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Iberian regional replication of Soroye et al. 2020 using open GBIF Bombus occurrence data
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Three intentional deviations from the original lme4/MCMC implementation:
(i) the species random effect is fit by variational Bayes (statsmodels.BinomialBayesMixedGLM) rather than full MCMC, a fast approximation that typically underestimates posterior credible-interval width by approximately 10–20%;
(ii) the climateLimits[[1]]/[[2]] precomputation step is reconstructed from the available R helper scripts because the precomputation script itself is not in the public Figshare release of the original code;
(iii) the input occurrence dataset is replaced with an open GBIF Iberian Bombus query (https://doi.org/10.15468/dl.3frmsq) rather than the authors' curated continental dataset; this is the deliberate experimental change that makes the study a regional replication.
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notebooks/01b_gbif_download_doi.py in the same repository.
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The complete claim — that local extirpation rate in bumble bee species rises with the frequency at which local temperatures exceed species-specific historically observed thermal tolerances — is tested on an independent regional dataset of bumble bee occurrences for the Iberian Peninsula (Spain and Portugal). The regression specification, response variable, grid resolution, and baseline-vs-recent period definitions all match those used in the Phase 2 Python port; only the input occurrence dataset is replaced.
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Anne Fouilloux
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