[ { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/provenance", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci claim tester (claude-fable-5.1; cursor/claim-tests-darwin-batch-b201)" } ], "http://www.w3.org/ns/prov#actedOnBehalfOf": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "https://w3id.org/delphi/ontology/usesModel": [ { "@id": "https://w3id.org/delphi/resource/model/claude-fable-5-1" } ] }, { "@id": "https://w3id.org/delphi/resource/model/claude-fable-5-1", "http://purl.org/dc/terms/identifier": [ { "@value": "claude-fable-5.1" } ], "@type": [ "https://w3id.org/delphi/ontology/LanguageModel" ] }, { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch04-13/result.json" } ], "http://www.w3.org/ns/prov#wasGeneratedBy": [ { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/test" } ] }, { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/test", "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/ns/prov#qualifiedAssociation": [ { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/plan" } ], "http://www.w3.org/ns/prov#wasAssociatedWith": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ] }, { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/plan", "http://www.w3.org/ns/prov#hadPlan": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md" } ] } ] }, { "@id": "https://w3id.org/np/RAg8Y5Z81Po8zQOnJ9bDaSwdbo6q3ZfDnRmvJoIRkkpTA/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch04-13--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "GIFT trait 3.4.1 (sexual system; 2,977 species) was joined to trait 1.2.1 (growth form; 222,598 species, 23 API pages) by work_ID, species were assigned to orders and to Angiospermae through the GIFT nested-set taxonomy, and 1,865 angiosperm species with a single growth-form value (146 trees, 242 shrubs, 1,477 herbs) were analysed. Separate sexes (dioecious or monoecious) in trees vs herbs was tested with a Fisher exact test (odds ratio), with trees vs shrubs and dioecy-only as supplementary comparisons, and the direction of the difference checked within each order having >= 10 trees and >= 10 herbs." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 13.062 odds ratio of separate sexes (dioecious or monoecious) in trees versus herbs, angiosperms in GIFT (n = 1623, Fisher exact p = 1.62e-43). Interpretation: Darwin's 'trees' is read as GIFT growth form 'tree'; 'other plants' primarily as herbs (the claim's scope says 'comparing trees with non-woody plants'), with shrubs reported separately; 'sexes separated' as dioecious or monoecious (both have unisexual flowers, which is what Darwin's argument about cross-pollination needs); 'belonging to all Orders' as the across-order replication test. Darwin's observation was for Britain ('in this country') with Hooker's report of failure in Australia; the GIFT data are global, so the test is of the generalisation rather than the British observation. Modern caveat known in advance: GIFT sexual-system coverage (~3,000 species) is a small, non-random subset of angiosperms, so coverage bias is possible in either direction." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch04-13: supports, confidence 0.7" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch04-13/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Planned datasets: gift-api-traits, gift-api-taxonomy" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "Pre-registered. The claim is REFUTED if the odds ratio is <= 1.0 or p >= 0.05, or if trees exceed herbs in fewer than half of the qualifying orders. Other outcomes are 'mixed'. Supplementary: the same odds ratio for trees vs shrubs, for dioecy alone, and the proportion of separate-sexed species in each growth form." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "GIFT sexual-system coverage is small (2,977 species, 1,865 usable angiosperms) and evidently enriched for dioecious species (55% of the trees and 7% of the herbs are dioecious, against roughly 6% of all angiosperms), so absolute proportions are not representative; the test relies on the contrast between growth forms, which would be biased only if the references coding sexual systems targeted dioecious trees more than dioecious herbs. Published syntheses with larger samples (e.g. Renner 2014; Vamosi et al. 2003) report the same association of dioecy with woody growth." }, { "@value": "Hooker's reported failure of the rule in Australia was not tested separately, since GIFT trait values are not regionalised." }, { "@value": "Only three orders (Apiales, Malpighiales, Rosales; derived/orders.csv) have >= 10 trees and >= 10 herbs with sexual-system data; trees exceed herbs in all three, but a sign test on three orders cannot be significant (p = 0.125), so the 'across all Orders' part of the claim is only weakly tested." }, { "@value": "Shrubs are intermediate (60% separate-sexed), and trees still exceed shrubs (OR 2.1, p = 0.001), so the effect is not just woody vs herbaceous." }, { "@value": "Species are treated as independent; no phylogenetic correction was applied, and the growth-form categories ignore within-species variation (species with mixed growth-form values were excluded)." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Pre-registered. Using the GIFT database public API, join the sexual-system trait (3.4.1: dioecious / monoecious / bisexual) to the growth-form trait (1.2.1: tree / shrub / herb / other) for angiosperm species (Angiospermae in the GIFT taxonomy), keeping species whose growth-form value is a single category. 'Separate sexes' = dioecious or monoecious. The claim is SUPPORTED if (i) the odds ratio of separate sexes in trees versus herbs is >= 1.5 with two-sided Fisher exact p < 0.01, and (ii) among orders with at least 10 trees and at least 10 herbs in the joined data, the proportion of species with separate sexes is higher in trees than in herbs in at least two-thirds of orders." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. The claim is REFUTED if the odds ratio is <= 1.0 or p >= 0.05, or if trees exceed herbs in fewer than half of the qualifying orders. Other outcomes are 'mixed'. Supplementary: the same odds ratio for trees vs shrubs, for dioecy alone, and the proportion of separate-sexed species in each growth form." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.7", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch04-13--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch04-13--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Among flowering plants, species that are trees have separate sexes (dioecy or monoecy, i.e. unisexual flowers) more often than non-woody (herbaceous) species, and this excess recurs across orders rather than being confined to one or two clades." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "GIFT trait 3.4.1 (sexual system; 2,977 species) was joined to trait 1.2.1 (growth form; 222,598 species, 23 API pages) by work_ID, species were assigned to orders and to Angiospermae through the GIFT nested-set taxonomy, and 1,865 angiosperm species with a single growth-form value (146 trees, 242 shrubs, 1,477 herbs) were analysed. Separate sexes (dioecious or monoecious) in trees vs herbs was tested with a Fisher exact test (odds ratio), with trees vs shrubs and dioecy-only as supplementary comparisons, and the direction of the difference checked within each order having >= 10 trees and >= 10 herbs." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. Using the GIFT database public API, join the sexual-system trait (3.4.1: dioecious / monoecious / bisexual) to the growth-form trait (1.2.1: tree / shrub / herb / other) for angiosperm species (Angiospermae in the GIFT taxonomy), keeping species whose growth-form value is a single category. 'Separate sexes' = dioecious or monoecious. The claim is SUPPORTED if (i) the odds ratio of separate sexes in trees versus herbs is >= 1.5 with two-sided Fisher exact p < 0.01, and (ii) among orders with at least 10 trees and at least 10 herbs in the joined data, the proportion of species with separate sexes is higher in trees than in herbs in at least two-thirds of orders." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch04-13--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "species-level sexual system and growth form" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC BY 4.0 (GIFT database terms)" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: GIFT (Global Inventory of Floras and Traits) public API: traits 3.4.1 (Reproduction sexual) and 1.2.1 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