https://w3id.org/np/RA_McE5sx1opeUEZqP0-DwL-MwqNns3kkX2A2OhNCLNXU
.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-ch12-16--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "WCVP version 16 supplied accepted non-hybrid species and accepted subspecies, varieties and forms, restricted to native, non-extinct, non-doubtful TDWG level-3 records. Countries with at least 200 such species were paired only when their level-1 continents differed (45,673 pairs among 329 countries). For each pair the script counted representative genera (shared genera with no species in common), identical species and shared infraspecific taxa, then applied the pre-registered quartile tests and size-controlled partial Spearman correlations. The percentile is the smallest observed value whose empirical cdf reaches 0.25 or 0.75. Pair rows are not stored; derived/bins.csv is a descriptive grouping.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 1 share of cross-continent pairs in the top quartile of representative genera that share at least one native species (n = 45673, 75th percentile of representative genera=162; partial Spearman shared-species rho=0.633188, scipy two-sided p underflowed to 0.0). Interpretation: Darwin's regions are TDWG level-3 botanical countries, and 'however distant' is read as different TDWG level-1 continents, so same-continent neighbours are not in the verdict. 'Closely allied or representative species' are not phylogenetic sisters: sister-species identity is not in this checklist. The proxy is a shared genus whose species in the two countries are not the same species, and it is labelled as a congener proxy. 'Identical species' are the same accepted binomial native in both countries. 'Doubtful forms' are accepted subspecies, varieties and forms native in both countries, a nomenclatural proxy rather than a count of names that two authors rank differently. The test is vascular plants only. Pairwise tests reuse countries, so the correlation p-values are anti-conservative; support therefore requires the pre-registered effect sizes, not significance alone. Flora size is controlled in the partial correlations because two large floras share names by opportunity.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch12-16: supports, confidence 0.6";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch12-16/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "A global vascular-plant checklist with accepted species, genus, infraspecific rank and native status at botanical-country resolution, open to reuse. A phylogeny is not required because the pre-registered proxy is congeners, not sisters.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Cross-continent pairs rich in representative genera usually share no species, or identical-species counts fall as representative genera rise once flora size is controlled.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Doubtful forms are accepted infraspecific names native in both countries, not names that two authorities rank differently.",
"Same-continent pairs were excluded by the pre-registered reading of 'however distant'. The verdict does not say how neighbouring countries behave.",
"The 45,673 pairs reuse 329 countries, so the correlation and Mann-Whitney p-values (both returned as 0.0 by underflow) are not independent-sample probabilities. The effect sizes are large: partial Spearman rho 0.633188 for shared species and 0.617002 for shared infraspecific taxa after flora-size control, top-quartile median shared species 92 against a pattern in which pairs with 0 representative genera (n=10) share no species.",
"The allied-species term is a congener proxy: genera native in both countries with no species in common. Sister species were not identified, and no phylogeny was used.",
"Vascular plants only. Animal regions in Darwin's chapter were not tested.";
<https://w3id.org/delphi/ontology/expectedObservation> "Cross-continent pairs with more representative genera share identical species more often, and share more infraspecific taxa, than pairs with few representative genera, including after flora size is controlled.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered. REFUTES if there are at least 100 eligible pairs and either the share of top-quartile pairs with S >= 1 is at most 0.40, or the size-controlled partial Spearman of log1p(S) with log1p(R) is less than or equal to 0 with two-sided p < 0.01. If the 75th percentile of R is 0, or fewer than 100 pairs are eligible, the verdict is inconclusive (underpowered): the 'many allied species' condition is absent or the sample is small. Any other computable outcome is MIXED. Animals are untested. An unobtainable WCVP file is inconclusive (data-unavailable).";
<https://w3id.org/delphi/ontology/hasConfidence> "0.6"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch12-16--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<https://w3id.org/delphi/ontology/hypothesis> "Among vascular-plant floras on different continents, pairs of botanical countries that share many genera of representative (non-identical) species also share at least some identical species and more accepted infraspecific taxa than pairs that share few such genera.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Among cross-continent pairs of countries with at least 200 native species, compare the top and bottom quartiles of representative-genus counts on the presence of shared species and on the count of shared infraspecific taxa, and compute size-controlled partial Spearman correlations. All four clauses must pass for support. A top-quartile shared-species rate of 0.40 or less, or a non-positive partial correlation of shared species with representative genera, refutes.";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered, before the pair counts are computed. Data: Kew WCVP wcvp_names.csv and wcvp_distribution.csv. Accepted non-hybrid species only (taxon_rank Species, taxon_status Accepted, genus_hybrid and species_hybrid empty); binomials that map to more than one species id are dropped. Infraspecific taxa are accepted non-hybrid names of rank Subspecies, Variety or Form. A record is native in a TDWG level-3 area only when introduced=0, extinct=0 and location_doubtful=0. An area is eligible if it has at least 200 qualifying native species and a single continent_code_l1. A pair is eligible if the two areas lie on different continents. A representative genus is a genus with at least one qualifying native species in each area and no species binomial in common; this congener count is the proxy for closely allied or representative species, and it is not a sister-species count. Identical species are shared species binomials. Doubtful forms are accepted infraspecific taxa native in both areas. Let R be the number of representative genera, S the number of identical species and D the number of shared infraspecific taxa. The top quartile is pairs with R at or above the 75th percentile of R; the bottom quartile is pairs with R at or below the 25th percentile. Clause identical passes if the 75th percentile of R is at least 1 and at least 75% of top-quartile pairs have S >= 1. Clause doubtful passes if the top-quartile median of D is at least 1 and at least twice the bottom-quartile median (a bottom median of 0 satisfies the ratio when the top median is at least 1) and a Mann-Whitney U test of top versus bottom, alternative greater, has p < 0.01. Clause species-partial passes if the partial Spearman correlation of log1p(S) with log1p(R), controlling for log of the geometric mean of the two species counts, is at least 0.15 with two-sided p < 0.01. The partial correlation is the Pearson correlation of rank residuals after linear residualizing both ranks on the rank of the size control; the p-value treats pairs as independent. Clause doubtful-partial uses log1p(D) in place of log1p(S) with the same threshold. SUPPORTS only if all four clauses pass and there are at least 100 eligible pairs.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
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dc:description "accepted species, genera and infraspecific names with native continent and botanical-country 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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dc:license <https://creativecommons.org/licenses/by/4.0/>;
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<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch12-16: supports, confidence 0.6";
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