https://w3id.org/np/RAWmy-lzdhQn3qTAGvCCBQ7llOKStbN3RmSsip7188m4Y
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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dc:description "analysis.py downloads the Dryad version zip, verifies the specimen CSV against Dryad's SHA-256 digest, keeps the 16,377 specimens with positive mass, SL, depth and width, and takes geometric species means (6,091 species). For the 5,670 species in the 195 families with >= 5 species it computes d = ln(depth/SL), w = ln(width/SL) and k = ln(mass/SL^3), centres each on its family mean, and computes the Spearman correlation of centred d and w and the SDs of centred d, w and k. Per-family correlations and SDs are written to derived/families.csv; the plaice/haddock ratios are reported separately.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.5274 Spearman rho between family-centred ln(body depth/SL) and ln(body width/SL) across teleost species (n = 5670, one-sided p (rho<0) = 1; 195 families with >= 5 species). Interpretation: Thompson's 'expansion in one transverse dimension compensated by compression in the other' is read as negative covariation of depth and width at a given length among related fishes; 'related' is operationalized as the same family (FishBase family names used in FishShapes). Length is standard length; 'thickness' is maximum fish width; 'volume at a given length' is mass/SL^3 (Thompson's k uses weight, so mass is the direct quantity). Family-centring removes between-family differences so that the comparison is among related species, as Thompson's haddock/plaice and shark/skate examples are. Because ln k is approximately d + w + ln(density x shape factor), condition B can hold only if d and w covary negatively; it is the 'volume less affected than the linear dimensions' clause. Secondary, reported but not part of the verdict: Thompson's named pair, plaice (Pleuronectes platessa) vs haddock (Melanogrammus aeglefinus), if both are in the data: depth ratio expected ~2, width ratio ~0.5, k ratio ~1. Note they are in different orders, so this pair is not 'related' by the family criterion.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of thompson1917-ch17-18: refutes, confidence 0.8";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch17-18/result.json>;
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<https://w3id.org/delphi/ontology/admissibleDatasets> "Measurements of standard length, maximum body depth, maximum body width and mass taken on the same fish specimens, across many species in many families, by a source independent of Thompson; species identified to FishBase taxonomy; public licence.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Relative depth and width covary positively or not at all within families, and mass/SL^3 varies at least as much as the less variable of the two transverse dimensions.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Both ratios are divided by standard length, so overall elongation (slender vs stocky species) makes them covary positively. The pre-registered test follows Thompson's own framing ('at a given length'), but it does not isolate depth-width compensation at fixed cross-sectional area; an analysis that removes elongation (e.g. using depth/width directly or a cross-section measure) was not pre-registered and was not run.",
"Species means rest on 1-3 specimens; intraspecific variation and measurement error inflate all three SDs, and k (three measurements combined) gets the most.",
"Specimens are preserved museum fish; mass and width can change with fixation and ethanol storage, and specimens were chosen as adult-sized, not at matched length. These add noise to k but are unlikely to reverse the sign of a +0.53 correlation across 5,670 species.",
"Thompson's named pair is partly borne out: plaice is 2.09 times as deep relative to length as haddock (expected ~2) and 0.64 times as wide (expected ~0.5, inside the pre-registered 0.35-0.7 band), but its k is 1.44 times haddock's, outside the pre-registered 0.8-1.25 'nearly equal' band. This pair is descriptive only and not part of the verdict.",
"Within families, relatively deep species are also relatively wide, not narrower: the family-centred correlation is +0.53, positive in 90% of the 195 families (median +0.56). As a result ln k varies more (SD 0.35) than ln depth/SL (0.22) or ln width/SL (0.18), the opposite of Thompson's 'volume less affected than the linear dimensions'.",
"preregistered_at is the time of the pre-registration commit (78fafafa); the committed pre-registration carried an estimated time (21:40Z) written before committing. The data were first downloaded after that commit; criteria are unchanged.";
<https://w3id.org/delphi/ontology/expectedObservation> "Within fish families, species that are relatively deeper are relatively narrower (negative family-centred correlation of ln(depth/SL) and ln(width/SL)), and ln(mass/SL^3) varies less than either.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES if the Spearman rho between family-centred d and w is >= 0 AND the SD of family-centred k is >= the smaller of the SDs of family-centred d and w. Any other outcome is MIXED. Fewer than 20 qualifying families or 200 species: inconclusive (underpowered).";
<https://w3id.org/delphi/ontology/hasConfidence> "0.8"^^xsd:double;
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<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "Among related teleost species (same family), relative body depth (depth/length) and relative body width (width/length) vary inversely, so that the length-weight coefficient k = W/L^3, a proxy for volume at a given length, varies less across species than either relative transverse dimension.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Species means, family-centring for families with >= 5 species, Spearman correlation of centred ln depth ratio vs ln width ratio (one-sided test for negative), and comparison of the SDs of centred ln k vs centred ln depth and width ratios, against the pre-registered thresholds.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered. Species means from FishShapes v1 specimens (standard length SL, maximum body depth BD, maximum fish width FW, mass M; specimens with all four > 0). Variables per species: d = ln(BD/SL), w = ln(FW/SL), k = ln(M/SL^3). Families with >= 5 species are kept and each variable is centred on its family mean. (A) Spearman rho between family-centred d and w is < 0 with one-sided p < 0.05. (B) the SD of family-centred k is smaller than the SDs of family-centred d and of family-centred w. SUPPORTS if A and B both hold.";
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dc:description "standard length, maximum body depth, maximum fish width and mass of 16,523 museum specimens (Smithsonian NMNH), 1-3 per species";
dc:license "CC0 1.0 (Dryad); the README asks users to cite Price et al. 2022, Ecology 103:e3829";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions (Price et al. 2022)";
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