Replication data for: “Applications of joint species distribution models in community ecology: a systematic literature review”

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Rojat, Margaux; Vieilledent, Ghislain; Schmitt, Sylvain; Pélissier, Raphaël; Pouteau, Robin, 2026, "Replication data for: “Applications of joint species distribution models in community ecology: a systematic literature review”", https://doi.org/10.23708/63UVSJ, DataSuds, V1, UNF:6:6WSHxj1XXFMoAy05ssH/Iw== [fileUNF]
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Description
Joint species distribution models (JSDMs) have emerged over the past decade as a vital biogeographic tool for incorporating multispecies co-occurrence data into species distribution modeling. However, a comprehensive synthesis of their practical applications has been lacking. This dataset contains the literature survey matrices and analytical criteria used to systematically review JSDM applications in peer-reviewed literature up to April 2024 via the Web of Science database. The provided data frames capture systematically extracted information across the following core dimensions:
• General study metadata: Publication date, geographic region (at the Biodiversity Information Standards TDWG4 resolution), and environmental context (latitude, insularity, and realm);
• Taxonomic representation: Classifications across major groups (amphibians, arthropods, birds, fishes, fungi, mammals, molluscs, plants, and reptiles);
• Data characteristics: Manual extractions of input dataset attributes, including occurrence type (presence-absence, abundance, or both), temporal depth (longitudinal vs. snapshot), and data origin (primary vs. secondary);
• Plant-specific sub-analyses: Species lists crossed with the Global Naturalized Alien Flora (GloNAF) database to evaluate the prevalence of alien species in plant-focused JSDMs;
• Biotic interaction and terminology text mining: Full-text keyword frequency analyses tracking instances of specific interaction terms (commensal*, compet*, facilit*, etc.);
• Interaction Focus Index (IFI): Calculated metrics evaluating how the type of input datasets influences the authors' interpretation of JSDM residuals. The IFI measures the ratio of the string interact* against more neutral terms like associat* and co-occur* to gauge interpretation preferences. (2026-09-23)
Subject Earth and Environmental Sciences
Keyword Biological interaction, Bias in scientific studies, Ecology, Datasets
Related Publication Rojat, M., Vieilledent, G., Schmitt, S., Pélissier, R., Pouteau, R. (2026). Applications of joint species distribution models in community ecology: a systematic literature review. Frontiers of Biogeography, under review.
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articles_interaction_focus_index_metric.tab
Tabular Data - 60.2 KB
Published Sep 24, 2026
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18 Variables, 269 Observations UNF:6:qMA3t9qSWodlJqS6Jz7Dkw==
Dataset containing text-mining keyword counts and the calculated Interaction Focus Index (IFI) for each analyzed article.
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dataset_all_articles_row_per_model.tab
Tabular Data - 112.1 KB
Published Sep 24, 2026
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16 Variables, 368 Observations UNF:6:7grUR9pdNzlAgVRsc5rBXw==
Dataset containing article metadata, and dataset characteristics.
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metadata.txt
Plain Text - 3.8 KB
Published Sep 24, 2026
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MD5: a27889656259e81c5cb54306731446af
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plant_species_lists_37_models.tab
Tabular Data - 1.0 MB
Published Sep 24, 2026
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8 Variables, 3765 Observations UNF:6:xTWru3vco39OisuOAThVRw==
Dataset containing extracted plant species lists across 37 plant-focused JSDMs.
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README.txt
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Published Sep 24, 2026
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MD5: e6f0e29984cb488f2ae199a7aae16501
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