[ { "@id": "https://w3id.org/np/RAIMULQWtvhSL2mnAd2kyNQG7LigUNif8dGML0Evfyv7Q/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/thompson1917-ch03-10--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "fetch.py requests one zip per survey year and quarter from the DATRAS Download API (50 files, 13.6 MB) and records their checksums. analysis.py pools all records, converts length classes to cm, drops plus-group and unaged records, and computes the CANoAtLngt-weighted mean length at age per species. For the 11 species with at least 7 consecutive age classes from age 1 each holding >= 50 aged fish, it fits by weighted least squares a 3-parameter von Bertalanffy curve and a 3-parameter quadratic-plateau curve whose maximum is reached at least one age class before the oldest included age, and compares them by AIC; it also records the sign of the three increments between the last four included age classes." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 0.6363636363636364 fraction of qualifying species in which the asymptotic model is favoured by dAIC > 2 (pre-registered threshold 2/3); fraction of late-age increments positive = 0.758 (threshold 0.75) (n = 11 species, 33 late-age increments, 1111408 aged fish from 986385 CA rows, species-level counts: 7 of 11 favour the asymptotic model, 2 of 11 (Merlangius merlangus, Microstomus kitt) favour the reached-maximum model, 2 indeterminate (|dAIC| <= 2); 25 of 33 late increments > 0). Interpretation: Thompson's 'size never actually reaches, but only approaches asymptotically, a maximal limit' is read as a contrast between an asymptotic growth curve (increments decline toward zero but stay positive at every age reached) and determinate growth (a maximum reached at a finite age, with zero increments thereafter while the animals are alive). 'Size' is taken as body length, the quantity recorded in surveys. The test uses cross-sectional survey means of length at age rather than individual growth histories; this is a modern reinterpretation forced by the data (Thompson's own fish examples were also population means). Fitted asymptotic parameters are not themselves used as evidence of an asymptote, as one assessor warned; the evidence is the model comparison against an explicit reached-maximum alternative and the sign of the late-age increments." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of thompson1917-ch03-10: mixed, confidence 0.6" } ], "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-ch03-10/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: ices-datras-ns-ibts-ca-2000-2024-q1q3" } ], "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. REFUTES if the determinate model is favoured (dAIC < -2) in at least half of the qualifying species, OR if at least half of the pooled late-age increments are zero or negative (growth has stopped at a reached maximum while fish are still well sampled). Anything between the supports and refutes conditions is 'mixed'. If the DATRAS download API is unreachable the verdict is inconclusive with reason data-unavailable." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Cross-sectional survey means pool cohorts and years (2000-2024, Q1 and Q3) and so mix cohort effects with age effects; the oldest age classes are sparsely sampled (>= 50 fish required) and trawl gear under-samples the largest fish." }, { "@value": "DATRAS 'Species' names are taken as delivered (AphiaID-based) and no taxonomic harmonisation was done." }, { "@value": "DATRAS is a live database; the API extract is reproducible only to the extent that ICES does not revise the 2000-2024 records. The 50 file checksums of the extract used are in derived/datras_file_manifest.json and in this file." }, { "@value": "In the two species where the reached-maximum model wins (whiting, lemon sole) mean length at age actually declines over the oldest ages, which neither model predicts for individual growth; the most likely cause is size-selective (fishing) mortality removing the faster growers (Lee's phenomenon) and ageing error, not cessation of growth. This biases the test against the claim." }, { "@value": "Scope: North Sea marine teleosts only (11 species); Thompson's scope was cold-blooded animals in general. For saithe and cod the oldest well-sampled fish are at only 48-65% of the fitted Linf, i.e. the data do not reach the asymptotic region at all." }, { "@value": "The determinate alternative had to be given a specific functional form (quadratic rise to a plateau); a different plateau model could change individual dAIC values. Model selection used AIC on 7-18 age-class means, not individual-level likelihoods." }, { "@value": "The pre-registered supports condition was narrowly missed: 7/11 = 0.636 species favour the asymptotic model against the required 2/3, while the late-increment condition (0.758 >= 0.75) was met. The result is therefore 'mixed' by rule, although most of the evidence points toward protracted growth." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Pre-registered. Data: ICES DATRAS North Sea IBTS (NS-IBTS) age records (CA record type), quarters 1 and 3, survey years 2000-2024, all species; length class converted to cm; records with a plus-group flag or missing age excluded. A species qualifies if it has at least 7 consecutive age classes starting at age 1, each with at least 50 aged fish (sum of CANoAtLngt); the included age range ends at the oldest class with at least 50 fish. For each species, mean length at age is computed (weighted by CANoAtLngt) and two 3-parameter models are fitted by weighted least squares (weights = number of fish): (i) asymptotic von Bertalanffy L = Linf (1 - exp(-K (a - t0))) with K > 0, and (ii) determinate quadratic-plateau L = Lmax - c (tc - a)^2 for a < tc, L = Lmax for a >= tc, with tc constrained to at most (oldest included age - 1) so that the model asserts a maximum actually reached inside the data. dAIC = AIC_det - AIC_VB (positive favours the asymptotic model). Late-age increments are the three increments of mean length between the last four included age classes. SUPPORTS if the asymptotic model is favoured (dAIC > 2) in at least two thirds of qualifying species AND at least 75% of all late-age increments pooled across species are positive. Requires at least 5 qualifying species; otherwise inconclusive (underpowered)." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. REFUTES if the determinate model is favoured (dAIC < -2) in at least half of the qualifying species, OR if at least half of the pooled late-age increments are zero or negative (growth has stopped at a reached maximum while fish are still well sampled). Anything between the supports and refutes conditions is 'mixed'. If the DATRAS download API is unreachable the verdict is inconclusive with reason data-unavailable." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.6", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch03-10--claim-test--dataset-1" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "mixed" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If fishes approach a maximal size only asymptotically, then mean length at age in well-sampled wild fish populations keeps increasing, by ever smaller but still positive increments, through the oldest well-sampled ages, and an asymptotic growth model fits the length-at-age means better than a model in which length reaches a fixed maximum at a finite age and then stays there." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "fetch.py requests one zip per survey year and quarter from the DATRAS Download API (50 files, 13.6 MB) and records their checksums. analysis.py pools all records, converts length classes to cm, drops plus-group and unaged records, and computes the CANoAtLngt-weighted mean length at age per species. For the 11 species with at least 7 consecutive age classes from age 1 each holding >= 50 aged fish, it fits by weighted least squares a 3-parameter von Bertalanffy curve and a 3-parameter quadratic-plateau curve whose maximum is reached at least one age class before the oldest included age, and compares them by AIC; it also records the sign of the three increments between the last four included age classes." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. Data: ICES DATRAS North Sea IBTS (NS-IBTS) age records (CA record type), quarters 1 and 3, survey years 2000-2024, all species; length class converted to cm; records with a plus-group flag or missing age excluded. A species qualifies if it has at least 7 consecutive age classes starting at age 1, each with at least 50 aged fish (sum of CANoAtLngt); the included age range ends at the oldest class with at least 50 fish. For each species, mean length at age is computed (weighted by CANoAtLngt) and two 3-parameter models are fitted by weighted least squares (weights = number of fish): (i) asymptotic von Bertalanffy L = Linf (1 - exp(-K (a - t0))) with K > 0, and (ii) determinate quadratic-plateau L = Lmax - c (tc - a)^2 for a < tc, L = Lmax for a >= tc, with tc constrained to at most (oldest included age - 1) so that the model asserts a maximum actually reached inside the data. dAIC = AIC_det - AIC_VB (positive favours the asymptotic model). Late-age increments are the three increments of mean length between the last four included age classes. SUPPORTS if the asymptotic model is favoured (dAIC > 2) in at least two thirds of qualifying species AND at least 75% of all late-age increments pooled across species are positive. Requires at least 5 qualifying species; otherwise inconclusive (underpowered)." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch03-10--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "individual-level aged fish (length class, age, number at length) for mean length at age per species" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC BY 4.0 (ICES Data Policy, open access data)" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: ICES DATRAS, North Sea International Bottom Trawl Survey (NS-IBTS), age-based biological records (CA), 2000-2024, quarters 1 and 3" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": 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