https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0/Head https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0/assertion https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0/provenance https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0/pubinfo https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAIVZJmE5C5zGECEnmkX1468XCoeHvi8sH-lK4Q_0pqI0/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://purl.org/dc/terms/description The BioTIME query table was streamed and summed to species-year within each study. Names without a species epithet were dropped, as were studies in which more than 95% of positive abundances equal 1. The first and last thirds of each study's years were compared. A species with no record in a third was treated as a mean of zero. Clause A kept the 159 studies in which some species at least doubled and asked whether a majority of the other early species declined. Clause B asked whether species present early and absent at the end had been below that study's early median. The fossil record was not opened. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.691824 share of studies with a species that at least doubled in which a majority of the other early species declined (n = 159, clause B share of local losses below the early median=0.617194 on 6421 losses). Interpretation: Darwin's favoured form is the species whose abundance at least doubles from the first third of a study to the last third, taking the largest such increase when several double. Less favoured forms are the other species that were already present. Decrease is a lower mean abundance, not necessarily rarity in absolute numbers. Rarity before disappearance is a within-study comparison to the median, so the chance level is one half. Disappearance from a BioTIME study is a local loss of records, not a geological extinction. The fossil half of the claim is untested. The test does not show that the increase caused the declines; it tests whether the declines accompany the increase. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch04-18: mixed, confidence 0.55 https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch04-18/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/admissibleDatasets A multi-species abundance time series with at least eight years, numeric counts rather than presence-only, public and reusable. A fossil occurrence database is required for the extinction clause and is not required for this verdict. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation When one species doubles, the other species usually do not decline, or the species that vanish were not the rarer ones. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Clause A meets its support rule: in 0.691824 of 159 studies where one species at least doubled, a majority of the other early species declined. The threshold was 0.65. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Clause B does not. Of 6421 local losses, 0.617194 had early abundance below the study median. That is above one half and below the support threshold of 0.65, and above the refute threshold of 0.45, so the rarity clause is intermediate. Support required both clauses. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The fossil statement is untested. A BioTIME absence is a local loss of records, not an extinction, and a year with no record was treated as zero. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The test does not show that the increase caused the declines. Studies are not independent of the way they were designed, and 172 studies passed the length and abundance filters. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/expectedObservation In most assemblage series where one species at least doubles, most other early species decline, and species that are absent at the end were already below the series median. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. REFUTES if clause A has at least 30 studies and the share in which a majority of the other species decline is at most 0.40, or if clause B has at least 50 losses and the share that were below the median is at most 0.45. If one clause passes and the other does not, the verdict is MIXED. If neither clause reaches its minimum sample, the verdict is inconclusive (underpowered). If the query zip cannot be fetched, the verdict is inconclusive (data-unavailable). An untested fossil clause does not by itself refute or support. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.55 https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch04-18--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/hypothesis In a modern assemblage time series, when one species at least doubles, most of the other species decline, and species that disappear from the series were already below the assemblage's median abundance. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/inferenceMethod Within each qualifying BioTIME study, compare the first and last thirds of years. Clause A is the share of studies, among those with a species that at least doubled, in which a majority of the other early species declined. Clause B is the share of local losses whose early abundance was below the study median. Both shares must be at least 0.65 for support. Clause A at or below 0.40, or clause B at or below 0.45, refutes. https://w3id.org/delphi/resource/assessment/darwin1859-ch04-18--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered, before opening the BioTIME table. Dataset: BioTIME Zenodo release 24_06_2021, record 5026943, the query zip (not the SQL dump). A study qualifies if it has at least 8 distinct years and at least 5 species with numeric abundance, and if no more than 95% of its positive abundance values equal 1 (presence-only series are dropped). Abundance is summed to species-year within a study. The first third and last third of the study's sorted years are compared. A species is favoured in a study if its mean abundance in the last third is at least twice its mean in the first third, and it is the species with the largest such log ratio; the study enters clause A only if such a species exists. Clause A passes if at least 30 studies enter and, in at least 65% of them, a majority of the other species that were present in the first third have a lower mean in the last third. Clause B: a local loss is a species with positive mean abundance in the first third and zero in the last third. It was rare beforehand if that first-third mean is strictly below the median first-third mean of species present then. Clause B passes if there are at least 50 losses and at least 65% of them were rare beforehand. SUPPORTS only if both clauses pass. 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