvePossibleFunction(this._config.content)}_getBasicClassPrefix(){return"bs-popover"}static jQueryInterface(t){return this.each((function(){const e=gn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(gn);const _n="scrollspy",bn={offset:10,method:"auto",target:""},vn={offset:"number",method:"string",target:"(string|element)"},yn="active",wn=".nav-link, .list-group-item, .dropdown-item",En="position";class An extends B{constructor(t,e){super(t),this._scrollElement="BODY"===this._element.tagName?window:this._element,this._config=this._getConfig(e),this._offsets=[],this._targets=[],this._activeTarget=null,this._scrollHeight=0,j.on(this._scrollElement,"scroll.bs.scrollspy",(()=>this._process())),this.refresh(),this._process()}static get Default(){return bn}static get NAME(){return _n}refresh(){const t=this._scrollElement===this._scrollElement.window?"offset":En,e="auto"===this._config.method?t:this._config.method,n=e===En?this._getScrollTop():0;this._offsets=[],this._targets=[],this._scrollHeight=this._getScrollHeight(),V.find(wn,this._config.target).map((t=>{const s=i(t),o=s?V.findOne(s):null;if(o){const t=o.getBoundingClientRect();if(t.width||t.height)return[U[e](o).top+n,s]}return null})).filter((t=>t)).sort(((t,e)=>t[0]-e[0])).forEach((t=>{this._offsets.push(t[0]),this._targets.push(t[1])}))}dispose(){j.off(this._scrollElement,".bs.scrollspy"),super.dispose()}_getConfig(t){return(t={...bn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}}).target=r(t.target)||document.documentElement,a(_n,t,vn),t}_getScrollTop(){return this._scrollElement===window?this._scrollElement.pageYOffset:this._scrollElement.scrollTop}_getScrollHeight(){return 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/dev/null +++ b/_freeze/data_model/libs/quarto-html/quarto-syntax-highlighting.css @@ -0,0 +1,203 @@ +/* quarto syntax highlight colors */ +:root { + --quarto-hl-ot-color: #003B4F; + --quarto-hl-at-color: #657422; + --quarto-hl-ss-color: #20794D; + --quarto-hl-an-color: #5E5E5E; + --quarto-hl-fu-color: #4758AB; + --quarto-hl-st-color: #20794D; + --quarto-hl-cf-color: #003B4F; + --quarto-hl-op-color: #5E5E5E; + --quarto-hl-er-color: #AD0000; + --quarto-hl-bn-color: #AD0000; + --quarto-hl-al-color: #AD0000; + --quarto-hl-va-color: #111111; + --quarto-hl-bu-color: inherit; + --quarto-hl-ex-color: inherit; + --quarto-hl-pp-color: #AD0000; + --quarto-hl-in-color: #5E5E5E; + --quarto-hl-vs-color: #20794D; + --quarto-hl-wa-color: #5E5E5E; + --quarto-hl-do-color: #5E5E5E; + --quarto-hl-im-color: #00769E; + --quarto-hl-ch-color: #20794D; + --quarto-hl-dt-color: #AD0000; + --quarto-hl-fl-color: #AD0000; + --quarto-hl-co-color: #5E5E5E; + --quarto-hl-cv-color: #5E5E5E; + --quarto-hl-cn-color: #8f5902; + --quarto-hl-sc-color: #5E5E5E; + --quarto-hl-dv-color: #AD0000; + --quarto-hl-kw-color: #003B4F; +} + +/* other quarto variables */ +:root { + --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; +} + +pre > code.sourceCode > span { + color: #003B4F; +} + +code span { + color: #003B4F; +} + +code.sourceCode > span { + color: #003B4F; +} + +div.sourceCode, +div.sourceCode pre.sourceCode { + color: #003B4F; +} + +code span.ot { + color: #003B4F; + font-style: inherit; +} + +code span.at { + color: #657422; + font-style: inherit; +} + +code span.ss { + color: #20794D; + font-style: inherit; +} + +code span.an { + color: #5E5E5E; + font-style: inherit; +} + +code span.fu { + color: #4758AB; + font-style: inherit; +} + +code span.st { + color: #20794D; + font-style: inherit; +} + +code span.cf { + color: #003B4F; + font-style: inherit; +} + +code span.op { + color: #5E5E5E; + font-style: inherit; +} + +code span.er { + color: #AD0000; + font-style: inherit; +} + +code span.bn { + color: #AD0000; + font-style: inherit; +} + +code span.al { + color: #AD0000; + font-style: inherit; +} + +code span.va { + color: #111111; + font-style: inherit; +} + +code span.bu { + font-style: inherit; +} + +code span.ex { + font-style: inherit; +} + +code span.pp { + color: #AD0000; + font-style: inherit; +} + +code span.in { + color: #5E5E5E; + font-style: inherit; +} + +code span.vs { + color: #20794D; + font-style: inherit; +} + +code span.wa { + color: #5E5E5E; + font-style: italic; +} + +code span.do { + color: #5E5E5E; + font-style: italic; +} + +code span.im { + color: #00769E; + font-style: inherit; +} + +code span.ch { + color: #20794D; + font-style: inherit; +} + +code span.dt { + color: #AD0000; + font-style: inherit; +} + +code span.fl { + color: #AD0000; + font-style: inherit; +} + +code span.co { + color: #5E5E5E; + font-style: inherit; +} + +code span.cv { + color: #5E5E5E; + font-style: italic; +} + +code span.cn { + color: #8f5902; + font-style: inherit; +} + +code span.sc { + color: #5E5E5E; + font-style: inherit; +} + +code span.dv { + color: #AD0000; + font-style: inherit; +} + +code span.kw { + color: #003B4F; + font-style: inherit; +} + +.prevent-inlining { + content: " { + // Find any conflicting margin elements and add margins to the + // top to prevent overlap + const marginChildren = window.document.querySelectorAll( + ".column-margin.column-container > * " + ); + + let lastBottom = 0; + for (const marginChild of marginChildren) { + if (marginChild.offsetParent !== null) { + // clear the top margin so we recompute it + marginChild.style.marginTop = null; + const top = marginChild.getBoundingClientRect().top + window.scrollY; + console.log({ + childtop: marginChild.getBoundingClientRect().top, + scroll: window.scrollY, + top, + lastBottom, + }); + if (top < lastBottom) { + const margin = lastBottom - top; + marginChild.style.marginTop = `${margin}px`; + } + const styles = window.getComputedStyle(marginChild); + const marginTop = parseFloat(styles["marginTop"]); + + console.log({ + top, + height: marginChild.getBoundingClientRect().height, + marginTop, + total: top + marginChild.getBoundingClientRect().height + marginTop, + }); + lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; + } + } +}; + +window.document.addEventListener("DOMContentLoaded", function (_event) { + // Recompute the position of margin elements anytime the body size changes + if (window.ResizeObserver) { + const resizeObserver = new window.ResizeObserver( + throttle(layoutMarginEls, 50) + ); + resizeObserver.observe(window.document.body); + } + + const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]'); + const sidebarEl = window.document.getElementById("quarto-sidebar"); + const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left"); + const marginSidebarEl = window.document.getElementById( + "quarto-margin-sidebar" + ); + // function to determine whether the element has a previous sibling that is active + const prevSiblingIsActiveLink = (el) => { + const sibling = el.previousElementSibling; + if (sibling && sibling.tagName === "A") { + return sibling.classList.contains("active"); + } else { + return false; + } + }; + + // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior) + function fireSlideEnter(e) { + const event = window.document.createEvent("Event"); + event.initEvent("slideenter", true, true); + window.document.dispatchEvent(event); + } + const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]'); + tabs.forEach((tab) => { + tab.addEventListener("shown.bs.tab", fireSlideEnter); + }); + + // fire slideEnter for tabby tab activations (for htmlwidget resize behavior) + document.addEventListener("tabby", fireSlideEnter, false); + + // Track scrolling and mark TOC links as active + // get table of contents and sidebar (bail if we don't have at least one) + const tocLinks = tocEl + ? [...tocEl.querySelectorAll("a[data-scroll-target]")] + : []; + const makeActive = (link) => tocLinks[link].classList.add("active"); + const removeActive = (link) => tocLinks[link].classList.remove("active"); + const removeAllActive = () => + [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link)); + + // activate the anchor for a section associated with this TOC entry + tocLinks.forEach((link) => { + link.addEventListener("click", () => { + if (link.href.indexOf("#") !== -1) { + const anchor = link.href.split("#")[1]; + const heading = window.document.querySelector( + `[data-anchor-id=${anchor}]` + ); + if (heading) { + // Add the class + heading.classList.add("reveal-anchorjs-link"); + + // function to show the anchor + const handleMouseout = () => { + heading.classList.remove("reveal-anchorjs-link"); + heading.removeEventListener("mouseout", handleMouseout); + }; + + // add a function to clear the anchor when the user mouses out of it + heading.addEventListener("mouseout", handleMouseout); + } + } + }); + }); + + const sections = tocLinks.map((link) => { + const target = link.getAttribute("data-scroll-target"); + if (target.startsWith("#")) { + return window.document.getElementById(decodeURI(`${target.slice(1)}`)); + } else { + return window.document.querySelector(decodeURI(`${target}`)); + } + }); + + const sectionMargin = 200; + let currentActive = 0; + // track whether we've initialized state the first time + let init = false; + + const updateActiveLink = () => { + // The index from bottom to top (e.g. reversed list) + let sectionIndex = -1; + if ( + window.innerHeight + window.pageYOffset >= + window.document.body.offsetHeight + ) { + sectionIndex = 0; + } else { + sectionIndex = [...sections].reverse().findIndex((section) => { + if (section) { + return window.pageYOffset >= section.offsetTop - sectionMargin; + } else { + return false; + } + }); + } + if (sectionIndex > -1) { + const current = sections.length - sectionIndex - 1; + if (current !== currentActive) { + removeAllActive(); + currentActive = current; + makeActive(current); + if (init) { + window.dispatchEvent(sectionChanged); + } + init = true; + } + } + }; + + const inHiddenRegion = (top, bottom, hiddenRegions) => { + for (const region of hiddenRegions) { + if (top <= region.bottom && bottom >= region.top) { + return true; + } + } + return false; + }; + + const categorySelector = "header.quarto-title-block .quarto-category"; + const activateCategories = (href) => { + // Find any categories + // Surround them with a link pointing back to: + // #category=Authoring + try { + const categoryEls = window.document.querySelectorAll(categorySelector); + for (const categoryEl of categoryEls) { + const categoryText = categoryEl.textContent; + if (categoryText) { + const link = `${href}#category=${encodeURIComponent(categoryText)}`; + const linkEl = window.document.createElement("a"); + linkEl.setAttribute("href", link); + for (const child of categoryEl.childNodes) { + linkEl.append(child); + } + categoryEl.appendChild(linkEl); + } + } + } catch { + // Ignore errors + } + }; + function hasTitleCategories() { + return window.document.querySelector(categorySelector) !== null; + } + + function offsetRelativeUrl(url) { + const offset = getMeta("quarto:offset"); + return offset ? offset + url : url; + } + + function offsetAbsoluteUrl(url) { + const offset = getMeta("quarto:offset"); + const baseUrl = new URL(offset, window.location); + + const projRelativeUrl = url.replace(baseUrl, ""); + if (projRelativeUrl.startsWith("/")) { + return projRelativeUrl; + } else { + return "/" + projRelativeUrl; + } + } + + // read a meta tag value + function getMeta(metaName) { + const metas = window.document.getElementsByTagName("meta"); + for (let i = 0; i < metas.length; i++) { + if (metas[i].getAttribute("name") === metaName) { + return metas[i].getAttribute("content"); + } + } + return ""; + } + + async function findAndActivateCategories() { + const currentPagePath = offsetAbsoluteUrl(window.location.href); + const response = await fetch(offsetRelativeUrl("listings.json")); + if (response.status == 200) { + return response.json().then(function (listingPaths) { + const listingHrefs = []; + for (const listingPath of listingPaths) { + const pathWithoutLeadingSlash = listingPath.listing.substring(1); + for (const item of listingPath.items) { + if ( + item === currentPagePath || + item === currentPagePath + "index.html" + ) { + // Resolve this path against the offset to be sure + // we already are using the correct path to the listing + // (this adjusts the listing urls to be rooted against + // whatever root the page is actually running against) + const relative = offsetRelativeUrl(pathWithoutLeadingSlash); + const baseUrl = window.location; + const resolvedPath = new URL(relative, baseUrl); + listingHrefs.push(resolvedPath.pathname); + break; + } + } + } + + // Look up the tree for a nearby linting and use that if we find one + const nearestListing = findNearestParentListing( + offsetAbsoluteUrl(window.location.pathname), + listingHrefs + ); + if (nearestListing) { + activateCategories(nearestListing); + } else { + // See if the referrer is a listing page for this item + const referredRelativePath = offsetAbsoluteUrl(document.referrer); + const referrerListing = listingHrefs.find((listingHref) => { + const isListingReferrer = + listingHref === referredRelativePath || + listingHref === referredRelativePath + "index.html"; + return isListingReferrer; + }); + + if (referrerListing) { + // Try to use the referrer if possible + activateCategories(referrerListing); + } else if (listingHrefs.length > 0) { + // Otherwise, just fall back to the first listing + activateCategories(listingHrefs[0]); + } + } + }); + } + } + if (hasTitleCategories()) { + findAndActivateCategories(); + } + + const findNearestParentListing = (href, listingHrefs) => { + if (!href || !listingHrefs) { + return undefined; + } + // Look up the tree for a nearby linting and use that if we find one + const relativeParts = href.substring(1).split("/"); + while (relativeParts.length > 0) { + const path = relativeParts.join("/"); + for (const listingHref of listingHrefs) { + if (listingHref.startsWith(path)) { + return listingHref; + } + } + relativeParts.pop(); + } + + return undefined; + }; + + const manageSidebarVisiblity = (el, placeholderDescriptor) => { + let isVisible = true; + let elRect; + + return (hiddenRegions) => { + if (el === null) { + return; + } + + // Find the last element of the TOC + const lastChildEl = el.lastElementChild; + + if (lastChildEl) { + // Converts the sidebar to a menu + const convertToMenu = () => { + for (const child of el.children) { + child.style.opacity = 0; + child.style.overflow = "hidden"; + } + + nexttick(() => { + const toggleContainer = window.document.createElement("div"); + toggleContainer.style.width = "100%"; + toggleContainer.classList.add("zindex-over-content"); + toggleContainer.classList.add("quarto-sidebar-toggle"); + toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom + toggleContainer.id = placeholderDescriptor.id; + toggleContainer.style.position = "fixed"; + + const toggleIcon = window.document.createElement("i"); + toggleIcon.classList.add("quarto-sidebar-toggle-icon"); + toggleIcon.classList.add("bi"); + toggleIcon.classList.add("bi-caret-down-fill"); + + const toggleTitle = window.document.createElement("div"); + const titleEl = window.document.body.querySelector( + placeholderDescriptor.titleSelector + ); + if (titleEl) { + toggleTitle.append( + titleEl.textContent || titleEl.innerText, + toggleIcon + ); + } + toggleTitle.classList.add("zindex-over-content"); + toggleTitle.classList.add("quarto-sidebar-toggle-title"); + toggleContainer.append(toggleTitle); + + const toggleContents = window.document.createElement("div"); + toggleContents.classList = el.classList; + toggleContents.classList.add("zindex-over-content"); + toggleContents.classList.add("quarto-sidebar-toggle-contents"); + for (const child of el.children) { + if (child.id === "toc-title") { + continue; + } + + const clone = child.cloneNode(true); + clone.style.opacity = 1; + clone.style.display = null; + toggleContents.append(clone); + } + toggleContents.style.height = "0px"; + const positionToggle = () => { + // position the element (top left of parent, same width as parent) + if (!elRect) { + elRect = el.getBoundingClientRect(); + } + toggleContainer.style.left = `${elRect.left}px`; + toggleContainer.style.top = `${elRect.top}px`; + toggleContainer.style.width = `${elRect.width}px`; + }; + positionToggle(); + + toggleContainer.append(toggleContents); + el.parentElement.prepend(toggleContainer); + + // Process clicks + let tocShowing = false; + // Allow the caller to control whether this is dismissed + // when it is clicked (e.g. sidebar navigation supports + // opening and closing the nav tree, so don't dismiss on click) + const clickEl = placeholderDescriptor.dismissOnClick + ? toggleContainer + : toggleTitle; + + const closeToggle = () => { + if (tocShowing) { + toggleContainer.classList.remove("expanded"); + toggleContents.style.height = "0px"; + tocShowing = false; + } + }; + + // Get rid of any expanded toggle if the user scrolls + window.document.addEventListener( + "scroll", + throttle(() => { + closeToggle(); + }, 50) + ); + + // Handle positioning of the toggle + window.addEventListener( + "resize", + throttle(() => { + elRect = undefined; + positionToggle(); + }, 50) + ); + + window.addEventListener("quarto-hrChanged", () => { + elRect = undefined; + }); + + // Process the click + clickEl.onclick = () => { + if (!tocShowing) { + toggleContainer.classList.add("expanded"); + toggleContents.style.height = null; + tocShowing = true; + } else { + closeToggle(); + } + }; + }); + }; + + // Converts a sidebar from a menu back to a sidebar + const convertToSidebar = () => { + for (const child of el.children) { + child.style.opacity = 1; + child.style.overflow = null; + } + + const placeholderEl = window.document.getElementById( + placeholderDescriptor.id + ); + if (placeholderEl) { + placeholderEl.remove(); + } + + el.classList.remove("rollup"); + }; + + if (isReaderMode()) { + convertToMenu(); + isVisible = false; + } else { + // Find the top and bottom o the element that is being managed + const elTop = el.offsetTop; + const elBottom = + elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight; + + if (!isVisible) { + // If the element is current not visible reveal if there are + // no conflicts with overlay regions + if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToSidebar(); + isVisible = true; + } + } else { + // If the element is visible, hide it if it conflicts with overlay regions + // and insert a placeholder toggle (or if we're in reader mode) + if (inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToMenu(); + isVisible = false; + } + } + } + } + }; + }; + + const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]'); + for (const tabEl of tabEls) { + const id = tabEl.getAttribute("data-bs-target"); + if (id) { + const columnEl = document.querySelector( + `${id} .column-margin, .tabset-margin-content` + ); + if (columnEl) + tabEl.addEventListener("shown.bs.tab", function (event) { + const el = event.srcElement; + if (el) { + const visibleCls = `${el.id}-margin-content`; + // walk up until we find a parent tabset + let panelTabsetEl = el.parentElement; + while (panelTabsetEl) { + if (panelTabsetEl.classList.contains("panel-tabset")) { + break; + } + panelTabsetEl = panelTabsetEl.parentElement; + } + + if (panelTabsetEl) { + const prevSib = panelTabsetEl.previousElementSibling; + if ( + prevSib && + prevSib.classList.contains("tabset-margin-container") + ) { + const childNodes = prevSib.querySelectorAll( + ".tabset-margin-content" + ); + for (const childEl of childNodes) { + if (childEl.classList.contains(visibleCls)) { + childEl.classList.remove("collapse"); + } else { + childEl.classList.add("collapse"); + } + } + } + } + } + + layoutMarginEls(); + }); + } + } + + // Manage the visibility of the toc and the sidebar + const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, { + id: "quarto-toc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, { + id: "quarto-sidebarnav-toggle", + titleSelector: ".title", + dismissOnClick: false, + }); + let tocLeftScrollVisibility; + if (leftTocEl) { + tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, { + id: "quarto-lefttoc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + } + + // Find the first element that uses formatting in special columns + const conflictingEls = window.document.body.querySelectorAll( + '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]' + ); + + // Filter all the possibly conflicting elements into ones + // the do conflict on the left or ride side + const arrConflictingEls = Array.from(conflictingEls); + const leftSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return false; + } + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + className.startsWith("column-") && + !className.endsWith("right") && + !className.endsWith("container") && + className !== "column-margin" + ); + }); + }); + const rightSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return true; + } + + const hasMarginCaption = Array.from(el.classList).find((className) => { + return className == "margin-caption"; + }); + if (hasMarginCaption) { + return true; + } + + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + !className.endsWith("container") && + className.startsWith("column-") && + !className.endsWith("left") + ); + }); + }); + + const kOverlapPaddingSize = 10; + function toRegions(els) { + return els.map((el) => { + const boundRect = el.getBoundingClientRect(); + const top = + boundRect.top + + document.documentElement.scrollTop - + kOverlapPaddingSize; + return { + top, + bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize, + }; + }); + } + + let hasObserved = false; + const visibleItemObserver = (els) => { + let visibleElements = [...els]; + const intersectionObserver = new IntersectionObserver( + (entries, _observer) => { + entries.forEach((entry) => { + if (entry.isIntersecting) { + if (visibleElements.indexOf(entry.target) === -1) { + visibleElements.push(entry.target); + } + } else { + visibleElements = visibleElements.filter((visibleEntry) => { + return visibleEntry !== entry; + }); + } + }); + + if (!hasObserved) { + hideOverlappedSidebars(); + } + hasObserved = true; + }, + {} + ); + els.forEach((el) => { + intersectionObserver.observe(el); + }); + + return { + getVisibleEntries: () => { + return visibleElements; + }, + }; + }; + + const rightElementObserver = visibleItemObserver(rightSideConflictEls); + const leftElementObserver = visibleItemObserver(leftSideConflictEls); + + const hideOverlappedSidebars = () => { + marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries())); + sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries())); + if (tocLeftScrollVisibility) { + tocLeftScrollVisibility( + toRegions(leftElementObserver.getVisibleEntries()) + ); + } + }; + + window.quartoToggleReader = () => { + // Applies a slow class (or removes it) + // to update the transition speed + const slowTransition = (slow) => { + const manageTransition = (id, slow) => { + const el = document.getElementById(id); + if (el) { + if (slow) { + el.classList.add("slow"); + } else { + el.classList.remove("slow"); + } + } + }; + + manageTransition("TOC", slow); + manageTransition("quarto-sidebar", slow); + }; + const readerMode = !isReaderMode(); + setReaderModeValue(readerMode); + + // If we're entering reader mode, slow the transition + if (readerMode) { + slowTransition(readerMode); + } + highlightReaderToggle(readerMode); + hideOverlappedSidebars(); + + // If we're exiting reader mode, restore the non-slow transition + if (!readerMode) { + slowTransition(!readerMode); + } + }; + + const highlightReaderToggle = (readerMode) => { + const els = document.querySelectorAll(".quarto-reader-toggle"); + if (els) { + els.forEach((el) => { + if (readerMode) { + el.classList.add("reader"); + } else { + el.classList.remove("reader"); + } + }); + } + }; + + const setReaderModeValue = (val) => { + if (window.location.protocol !== "file:") { + window.localStorage.setItem("quarto-reader-mode", val); + } else { + localReaderMode = val; + } + }; + + const isReaderMode = () => { + if (window.location.protocol !== "file:") { + return window.localStorage.getItem("quarto-reader-mode") === "true"; + } else { + return localReaderMode; + } + }; + let localReaderMode = null; + + const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded"); + const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1; + + // Walk the TOC and collapse/expand nodes + // Nodes are expanded if: + // - they are top level + // - they have children that are 'active' links + // - they are directly below an link that is 'active' + const walk = (el, depth) => { + // Tick depth when we enter a UL + if (el.tagName === "UL") { + depth = depth + 1; + } + + // It this is active link + let isActiveNode = false; + if (el.tagName === "A" && el.classList.contains("active")) { + isActiveNode = true; + } + + // See if there is an active child to this element + let hasActiveChild = false; + for (child of el.children) { + hasActiveChild = walk(child, depth) || hasActiveChild; + } + + // Process the collapse state if this is an UL + if (el.tagName === "UL") { + if (tocOpenDepth === -1 && depth > 1) { + el.classList.add("collapse"); + } else if ( + depth <= tocOpenDepth || + hasActiveChild || + prevSiblingIsActiveLink(el) + ) { + el.classList.remove("collapse"); + } else { + el.classList.add("collapse"); + } + + // untick depth when we leave a UL + depth = depth - 1; + } + return hasActiveChild || isActiveNode; + }; + + // walk the TOC and expand / collapse any items that should be shown + + if (tocEl) { + walk(tocEl, 0); + updateActiveLink(); + } + + // Throttle the scroll event and walk peridiocally + window.document.addEventListener( + "scroll", + throttle(() => { + if (tocEl) { + updateActiveLink(); + walk(tocEl, 0); + } + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 5) + ); + window.addEventListener( + "resize", + throttle(() => { + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 10) + ); + hideOverlappedSidebars(); + highlightReaderToggle(isReaderMode()); +}); + +// grouped tabsets +window.addEventListener("pageshow", (_event) => { + function getTabSettings() { + const data = localStorage.getItem("quarto-persistent-tabsets-data"); + if (!data) { + localStorage.setItem("quarto-persistent-tabsets-data", "{}"); + return {}; + } + if (data) { + return JSON.parse(data); + } + } + + function setTabSettings(data) { + localStorage.setItem( + "quarto-persistent-tabsets-data", + JSON.stringify(data) + ); + } + + function setTabState(groupName, groupValue) { + const data = getTabSettings(); + data[groupName] = groupValue; + setTabSettings(data); + } + + function toggleTab(tab, active) { + const tabPanelId = tab.getAttribute("aria-controls"); + const tabPanel = document.getElementById(tabPanelId); + if (active) { + tab.classList.add("active"); + tabPanel.classList.add("active"); + } else { + tab.classList.remove("active"); + tabPanel.classList.remove("active"); + } + } + + function toggleAll(selectedGroup, selectorsToSync) { + for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) { + const active = selectedGroup === thisGroup; + for (const tab of tabs) { + toggleTab(tab, active); + } + } + } + + function findSelectorsToSyncByLanguage() { + const result = {}; + const tabs = Array.from( + document.querySelectorAll(`div[data-group] a[id^='tabset-']`) + ); + for (const item of tabs) { + const div = item.parentElement.parentElement.parentElement; + const group = div.getAttribute("data-group"); + if (!result[group]) { + result[group] = {}; + } + const selectorsToSync = result[group]; + const value = item.innerHTML; + if (!selectorsToSync[value]) { + selectorsToSync[value] = []; + } + selectorsToSync[value].push(item); + } + return result; + } + + function setupSelectorSync() { + const selectorsToSync = findSelectorsToSyncByLanguage(); + Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => { + Object.entries(tabSetsByValue).forEach(([value, items]) => { + items.forEach((item) => { + item.addEventListener("click", (_event) => { + setTabState(group, value); + toggleAll(value, selectorsToSync[group]); + }); + }); + }); + }); + return selectorsToSync; + } + + const selectorsToSync = setupSelectorSync(); + for (const [group, selectedName] of Object.entries(getTabSettings())) { + const selectors = selectorsToSync[group]; + // it's possible that stale state gives us empty selections, so we explicitly check here. + if (selectors) { + toggleAll(selectedName, selectors); + } + } +}); + +function throttle(func, wait) { + let waiting = false; + return function () { + if (!waiting) { + func.apply(this, arguments); + waiting = true; + setTimeout(function () { + waiting = false; + }, wait); + } + }; +} + +function nexttick(func) { + return setTimeout(func, 0); +} diff --git a/_freeze/data_model/libs/quarto-html/tippy.css b/_freeze/data_model/libs/quarto-html/tippy.css new file mode 100644 index 0000000..e6ae635 --- /dev/null +++ b/_freeze/data_model/libs/quarto-html/tippy.css @@ -0,0 +1 @@ +.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 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