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Updating the radiocarbon folder.
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‎Proposals/ostracode_support/ostracode_DataBUS_additions.qmd‎

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@@ -62,3 +62,12 @@ VALUES('AquaticSystem', 'Aquatic System');
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## Depositional Environments
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We need to check the following parameters against Neotoma:
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```{r depositionalenvts}
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habitats <- c(eanode$habitat, node$`NATURAL HABITAT`, node$`ARTIFICIAL HABITAT`) |>
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unique() |>
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na.omit() |>
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write.csv('habitat_equiv.csv')
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```

‎Proposals/radiocarbon/examining_radiocarbon.qmd‎

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---
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title: "Radiocarbon Data Formats"
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format: html
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---
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## Reporting Standards
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### Standards from Millard (2014)
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1. The laboratory measurement should be reported as a conventional 14C age in 14C yr BP or a
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fractionation-corrected fraction modern (the F14C value of Reimer et al. 2004) according to
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the amended conventions of Stuiver and Polach (Stuiver and Polach 1977; Stuiver 1980, 1983;
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Reimer et al. 2004).
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2. The laboratory code for the determination should be included.
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3. The sample material dated, the pretreatment method applied, and quality control measurements
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should be reported.
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4. The calibration curve and any reservoir offset used.
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5. The software used for calibration, including version number, the options and/or models used,
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and wherever possible a citation of a published description of the software.
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6. The calibrated date given as a range (or ranges) with an associated probability on a clearly
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identifiable calendar timescale.
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## Data Souces
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* [Cross-References p3k14c Data Table](https://opencontext.org/tables/e7fce3cb-eb78-4a36-8b70-da0323da23b3)
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* [Neotoma Radiocarbon Data](https://www.neotomadb.org)
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* [East African Radiocarbon Database](https://openquaternary.com/articles/10.5334/oq.22)
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* [IntCal aalen Record](https://intchron.org/schema.html)
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* [DarwinCore Chronometric Extension](https://www.tdwg.org/community/esp/chrono/)
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* [UC Irvine Records]()
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* [Nerd Database](https://openarchaeologydata.metajnl.com/articles/10.5334/joad.90#T1)
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## Data Columns
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### CARD
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Lab Number
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Field Number
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Material Dated
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Taxa Dated
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Type of Date
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Locality
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Latitude
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Longitude
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Map Sheet
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Elevation (m ASL)
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Submitter
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Date Submitted
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Collector
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Date Collected
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Updater
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Date Updated
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Measured Age
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MA Sigma
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Normalized Age
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NA Sigma
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Delta 13C (per mil)
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Delta 13 C Source
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Significance
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Site Identifier
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Site Name
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Stratigraphic Component
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Context
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Associated Taxa
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Additional Information
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Comments
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References
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### NERD
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DateID
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LabID
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OthLabID
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Problems
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CRA
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Error
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DC13
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Material
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Species
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SiteID
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SiteName
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SiteContext
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SiteType
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Country
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Longitude
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Latitude
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LocQual
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Source
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Comments
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### IntCAL Standard Reporting
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* Standards are reported on the [IntCal Instructions](https://intchron.org/tools/integrate/help_IntCal.html) page and in the [schema](https://intchron.org/schema.html)
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Record Metadata
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* site: the site name
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* country (blank if marine)
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* longitude (optional but desirable)
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* latitude (optional but desirable)
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* elevation (optional but desirable)
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* site_type (optional but desirable)
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* record: the record name
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* changed (optional - if set implies file_data is different from the original file)
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* refs: DOIs
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Key Intcal parameters
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* z (Depth/Ring): general depth or ring measurement (see below)
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* z_range (z range): range in z (see below)
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* t (Date): general date parameter - the timescale is defined at the record level; internally this is stored as fractional astronomical years but can be displayed in a number of different formats (calBP, fractional years, BC/AD etc)
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* t_sigma (±1σ): one sigma uncertainty in t
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* sample (Sample): the sample name (see below)
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* ring_segment (Seg.): the segment of a ring measured (EW, LW, EW/LW, EW1, EW2, LW1, LW2 etc.)
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* labcode (Lab code): the radiocarbon lab code in standard format
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* batch (Batch): the measurement batch (magzine/wheel) in which the measurements were made
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* r_date (R_Date): the uncalibrated radiocarbon date in 14C years BP
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* r_date_sigma (±1σ): the one sigma uncertainty in r_date
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Special IntCal parameters
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* calage (CalAge): required for all data - this is the age of the sample in years calBP; in normal circumstances t will be 1950.5 - calage
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* calage_range (CalSpan): this is the range of the sample material (see below); the default value is 1
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* calage_sigmaI (±1σ): this is the one sigma independent uncertainty in the age (0 for dendrochronologically dated material)
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* calage_sigmaD (±1σ): this is the one sigma systematic uncertainty in the age of the entire dataset (typically for tree ring series)
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* calage_sigmaC (±1σ): correlated uncertainty (used for example in the Cariaco Basin varved sediments)
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* intcal_reservoir (Reservoir): the marine reservoir offset (relative to the atmosphere) of this sample set
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* intcal_reservoir_sigma (±1σ): the one sigma uncertainty in intcal_reservoir_sigma
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The following parameters are used internally in the IntCal curve process and are typically not set on submission of data
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* intcal_data_id (Id): the unique ID number for this data point in IntCal
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* intcal_seq_no (Seq): the sequence number (for series with multiple sequences)
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* r_date_sigma_extra (+ ±1σ): extra uncertainty in the radiocarbon value
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* r_date_sigma_mult (× ±1σ): an error multiplier (typically 1 as a default)
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### Chronometric Reporting (DWC)
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* chronometricAgeID: URL or unique id for the record.
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* verbatimChronometricAge: The verbatim age for a specimen, whether reported by a dating assay, associated references, or legacy information.
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* chronometricAgeProtocol: A description of or reference to the methods used to determine the chronometric age.
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* uncalibratedChronometricAge: The output of a dating assay before it is calibrated into an age using a specific conversion protocol.
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* chronometricAgeConversionProtocol: The method used for converting the uncalibratedChronometricAge into a chronometric age in years, as captured in the earliestChronometricAge, earliestChronometricAgeReferenceSystem, latestChronometricAge, and latestChronometricAgeReferenceSystem fields.
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* earliestChronometricAge: The maximum/earliest/oldest possible age of a specimen as determined by a dating method.
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* earliestChronometricAgeReferenceSystem: The reference system associated with the earliestChronometricAge.
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* latestChronometricAge: The minimum/latest/youngest possible age of a specimen as determined by a dating method.
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* latestChronometricAgeReferenceSystem: The reference system associated with the latestChronometricAge.
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* chronometricAgeUncertaintyInYears: The temporal uncertainty of the earliestChronometricAge and latestChronometicAge in years.
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* chronometricAgeUncertaintyMethod: The method used to generate the value of chronometricAgeUncertaintyInYears.
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* materialDated: A description of the material on which the chronometricAgeProtocol was actually performed, if known.
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* materialDatedID: An identifier for the MaterialSample on which the chronometricAgeProtocol was performed, if applicable.
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* materialDatedRelationship: The relationship of the materialDated to the subject of the ChronometricAge record, from which the ChronometricAge of the subject is inferred.
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* chronometricAgeDeterminedBy: A list (concatenated and separated) of names of people, groups, or organizations who determined the ChronometricAge.
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* chronometricAgeDeterminedDate: The date on which the ChronometricAge was determined.
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* chronometricAgeReferences: A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the ChronometricAge.
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* chronometricAgeRemarks: Notes or comments about the ChronometricAge.
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### Neotoma Reporting
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See JSON (we need to do this better though)
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### p2k21 [in OpenContext]
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Item URI
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Item Label
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Persistent ID (ARK)
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Item Category
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Project Label
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Project URI
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Item Context URI
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Site Wikidata URI
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Site Pleiades URI
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Latitude (WGS-84)
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Longitude (WGS-84)
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Geospatial Note
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Geospatial Inference
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Earliest Year (-BCE/+CE)
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Latest Year (-BCE/+CE)
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Chronology Inference
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Context (1)
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Context (2)
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Context (3)
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Context (4)
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Context (5)
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Authors and Contributors
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Material Type [https://opencontext.org/predicates/b342d8f3-c47c-4ab0-a6dc-39413e373c7d]
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LabID [https://opencontext.org/predicates/ac06a96f-a41d-4fd8-be1f-86642336f375]
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Consists of [https://erlangen-crm.org/current/P45_consists_of]
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Age [https://opencontext.org/predicates/3101d7ea-b28c-4262-adf1-12c609ed5e7a]
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Has taxonomic identifier [https://purl.obolibrary.org/obo/FOODON_00001303]
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Error [https://opencontext.org/predicates/25858351-ff6b-4b59-877f-b2cfe020caa2]
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Longitude (WGS84, sample) [https://opencontext.org/predicates/6c6a6ae0-cb7d-4558-bb82-3a5e85152cf1]
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Longitude (WGS84, sample) [Note] [https://opencontext.org/predicates/6dbdd6c1-7dbf-4b66-bf50-485c9044e5b9]
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Latitude (WGS84, sample) [https://opencontext.org/predicates/2f24017e-1b5c-4554-8908-5d7107412099]
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Material (original) [https://opencontext.org/predicates/2d4fd385-12e6-429a-a965-9d401d15c80f]
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Taxa [https://opencontext.org/predicates/63b5403a-41fc-471c-97f7-c36789398217]
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d13C [Note] [https://opencontext.org/predicates/e3f16d13-91d3-499d-afcd-6c41d7ec7451]
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d13C [https://opencontext.org/predicates/84d688d1-1fd3-433d-9e69-b1b8547bf248]
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Method [https://opencontext.org/predicates/07717fe1-6b85-4bf5-a378-9027a2c578b3]
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Location Note [https://opencontext.org/predicates/894aa7a2-27cb-4c7e-a1a3-855e4a841a40]
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LocAccuracy [https://opencontext.org/predicates/9615a4a5-8075-4f5b-a056-1ecf3fc416a2]
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Period [https://opencontext.org/predicates/1d48f6f4-7006-4a20-a785-bc12fa671a52]
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SiteID [https://opencontext.org/predicates/4060cc11-9a31-4dfd-a85e-652b5d0ef186]
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SiteName [https://opencontext.org/predicates/1b857265-f7e7-4bc9-bf71-e01c9e50425b]
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Country [https://opencontext.org/predicates/6c4f05b3-3f67-4c72-bb09-f4487bfcf514]
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Province [https://opencontext.org/predicates/3a58765e-dc57-4b58-9cf7-8bebdf3c5546]
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Continent [https://opencontext.org/predicates/9a5ef89f-3ca8-4e42-be97-340eccbdf23b]
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Source [https://opencontext.org/predicates/d6bdccfe-0609-486d-918e-3242f8b1465c]
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Reference [https://opencontext.org/predicates/1d319fd8-0a5d-4318-81dd-6658a9098eea]
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## Aligned Records
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CARD Field | Neotoma Fields | DwC | IntCal |
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----------| ------- |
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Lab Number | ndb.geochronology.labnumber | | |
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Field Number | | | |
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Material Dated | ndb.geochronology.materialdated | materialDated | |
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Taxa Dated | | | |
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Type of Date | ndb.geochronology.agetypeid | | |
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Locality | ndb.collectionunits. |
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Latitude | ndb.sites.geog |
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Longitude | ndb.sites.geog |
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Map Sheet | API? |
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Elevation (m ASL) | ndb.sites.altitude |
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Submitter | ndb.datasets.datasetsubmitter |
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Date Submitted | ndb.datasets.redatecreated |
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Collector | ndb.collectionunits |
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Date Collected | ndb.collectionunits |
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Updater | ndb.??? |
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Date Updated | ndb.datasets.recdateupdated |
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Measured Age | ndb.geochronology.geochronage | uncalibratedChronometricAge
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MA Sigma | ndb.geochronology.errorolder |
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Normalized Age | |
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NA Sigma | |
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Delta 13C (per mil) | |
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Delta 13 C Source | |
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Significance | |
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Site Identifier | ndb.sites.siteid |
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Site Name | ndb.sites.sitename |
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Stratigraphic Component | |
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Context | ndb.sites.sitedescription |
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Associated Taxa | ndb.variables |
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Additional Information | |
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Comments | ndb.geochronology.notes | chronometricAgeRemarks |
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References | ndb.datasetpublications | chronometricAgeReferences |
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| geochrontype |
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| infinite |
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| percentc |
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| percentcollagen |
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| percentn |
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| radiocarbonmethod | chronometricAgeProtocol
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| reservoir |
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| geochronologyid | chronometricAgeID |
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| | earliestChronometricAge |
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| | latestChronometricAge |
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| | chronometricAgeConversionProtocol |
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| ndb.chroncontrols.recdatecreated | chronometricAgeDeterminedDate |
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| ndb.chronologies.contactid | chronometricAgeDeterminedBy |
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| ndb.analysisunit.analysisunitd | materialDatedID
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* verbatimChronometricAge: The verbatim age for a specimen, whether reported by a dating assay, associated references, or legacy information.
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* : The method used for converting the uncalibratedChronometricAge into a chronometric age in years, as captured in the earliestChronometricAge, earliestChronometricAgeReferenceSystem, latestChronometricAge, and latestChronometricAgeReferenceSystem fields.
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* earliestChronometricAge: The maximum/earliest/oldest possible age of a specimen as determined by a dating method.
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* earliestChronometricAgeReferenceSystem: The reference system associated with the earliestChronometricAge.
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* latestChronometricAge: The minimum/latest/youngest possible age of a specimen as determined by a dating method.
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* latestChronometricAgeReferenceSystem: The reference system associated with the latestChronometricAge.
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* chronometricAgeUncertaintyInYears: The temporal uncertainty of the earliestChronometricAge and latestChronometicAge in years.
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* chronometricAgeUncertaintyMethod: The method used to generate the value of chronometricAgeUncertaintyInYears.
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* materialDatedID: An identifier for the MaterialSample on which the chronometricAgeProtocol was performed, if applicable.
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* materialDatedRelationship: The relationship of the materialDated to the subject of the ChronometricAge record, from which the ChronometricAge of the subject is inferred.
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‎Proposals/radiocarbon/geochron_small_mammals.qmd‎

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# Loading in the data
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We want to pull in the full compliment of columns, add new publications where neccessary, and reassign dates & cetera.
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```{r loadtsv}
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raw_data <- readr::read_tsv('data/syverson_14c.tsv')
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```
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# Fields & Considerations
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Most columns directly map onto existing Neotoma columns, overwriting some data, or adding additional information to the records.
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Some considerations:
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* We don't have the dataset ID.
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We can build a SQL Query to access this data as a flat file in the following way:
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```
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SELECT st.siteid,
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st.sitename,
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cu.collectionunitid,
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cu.handle,
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au.analysisunitid,
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au.analysisunitname,
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gc.geochronid,
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gc.materialdated,
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gc.labnumber,
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gc.age,
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gc.errorolder,
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gc.erroryounger,
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gc.infinite,
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gc.agetypeid,
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gc.geochrontypeid,
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gc.notes,
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rc.radiocarbonmethodid,
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rc.delta13c,
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rc.delta15n,
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rc.cnratio,
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tx.taxonname,
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spd.elementtypeid,
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pub.publicationid,
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pub.doi,
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pub.isbn,
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pub.citation,
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pub.pubtypeid
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FROM ndb.sites AS st
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INNER JOIN ndb.collectionunits AS cu ON cu.siteid = st.siteid
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INNER JOIN ndb.analysisunits AS au ON au.collecitonunitid = cu.collectionunitid
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INNER JOIN ndb.samples AS smp ON smp.analysisunitid = au.analysisunitid
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INNER JOIN ndb.geochronology AS gc ON gc.sampleid = smp.sampleid
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LEFT JOIN ndb.radiocarbon AS rc ON rc.geochronid = gc.geochronid
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LEFT JOIN ndb.specimendates AS spd ON spd.sampleid = smp.sampleid AND spd.geochronid = gc.geochronid
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LEFT JOIN ndb.taxa AS tx ON spd.taxonid = tx.taxonid
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LEFT JOIN ndb.specimens AS spc ON spc.specimenid = spd.specimenid
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LEFT JOIN ndb.repositoryinstitutions AS ri ON ri.repositoryid = spc.repositoryid
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INNER JOIN ndb.datasets AS ds ON ds.collectionunitid = cu.collectionunitid
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LEFT JOIN ndb.datasetpublications AS dspb ON dspb.datasetid = ds.datasetid
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LEFT JOIN ndb.publications AS pub ON pub.publicationid = dspb.publicationid;
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```
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This results in row duplication for some fields, particularly as a result of multiple datasets associated with a single sampleid, or multiple publications associated with a datasetid.

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