https://w3id.org/np/RAtbYEapr1lwOTgRZnKOWAQqteSprVt6Qhj4DpVclVlw4
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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np:hasAssertion sub:assertion;
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/darwin1859-ch09-09--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "Paleobiology Database marine Bivalvia occurrences resolved to species were counted for the Pliocene (7224 records_found). The occurrence table was downloaded with show=strat,coords,time,loc because the country code cc2 is absent from strat,coords,time (3127162 bytes, not committed). Early age is max_ma or eag, the older bound. 7090 rows kept a species name, a collection id and an early age at least the late age. 3 formation-continent groups have a span of at least 3 Ma and at least 8 collections. One case per species per continent uses the formation with the most occurrences of that species. Partway cases: 21, of which 2 have an older other-continent record. Basal cases: 105, of which 0 do.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.095238 p_mid minus p_base (n = 21). Interpretation: Full quote (Origin, 1st ed., ch. IX): \"when we see a species first appearing in any formation, the probability is that it only then first immigrated into that area.\" Darwin's example is species appearing earlier in North American palaeozoic beds than in Europe. This test asks whether a first appearance partway through a formation is preceded by an older record on another modern continent, more often than a first appearance at the base of a formation. The base cases are the control. If they have older extralimital records just as often, the data do not separate immigration from the ordinary fact that species have records elsewhere, or from sampling. Bed-by-bed position is not in the database. Position is the species' oldest age bound inside the formation's age span on one modern continent. Scope is narrower than all marine species: Pliocene bivalves, or the Piacenzian if the Pliocene file is too large. One case per species per continent, the formation where that species has the most occurrences, so a widespread species is not counted many times. A formation needs a non-empty name, an age span of at least 3 Ma, and at least 8 collections.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch09-09: inconclusive, confidence 0.35";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch09-09/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Public marine occurrences with species names, formation names, country or coordinates, and early and late age bounds. A dataset with bed-level heights would also be admissible. A dataset with no formation name is not.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Most partway appearances have no older record elsewhere, or the partway and basal rates differ by less than 15 percentage points so immigration is not separated from sampling.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "A missing older record is not evidence that the species was created in place. The basal fraction is only a control for how often older extralimital records occur anyway.",
"An older record must fall inside this interval download and be at least 1 Ma older. A first appearance at the old edge of the interval cannot meet that test, so basal cases near the base of the window are less able to count as immigration.",
"Country codes are modern. Russia, Turkey, Kazakhstan, Egypt, Indonesia and Cyprus are ignored. Coordinates are not used to assign a continent.",
"Position is the species' oldest early-age inside the formation's age span, not a bed height. The database has no bed-by-bed section for this comparison.",
"Scope is Pliocene marine bivalves, or the Piacenzian only if the Pliocene count had exceeded 80000.",
"The country code is not in show=strat,coords,time. The download adds the loc block so the pre-registered cc2 continent map can be applied. Thresholds are unchanged.",
"The response has no license field, so license is null. The count response includes elapsed_time, so its sha256 changes on a later download. The occurrence table is the file the fractions are computed from.",
"The same stage age on many collections makes a partway position rare. Twenty-one partway cases is below the pre-registered minimum of 30, so the fractions are reported and are not a pass or a fail. Those 21 cases are one formation and one shared position, not 21 independent sections. The minimum is not lowered. The descriptive difference is also under 0.15.";
<https://w3id.org/delphi/ontology/expectedObservation> "Species that appear well above the base of a formation have an older record on another continent at least 15 percentage points more often than species that appear at the base, and in at least 60% of the partway cases.";
<https://w3id.org/delphi/ontology/failCriterion> "Refute if p_mid < 0.40. If the absolute difference between p_mid and p_base is under 0.15, the verdict is inconclusive with reason other: immigration is not separated from the background rate of older extralimital records, which is the sampling-confounded pattern. Any other non-pass is mixed. If fewer than 30 partway cases remain, inconclusive with reason underpowered. If the Pliocene download reports more than 80000 occurrences, use the Piacenzian instead. If that count is also above 80000, inconclusive with reason data-unavailable rather than truncating.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.35"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch09-09--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "inconclusive";
<https://w3id.org/delphi/ontology/hypothesis> "Pliocene marine bivalve species that first show up well above the base of a formation already occur at least 1 Ma earlier on another modern continent, more often than species that are present at the base of the same kind of formation.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Difference of two fractions, partway minus basal, of cases with an occurrence on another modern continent at least 1 Ma older. Pass at a difference of 0.15 and a partway fraction of 0.60. A difference under 0.15 is inconclusive rather than a pass or a fail.";
<https://w3id.org/delphi/ontology/passCriterion> "Let p_mid be the fraction of partway appearances with an older occurrence on another continent, and p_base the same fraction for basal appearances. Pass if p_mid >= 0.60 and p_mid - p_base >= 0.15. Partway means the species' oldest early-age in that formation-continent is at least 40% of the way down from the formation's oldest age toward its youngest, and at least three collections in the formation are older than that local first appearance. Basal means the local first appearance is in the oldest 20% of the formation's age span.";
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<https://w3id.org/delphi/resource/evidence/darwin1859-ch09-09--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "species, formation, country and age bounds for local first appearance and older extralimital records";
dc:license "";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Paleobiology Database marine bivalve occurrences, Pliocene";
prov:atLocation <https://paleobiodb.org/data1.2/occs/list.csv?base_name=Bivalvia&interval=Pliocene&envtype=marine&taxon_reso=species&show=strat%2Ccoords%2Ctime%2Cloc&limit=all>,
<https://paleobiodb.org/data1.2/occs/list.json?base_name=Bivalvia&interval=Pliocene&envtype=marine&taxon_reso=species&show=strat%2Ccoords%2Ctime&limit=1&rowcount=true>;
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prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch09-09/result.json>;
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sub:test a prov:Activity;
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sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.818Z"^^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-ch09-09--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch09-09: inconclusive, confidence 0.35";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/darwin-origin-1859> .
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