https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/Head https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/assertion https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/provenance https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/pubinfo https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/assertion https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://purl.org/dc/terms/description Fetched the two files, checked md5 and size against figshare's, matched species to the tree by name, regressed log10(MeanArea) on log10(BM) for Te species by PGLS (Brownian motion scaled by Pagel's lambda, ML on [0,1]) and by OLS, and applied the pre-registered decision rule. Secondary analyses are descriptive; see derived/measured.json. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.7092 exponent b in A proportional to M^b (log-log PGLS slope) (n = 84, 95% CI [0.6728, 0.7457]). Interpretation: The test covers the empirical part of the claim, that large terrestrial animals need disproportionately thick limb bones, and not the existence of a definite maximum size, which the dataset cannot show (it contains no extinct giants). The claim's arithmetic (strength proportional to L^2, weight to L^3) is proved separately in Lean (ThompsonLaws.Magnitude) and is not tested here. MeanArea is the humeral mean cross-sectional area reported in the deposit; whether it is total or cortical area is as defined by the dataset's authors, and either is a bone cross-section relevant to crushing resistance. Exponents of area and of circumference are related by A proportional to C^2, so b = 2 x (circumference exponent): 2/3, 3/4 and 1 correspond to 1/3, 3/8 and 1/2. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://www.w3.org/2000/01/rdf-schema#label Claim test of thompson1917-ch02-03 (limb-bone-pgls-01): supports, confidence 0.6 https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch02-03/limb-bone-pgls-01/result.json https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-sonnet-5-5 https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/admissibleDatasets Published, openly licensed measurements of limb-bone cross-sectional area and body mass of mammals, measured independently of Thompson's text, with a phylogeny that covers at least 90 % of the species. Terrestrial species only for the primary analysis (the claim's scope is terrestrial animals under gravity). https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/disconfirmingObservation An exponent interval whose upper bound is at or below 2/3 under phylogenetic regression: the limb skeleton would then scale like the geometric-similarity case and not compensate for the square-cube penalty. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst A positive-allometry result with a margin this small is a statement about this mammal set and this lifestyle restriction, not a measurement of the exponent for large terrestrial animals. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst Before this registration was written the CSV header, the row count, the Lifestyle, Lineage and Order labels, the blank-cell counts for BM and MeanArea and the match of taxon names to the tree tips (159 of 159) were inspected, and the files' checksums were confirmed against figshare's. No values of BM or MeanArea were viewed and no regression of any kind was run. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst Campione and Evans 2012 (BMC Biology 10:60) was planned as a second dataset and dropped before analysis because its data package (MASSTIMATE) has been archived from CRAN and the journal's supplementary file could not be retrieved within the session. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst Implementation history: the first run failed before producing any output because V is singular at lambda = 1 (zero-length terminal branches); a 1e-8 diagonal ridge was added, and a later change made the optimiser treat a non-finite likelihood as infinitely bad. Neither changed the estimates. The code was validated beforehand on simulated traits with a known slope on this tree (95% interval coverage 0.947 at both lambda 1 and lambda 0; lambda recovered as 0.99 and 0.01). https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst Positive allometry of area does not show which mechanical similarity holds, nor that bone stress sets a maximum size. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst The author of this registration knows from the literature that limb-bone dimensions of tetrapods are generally reported to scale with positive allometry relative to geometric similarity (for example Campione and Evans 2012, whose supplementary table could not be retrieved for this test). A pass is therefore the expected outcome, and the test is a replication on an independent mammal dataset more than a surprise. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/evidenceAgainst The dataset contains small mammals mostly: whether the terrestrial set reaches large body masses is not known before analysis, and a positive-allometry result driven by a few large animals would be fragile; a leave-largest-species-out check is run and reported but is not part of the verdict. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/expectedObservation Humeral cross-sectional area of terrestrial mammals scales with body mass with an exponent clearly above 2/3, with a lower confidence bound above 2/3 and a point estimate of at least 0.70, under both phylogenetic and ordinary regression. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/failCriterion Pre-registered (claim refuted). The PGLS 95 % confidence interval of b has an upper bound at or below 2/3 (isometry or negative allometry: no compensation by bone thickness). If the PGLS interval includes 2/3, or has a lower bound above 2/3 but a point estimate below 0.70, or PGLS and OLS disagree on whether the interval lies above 2/3, the verdict is 'mixed'. If fewer than 60 terrestrial species can be matched to the tree with a positive BM and MeanArea, or the downloaded files do not match the checksums recorded below, the verdict is 'inconclusive' with reason 'data-unavailable' or 'underpowered'. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/hasConfidence 0.6 https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/hypothesis If Thompson's square-cube argument describes real terrestrial mammals, geometric scaling of the limb skeleton would leave large animals under-strengthened, so they must compensate with disproportionately thick limb bones: the cross-sectional area A of the humerus scales with body mass M with an exponent greater than the geometric-similarity value 2/3 (A proportional to M^b with b > 2/3), as for the elephant's 'disproportionately thick limb bones'. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/inferenceMethod log10(MeanArea) regressed on log10(BM) by phylogenetic GLS under a Brownian-motion covariance scaled by Pagel's lambda (maximum likelihood on [0, 1], profile likelihood), slope and 95 % CI from the t distribution with n - 2 degrees of freedom; the same by ordinary least squares as a check. Thresholds as stated in pass_criterion and fail_criterion. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/passCriterion Pre-registered (claim supported). In the primary analysis (terrestrial species, Lifestyle code Te, humeral MeanArea against body mass BM, both log10-transformed, phylogenetic GLS on the supplied timetree with Pagel's lambda estimated by maximum likelihood on [0, 1]) the 95 % confidence interval of the slope b lies entirely above 2/3 and its point estimate is at least 0.70; and the ordinary least squares slope on the same species also has its 95 % interval entirely above 2/3. https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/thompson1917-ch02-03 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/thompson1917-ch02-03--claim-test--limb-bone-pgls-01 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://purl.org/dc/terms/description body mass and humeral mean cross-sectional area of 159 mammal species, with the timetree used for the phylogenetic covariance https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Raw data for: Differing effects of size and lifestyle on bone structure in mammals (RawDataHumerusR1.csv and AlteredTimetree.nex) https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://www.w3.org/ns/prov#atLocation https://ndownloader.figshare.com/files/23612879 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://www.w3.org/ns/prov#atLocation https://ndownloader.figshare.com/files/25463282 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://doi.org/10.6084/m9.figshare.12600440.v3 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:1ddb7571c3478e5f3e64dbcd9ca1802b431d3c080b8c7363eba2655ca595c948 https://w3id.org/delphi/resource/evidence/thompson1917-ch02-03--claim-test--limb-bone-pgls-01--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:a0b1e6b68d8517f26d0557d903dbe2c7cc6809ab655373038378aad5032d4fca https://w3id.org/np/RACDO88WaTvFx_xsZAD3aTfx10yqvABRUaFkgnS9GTqcQ/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-sonnet-5-5 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/ns/prov#SoftwareAgent https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-sonnet-5-5 http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (claude-sonnet-5-5; 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