https://w3id.org/np/RA9j-_YX-xn8PuI70q_MU9xN0T_N90wwZhhDN4uTDh_A0
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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@prefix prov: <http://www.w3.org/ns/prov#> .
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@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
<https://w3id.org/delphi/resource/assessment/darwin1859-ch10-09--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "The Harnik genus-by-bin CSV was read in memory and not written into the repo (5077949 bytes). Deviation from the pre-registered name match: the README defines bin as the stage-base age in Ma and the values are numbers, so the window (2.58, 23.03] is applied to that base age rather than to a midpoint. A genus enters only if its youngest bin base lies in that window. Occupancy is raw.cell.occupancy. Victims are those with victim=1 on that bin; survivors have 0. Singletons are dropped when the singleton column is 1. The previous bin is the next-older matched bin. Decline means last occupancy is strictly lower. Ratios omit a previous occupancy of zero. Victim fraction 0.24549098196392785, median ratio 1.0, survivor fraction None, n victims 998, n survivors 0. The human-extermination clause is not scored.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.245491 fraction of victim genera with lower occupancy in the last Neogene bin (n = 998). Interpretation: Full quote (Origin, 1st ed., ch. X): \"We see in many cases in the more recent tertiary formations, that rarity precedes extinction; and we know that this has been the progress of events with those animals which have been exterminated, either locally or wholly, through man's agency.\" This test scores only the recent-Tertiary clause. 'More recent tertiary' is the Neogene, bins whose matched age midpoint lies after 23.03 Ma and at or before 2.58 Ma is excluded (the Quaternary is not Tertiary). The human-extermination clause is not scored: no open pre-extinction abundance series for those species is in the planned data, and another claim's modern abundance test is not reused. The Harnik table is genera of marine animals, not species. Occupancy is geographic cell occupancy, a rarity proxy, not a count of individuals. One row per genus: its youngest Neogene bin. Victims are genera flagged extinct at the end of that bin. The previous bin is the same genus's next-older bin anywhere in the table. Singletons are excluded. The survivor comparison is the control for a sampling decline that hits every genus. Scope is narrower than the quote: Neogene marine genera.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch10-09: refutes, confidence 0.5";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-09/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "A public genus-by-bin table of marine fossils with an occupancy measure, a flag for extinction at the end of the bin, and bin names that can be matched to numerical ages. A modern living-population index is not admissible for this quote.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Those last bins are not less occupied than the previous bin, or survivors lose occupancy just as often.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Bins that do not match an international interval name are dropped. A genus whose youngest matched bin is Quaternary is outside the recent Tertiary window.",
"Deviation: bin is a stage-base age in Ma, per the README in the same Zenodo record, not an interval name and not a midpoint. The pre-registered window was applied to that base age.",
"No survivor genera have their youngest bin inside the Neogene window. Genera that continue into the Quaternary fall outside it, so the survivor control is empty and the verdict uses only the victim decline.",
"Rows are genera of marine animals, not species, and occupancy is a count of geographic cells, not individuals.",
"The CSV is larger than 1 MB and is not committed. The script downloads it again on each run.",
"The human-extermination sentence is not scored. No open abundance series for those species was used, and a separate modern-abundance test of another claim was not copied.",
"The survivor gap is a control for a decline that sampling would impose on everyone. It is not a full Signor-Lipps correction.";
<https://w3id.org/delphi/ontology/expectedObservation> "Genera that vanish at the end of a Neogene bin are usually less widespread in that bin than in their previous bin, by a margin survivors do not share.";
<https://w3id.org/delphi/ontology/failCriterion> "Refute if the victim decline fraction is < 0.45 or the victim median occupancy ratio is >= 1. If victims decline at the pass rate but survivors decline nearly as often (gap < 0.15), the verdict is mixed. Any other non-passing, non-refuting outcome is mixed. If fewer than 40 victim genera have a previous bin, inconclusive with reason underpowered.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.5"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch10-09--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/darwin1859-ch10-09--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "In the more recent Tertiary, marine genera that disappear at the end of a bin occupy fewer geographic cells in that last bin than in their previous bin, and survivors in the same bins do not decline as often.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Victim decline fraction, median last/previous occupancy, and the same decline fraction for survivors. Pass needs fraction >= 0.60, median ratio <= 0.8, and a survivor gap of at least 0.15. Refute if the victim fraction is < 0.45 or the median ratio is >= 1.";
<https://w3id.org/delphi/ontology/passCriterion> "Using raw.cell.occupancy, among victim genera whose youngest bin has a midpoint in (2.58, 23.03] Ma and that have an earlier bin, at least 60% have lower occupancy in the last bin than in the previous bin, the median of last/previous occupancy is <= 0.8, and the fraction of survivor genera that decline is at least 0.15 lower than the victim fraction. If the column raw.cell.occupancy is absent, the test is inconclusive with reason not-operationalizable rather than switching to raw occurrence counts.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/darwin1859-ch10-09> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/darwin1859-ch10-09--claim-test> .
<https://w3id.org/delphi/resource/evidence/darwin1859-ch10-09--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "genus-by-bin geographic occupancy and extinction flag";
dc:license "{\"id\": \"cc-zero\"}";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Harnik, Simpson and Payne Phanerozoic genus occupancy table";
prov:atLocation <https://zenodo.org/api/records/4969866>, <https://zenodo.org/api/records/4969866/files/Harnik-et-al-Phanerozoic-rarity-data.csv/content>,
<https://zenodo.org/api/records/4969866/files/README_for_Harnik-et-al-Phanerozoic-rarity-data.txt/content>;
prov:wasDerivedFrom <https://zenodo.org/records/4969866>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:39b597d0b7c95392ff57e3f7784f4f19f85ff6e830cb5e77bbfcff6ea18b856f",
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<https://w3id.org/delphi/resource/evidence/darwin1859-ch10-09--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "numerical midpoints for bin names";
dc:license "";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Paleobiology Database international timescale";
prov:atLocation <https://paleobiodb.org/data1.2/intervals/list.json?scale_id=1&vocab=pbdb>;
prov:wasDerivedFrom <https://paleobiodb.org/data1.2/intervals/list_doc.html>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:b1218478d33d8315f9ca4882f29e66b94bd45712ef376c8016ceeee0561ef209" .
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sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7> a prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (grok-4.7; cursor/darwin-geology-claims-5fad)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/grok-4-7> .
<https://w3id.org/delphi/resource/model/grok-4-7> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "grok-4.7" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-09/result.json>;
prov:wasGeneratedBy sub:test .
sub:plan prov:hadPlan <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md> .
sub:test a prov:Activity;
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prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7> .
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sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.822Z"^^xsd:dateTime;
dc:creator <https://orcid.org/0009-0007-4948-9192>;
dc:license <https://creativecommons.org/licenses/by/4.0/>;
npx:hasNanopubType <https://w3id.org/delphi/ontology/Assessment>;
npx:introduces <https://w3id.org/delphi/resource/assessment/darwin1859-ch10-09--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch10-09: refutes, confidence 0.5";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/darwin-origin-1859> .
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