[ { "@id": "https://w3id.org/np/RAOU89RwyYE7_0JaXXLq2HmTd6RvBvFhnfMxCbYGDJVfA/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/thompson1917-ch03-35--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "Downloaded Dryad version 3888 and checked WatanabeSlice_JEB_PreGPA.nts against the Dryad MD5. The file holds 204 specimens and 78 landmarks that still have their original size. Centroid size was computed and the configurations were aligned by generalized Procrustes analysis. Each species with at least 4 specimens contributed the least-squares slope of aligned shape on the natural log of centroid size, and the interspecific axis was the first principal component of the unweighted species-mean shapes, signed to increase with mean log centroid size. Acute angles and a 999-draw within-species shuffle of log size were scored with the pre-registered thresholds; p = (1 + count of null median angles at or below the observed median) / 1000." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: undefined undefined. Interpretation: Thompson's 'same phenomenon' in individual development and in the differences between species is read as a shared direction in cranial shape space: allometric trajectories and the leading axis of species means. A straight allometric vector is the course that is tested. Curved paths, heterochrony of timing, and clades other than Crocodylia are outside this test. Centroid size is the growth measure when the file does not carry age; age is used instead of centroid size only if the file has age and no size. The sign of the interspecific axis is tied to size so that 'larger species' and 'growth' point the same way when size and that axis are associated." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of thompson1917-ch03-35: refutes, confidence 0.45" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch03-35/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7-high-fast" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "The same 3D landmark scheme on an ontogenetic series of several species in one clade, with a size or age for each specimen. Public and licensed for reuse. A phylogeny is admissible as a reported check and is not required for the direction test." } ], "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": "Ontogenetic vectors sit at a large angle to the axis of species differences, and that angle is no smaller than angles from size-shuffled data." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Each ontogeny is one straight slope. Curved paths were not tested. The interspecific direction is the leading axis of species-mean shapes (about 76 percent of the variance among those means), not a phylogenetic path. The version zip contains no tree." }, { "@value": "Growth is centroid size. The file has no age. The Dryad usage note says the coordinates were not Procrustes-superimposed and still carry size, and that the series is post-natal." }, { "@value": "Species are the file's own codes. The Dryad usage note defines a code as the first three letters of the genus and of the species, and gives allmis as Alligator mississippiensis. That note also says Gavialis and Tomistoma include captive animals; they were not dropped." }, { "@value": "The data are one clade, Crocodylia, and the claim is about organic form in general. Confidence is reduced for that." }, { "@value": "The median acute angle is 76.3 degrees, above the pre-registered 60 degree line, and 395 of 999 size-shuffled medians were at least as small (p = 0.396). Seven of ten species have a positive dot product with the interspecific axis, but every acute angle is above 65 degrees, so the lean is not a shared course. The locked rule refutes; the positive dots do not meet the support rule." }, { "@value": "The test does not score von Baer's law as an order of ancestral characters. It scores only whether cranial shape change from small to large individuals shares a direction with the differences among these species." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Within crocodylians, the cranial shape change from small to large individuals lies along the same direction as the shape differences among species, with a median angle below 45 degrees." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. REFUTES if at least 6 species qualify, the median angle is above 60 degrees, and the permutation p is not below 0.05. MIXED if the median angle is below 45 degrees but the permutation p is not below 0.05, or the permutation p is below 0.05 but the median angle is 45 degrees or more, or the angle criteria would support but a majority of species point against the interspecific vector. Inconclusive, reason underpowered, if fewer than 6 species have at least 4 specimens; data-unavailable if the landmark file cannot be fetched; not-operationalizable if landmarks, specimen identity, or a size or species label cannot be read. The claim about animals in general is not tested by one clade. Thresholds are not revised after the landmarks are opened." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.45", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch03-35--claim-test--dataset-1" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "In one shape space, the direction of cranial change through a crocodylian's growth is the same direction as the differences among crocodylian species." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Procrustes shape coordinates, species-wise multivariate regression on log centroid size, the leading principal component of species means, acute angles, and a within-species size-shuffle permutation of the median angle. Thresholds: median angle below 45 degrees, majority of species positively aligned, permutation p below 0.05, at least 6 species with at least 4 specimens." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered for Crocodylia only. Generalized Procrustes alignment of the 3D cranial landmarks, keeping centroid size. A species is included if it has at least 4 specimens with landmarks and a size. Its ontogenetic vector is the least-squares slope of the aligned shape coordinates on the natural log of centroid size, oriented from smaller to larger. The interspecific vector is the first principal component of the unweighted species-mean shapes, sign-flipped so that it increases with the species' mean log centroid size when that correlation is nonzero. The angle between a species vector and the interspecific vector is the acute angle, 0 to 90 degrees. 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