https://w3id.org/np/RAwakSiAxb3RIuwpVxfDTItPNrcYcnHLuVbtqFugRa9VM
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/darwin1859-ch02-08--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "WCVP version 16 was downloaded as one zip and the names and distribution tables were read from it. Accepted non-hybrid species, after dropping three binomials that mapped to two species ids, were compared with accepted subspecies, varieties and forms that are themselves native in the same TDWG level-3 area. Within each area, genera above the median size were compared with genera at or below it on the infraspecific rate and, among species that have at least one infraspecific taxon, on the mean count, using a one-sided Wilcoxon signed-rank test (normal approximation, zero differences dropped). The same thresholds were applied to variety-rank names only, as a sensitivity that does not change the verdict. No occurrence-effort covariate was applied.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.160819 share of qualifying TDWG level-3 areas where the infraspecific rate is higher in above-median genera than in at-or-below-median genera (n = 342, Wilcoxon one-sided p (approx, zeros dropped)=1.0; median p_large-p_small=-0.030544). Interpretation: Darwin's 'country' is a TDWG level-3 botanical country, the unit of the WCVP distribution table. 'Larger genera' and 'smaller genera' are the above-median and at-or-below-median genera of that country, not a global size cut. 'Present varieties' is the presence of an accepted infraspecific taxon (subspecies, variety or form) native in the same country; Darwin's 'variety' was broader than the modern variety rank, so subspecies and forms are included and the variety rank alone is only a sensitivity. 'More varieties' is the mean count of those taxa among species that have at least one. The test is vascular plants only. Darwin also tabulated beetles; that half is untested. Collection and taxonomic effort, which can name more infraspecific taxa in large or well-studied genera, is not controlled: no GBIF occurrence covariate is in the pre-registered test. The verdict therefore does not extend to animals and does not claim that the plant pattern is free of taxonomic-effort bias.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch02-08: refutes, confidence 0.55";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch02-08/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "A global expert checklist of accepted vascular-plant names with infraspecific rank and a native/introduced flag at botanical-country resolution, independent of this analysis, with a licence that permits reuse. Occurrence counts are not required for the verdict.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "In most botanical countries the infraspecific rate is higher in the smaller genera, at the pre-registered thresholds.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Genus size is the number of accepted native species in that botanical country, which is Darwin's within-country comparison and is not global genus size.",
"Infraspecific ranks are applied unevenly across families. The variety-rank-only sensitivity also meets the refutation rule for the rate (share 0.342105) and the support rule for the mean count.",
"No GBIF occurrence count was used. Taxonomic effort is uncontrolled. Effort would be expected to name more infraspecific taxa in larger genera, which is the direction of the claim, not the direction observed for the rate.",
"The refutation is the pre-registered rate clause: in 342 botanical countries the share with a higher infraspecific rate in larger genera is 0.160819, median difference -0.030544, opposite-direction Wilcoxon p 7.02e-41. The effect is a few percentage points.",
"The second clause goes the other way and meets its support threshold: among species that have at least one infraspecific taxon, the mean count is higher in larger genera in 0.874251 of 334 countries (median difference 0.08829). The pre-registered rule makes the rate clause decisive for refutation.",
"Vascular plants only. Beetle faunas in Darwin's section were not tested, so this is not a verdict about animals.";
<https://w3id.org/delphi/ontology/expectedObservation> "In most botanical countries, species in above-median genera have a higher rate of native infraspecific taxa than species in at-or-below-median genera, and a higher mean count of those taxa among the species that have any.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES if clause A has >= 30 areas, the share with p_large > p_small is <= 0.35, and the Wilcoxon signed-rank test of (p_small - p_large) greater than 0 has one-sided p < 0.01. If a signed-rank test cannot be computed because fewer than 10 differences are non-zero, that clause neither passes nor refutes. Any other computable outcome is MIXED. Fewer than 30 areas for clause A, or an unobtainable WCVP file, is inconclusive (underpowered or data-unavailable). Beetles, the other group in Darwin's section, are outside this dataset and are not part of the verdict. A variety-rank-only sensitivity (taxon_rank Variety alone) is reported and does not change the verdict.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.55"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch02-08--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "refutes";
<https://w3id.org/delphi/ontology/hypothesis> "Within a botanical country, accepted vascular-plant species that belong to the larger genera of that country more often have at least one accepted infraspecific taxon recorded in the same country, and those that do have more such taxa on average, than species in the smaller genera of that country.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Within each TDWG level-3 area, compare above-median and at-or-below-median genera on the species-level infraspecific rate and, among species that vary, on the mean infraspecific count. Combine areas with a one-sided Wilcoxon signed-rank test and a share threshold of 0.65 (support) or 0.35 (refutation) at alpha 0.01. Both clauses must pass for support; only the rate clause, in the opposite direction, refutes.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered, before any download. Data: Kew WCVP bulk zip (wcvp_names.csv and wcvp_distribution.csv). Accepted non-hybrid species only (taxon_rank Species, taxon_status Accepted, genus_hybrid and species_hybrid empty). A binomial with more than one such species id is dropped. An infraspecific taxon is an accepted non-hybrid name of taxon_rank Subspecies, Variety or Form, parented by genus + species. A record counts in a TDWG level-3 area only when introduced=0, extinct=0 and location_doubtful=0. Genus size is the number of qualifying native species of that genus in that area. Within an area, the median is taken over genera (one observation per genus). Large genera have size strictly above that median; small genera have size at or below it. For each species, n_var is the number of its infraspecific taxa that are themselves native in that area. p is the proportion of species with n_var >= 1. m is the mean n_var among species with n_var >= 1. An area enters clause A if it has >= 100 qualifying native species and >= 20 species in each of the large and small classes. Clause A passes if at least 30 such areas exist, the share with p_large > p_small is >= 0.65, and a Wilcoxon signed-rank test on the non-zero differences (alternative greater, zero_method wilcox) has one-sided p < 0.01. An area enters clause B if it enters clause A and both classes have >= 10 species with n_var >= 1. Clause B passes if at least 30 such areas exist, the share with m_large > m_small is >= 0.65, and the same Wilcoxon test has one-sided p < 0.01. SUPPORTS only if both clauses pass. No GBIF occurrence count is fetched; taxonomic effort is uncontrolled and is a caveat, not a covariate in the verdict.";
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dc:description "accepted species and infraspecific names with genus, and native TDWG level-3 distributions";
dc:license "CC BY 3.0 (README_WCVP.xlsx in the zip links to http://creativecommons.org/licenses/by/3.0)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: World Checklist of Vascular Plants (WCVP), Royal Botanic Gardens, Kew";
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