https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/Head https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/assertion https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/provenance https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/pubinfo https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/assertion https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://purl.org/dc/terms/description fetch.py downloads the RData file and exports metadata and U, F, C submatrices to JSON with an R script (jsonlite). analysis.py keeps age-classified, divided, unmanipulated, wild, individual-or-mean matrices of dimension >= 5 with finite entries; averages a species' matrices of its most common dimension; takes survival per class as the U column sum, drops a terminal class with a self-loop (open plus group), defines mature classes by positive F column sums, and computes Spearman rho between class index and mortality over >= 4 mature classes (constant mortality counted as rho = 0). Bird species are excluded before the verdict. The pre-registered rule is applied. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.5714285714285714 fraction of qualifying non-bird species with Spearman rho(age, adult mortality) > 0 (n = 35 species (classes: {'Mammalia': 20, 'Actinopterygii': 9, 'Amphibia': 2, 'Reptilia': 2, 'Bivalvia': 1, 'Gastropoda': 1}), 20 rising, 13 falling, 2 flat; 12 significantly rising and 6 significantly falling at p < 0.05). Interpretation: The proved part of the claim is the formula for s(a); the biological assertion tested is that senescence (rising mortality with adult age) is the inevitable result, which is how Jones et al. (2013) tested it across the tree of life and the reason the claim is already marked refuted in the claim graph. Matrix models average over years and individuals, late age classes are estimated from few animals, and many published matrices truncate age at a plus group; these all add noise rather than a systematic sign. Age classes are the model's classes (usually years), not ages since maturity, which is adequate for a monotonic-trend test. The RData file is converted to JSON with an R script (R 4.x) because the matrices are stored as R lists; analysis.py reads the committed JSON. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of hamilton-senescence: mixed, confidence 0.6 https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/hamilton-senescence/result.json https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: comadre-animal-matrix-database-4.26.4.0, holdout: class Aves rows excluded from fitting (see holdout/README.md) https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered. REFUTES if fewer than 50% of qualifying species show rising adult mortality. MIXED otherwise (50% to 80%, or >= 80% with mean rho <= 0.3). INCONCLUSIVE (underpowered) if fewer than 15 species qualify; INCONCLUSIVE (data-unavailable) if the file cannot be downloaded or read. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Published age-classified matrices usually truncate age with a plus group, so the oldest ages, where senescence is strongest, are often missing; this biases the test against the claim. Conversely, class index is calendar age for most studies but not all. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Sample is small (35 non-bird species, 20 of them mammals) and dominated by well-studied ungulates, carnivores and fishes; it is not a random sample of animal life histories. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The proved part of the claim (the formula for the age-specific force of selection) is not tested; only the biological corollary that mortality must rise with adult age. Class Aves (8 species) is held out and scorable later with 'analysis.py --exam'; the first run of the script, before the gate was added, printed the birds' fraction rising once and it was not used. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Verdict 'mixed' by the pre-registered rule (57% rising, between the 50% refute and 80% support thresholds): adult mortality rises with age in a majority of species but far from the 'great majority' that 'inevitable senescence' implies, and 13 of 35 species show falling adult mortality. This is the same direction as Jones et al. (2013) but weaker evidence, because matrix models have few age classes and noisy late-age estimates. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered. Data: COMADRE Animal Matrix Database v4.26.4.0 (RData file served at compadre-db.org/Data/ComadreDownload; data user agreement and citation guidelines accepted). Matrix selection: MatrixCriteriaAge == 'Yes' (age-classified), MatrixSplit == 'Divided' (U and F submatrices available), MatrixComposite in {'Individual', 'Mean'}, MatrixTreatment == 'Unmanipulated', MatrixCaptivity == 'W' (wild), matrix dimension >= 5, no missing entries in U or F. For each qualifying matrix, survival of age class a is the column sum of U for class a; the last class is dropped from the trend if U has a non-zero diagonal entry there (an open-ended plus group whose survival mixes ages). Mature classes are those whose F column sum is > 0. For each species, qualifying matrices of the same dimension are averaged element-wise (so each species contributes once); species with fewer than 4 mature age classes after dropping the plus group are excluded. Rising adult mortality = Spearman rho between age-class index and mortality (1 - survival) over the mature classes is > 0. SUPPORTS if at least 80% of qualifying species show rising adult mortality AND the mean rho across species is > 0.3. AMENDMENT (2026-10-31, before any data were downloaded, at the request of the holdout thread): species of class Aves are excluded from the primary analysis and from all criteria above; bird species are held out and only reported separately, unfitted, as a holdout check. Class is taken from COMADRE's 'Class' metadata column. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. REFUTES if fewer than 50% of qualifying species show rising adult mortality. MIXED otherwise (50% to 80%, or >= 80% with mean rho <= 0.3). INCONCLUSIVE (underpowered) if fewer than 15 species qualify; INCONCLUSIVE (data-unavailable) if the file cannot be downloaded or read. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.6 https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/hypothesis If the force of selection on survival declines with age after reproduction begins so that senescence is inevitable, then in age-structured matrix population models of unmanipulated wild animal populations, age-specific mortality should rise across the adult (reproductive) age classes in the great majority of species. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/inferenceMethod fetch.py downloads the RData file and exports metadata and U, F, C submatrices to JSON with an R script (jsonlite). analysis.py keeps age-classified, divided, unmanipulated, wild, individual-or-mean matrices of dimension >= 5 with finite entries; averages a species' matrices of its most common dimension; takes survival per class as the U column sum, drops a terminal class with a self-loop (open plus group), defines mature classes by positive F column sums, and computes Spearman rho between class index and mortality over >= 4 mature classes (constant mortality counted as rho = 0). Bird species are excluded before the verdict. The pre-registered rule is applied. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered. Data: COMADRE Animal Matrix Database v4.26.4.0 (RData file served at compadre-db.org/Data/ComadreDownload; data user agreement and citation guidelines accepted). Matrix selection: MatrixCriteriaAge == 'Yes' (age-classified), MatrixSplit == 'Divided' (U and F submatrices available), MatrixComposite in {'Individual', 'Mean'}, MatrixTreatment == 'Unmanipulated', MatrixCaptivity == 'W' (wild), matrix dimension >= 5, no missing entries in U or F. For each qualifying matrix, survival of age class a is the column sum of U for class a; the last class is dropped from the trend if U has a non-zero diagonal entry there (an open-ended plus group whose survival mixes ages). Mature classes are those whose F column sum is > 0. For each species, qualifying matrices of the same dimension are averaged element-wise (so each species contributes once); species with fewer than 4 mature age classes after dropping the plus group are excluded. Rising adult mortality = Spearman rho between age-class index and mortality (1 - survival) over the mature classes is > 0. SUPPORTS if at least 80% of qualifying species show rising adult mortality AND the mean rho across species is > 0.3. AMENDMENT (2026-10-31, before any data were downloaded, at the request of the holdout thread): species of class Aves are excluded from the primary analysis and from all criteria above; bird species are held out and only reported separately, unfitted, as a holdout check. Class is taken from COMADRE's 'Class' metadata column. https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/hamilton-senescence https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/hamilton-senescence--claim-test https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 http://purl.org/dc/terms/description age-classified U (survival) and F (fertility) submatrices with study metadata https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 (COMPADRE/COMADRE data user agreement) https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--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/hamilton-senescence--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: COMADRE Animal Matrix Database v4.26.4.0 (3548 matrix population models, 445 species) https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://compadre-db.org/Data/ComadreDownload https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://compadre-db.org/Data/Comadre https://w3id.org/delphi/resource/evidence/hamilton-senescence--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:490666bacce563c2f8ed43467634b6a60c4fee2d1389900d22b087fe665d313f https://w3id.org/np/RAmIetNdPN-QUaJfp9zvc0OS16cInlvo6XlWV6K0QnPYQ/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 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-fable-5-1 http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (claude-fable-5-1; 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