d08b564b-7b5c-4f39-9b28-9684dfc83cf5 Sextant Ifremer ZI Pointe du Diable Plouzane Brittany 29280 France sextant@ifremer.fr https://sextant.ifremer.fr/eng pointOfContact 2025-05-16T00:13:30.764279Z ISO 19115-3 - SEXTANT 1.0 GAM-NICHE: Shape-Constrained GAMs to build Species Distribution Models under the ecological niche theory 2023-05-14 publication To populate GAM-NICHE is a new tool developed by AZTI (Valle et al. 2023) to build Species Distribution Models (SDMs) under the ecological niche theory (Citores et al. 2020). It provides a GitHub tutorial in R language with an application to marine fish. Species Distribution Models (SDMs) are numerical tools that combine observations of species occurrence or abundance at known locations with information on the environmental and/or spatial characteristics of those locations (Elith and Leathwick 2009). SDMs are widely used as a tool for understanding species spatial ecology and are also known as ecological niche models (ENM) or habitat suitability models. According to ecological niche theory, species response curves are unimodal with respect to environmental gradients (Hutchinson 1957). While a variety of statistical methods have been developed for species distribution modelling, a general problem with most of these habitat modelling approaches is that the estimated response curves can display biologically implausible shapes which do not respect ecological niche theory. This is because species response curves are fit statistically with any assumption or restriction, which sometimes do not respect the ecological niche theory. To better understand species response to environmental changes, SDMs should consider theoretical background such as the ecological niche theory and pursue the unimodality of the response curves with respect to environmental gradients. This book provides a tutorial on how to use Shape-Constrained Generalized Additive Models (SC-GAMs) to build SDMs under the ecological niche theory framework (Citores et al. 2020). SC-GAMs impose monotonicity and concavity constraints in the linear predictor of the GAMs and avoid overfitting. SC-GAM is an effective alternative to fitting nonsymmetric parametric response curves, while retaining the unimodality constraint, required by ecological niche theory, for direct variables and limiting factors. The book is organised following the key steps in good modelling practice of SDMs (Elith and Leathwick 2009). First, presence data of a selected species are downloaded from GBIF/OBIS global public datasets and pseudo-absence data are created. Then, environmental data are downloaded from public repositories and extracted at each of the presence/pseudo-absence data points. Based on this dataset, an exploratory analysis is conducted to help deciding on the best modelling approach. The model is fitted to the dataset and the quality of the fit and the realism of the fitted response function are evaluated. After selecting a threshold to transform the continuous probability predictions into binary responses, the model is validated using a k-fold approach. Finally, the predicted maps are generated for visualization. The code is available in AZTI’s github repository and the book is readily available. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0) To cite the book, please use: Valle, M., Citores, L., Ibaibarriaga, L., Chust, C. (2023) GAM-NICHE: Shape-Constrained GAMs to build Species Distribution Models under the ecological niche theory. AZTI. https://doi.org/10.57762/fzpy-6w51 References Citores, L, L Ibaibarriaga, DJ Lee, MJ Brewer, M Santos, and G Chust. 2020. “Modelling Species Presence–Absence in the Ecological Niche Theory Framework Using Shape-Constrained Generalized Additive Models.” Ecological Modelling 418: 108926. https://doi.org/10.1016/j.ecolmodel.2019.108926. AZTI, Marine Research (Spain) Mireia Valle AZTI, Marine Research mvalle@azti.es originator Leire Citores AZTI, Marine Research originator Leire Ibaibarriaga AZTI, Marine Research originator Guillem Chust AZTI, Marine Research originator https://sextant.ifremer.fr/geonetwork/srv/api/records/d08b564b-7b5c-4f39-9b28-9684dfc83cf5/attachments/Picture2.jpg /Biological Environment/Species/Fish Species of Commercial Interest Thèmes Sextant 2024-07-26 publication geonetwork.thesaurus.local.theme.sextant-theme Species distribution GEMET - INSPIRE themes, version 1.0 2018-07-27T14:39:48 publication geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme Tool MISSION ATLANTIC Results Mission Atlantic - Resources 2024-07-26 publication geonetwork.thesaurus.local.theme.mission-atlantic-resources Celtic Seas Norwegian Sea South Brazilian Shelf Canary Current system Southern Benguela Atlantic Ocean North Mid-Atlantic Ridge South Mid-Atlantic Ridge Mission Atlantic - Case Studies 2024-07-26 publication geonetwork.thesaurus.local.theme.mission-atlantic-case-studies /Chemical oceanography /Physical oceanography /Biological oceanography Mission Atlantic - BODC Parameters 2024-07-26 publication geonetwork.thesaurus.local.theme.mission-atlantic-bodc-parameters Environmental data Modelling data Biological data Mission Atlantic - Data type (DMP) 2024-07-26 publication geonetwork.thesaurus.local.theme.mission-atlantic-data-type WP3 Pelagic Mapping Mission Atlantic - Work Package 2024-07-26 publication geonetwork.thesaurus.local.theme.mission-atlantic-work-package grid utf8 oceans biota -180.00 180.00 -90.00 90.00 https://gam-niche.azti.es/ WWW:LINK Gam-niche website https://fundacion-azti.github.io/gam-niche/ WWW:LINK Online book https://github.com/Fundacion-AZTI/gam-niche WWW:LINK GitHub RÈGLEMENT (UE) N o 1089/2010 DE LA COMMISSION du 23 novembre 2010 portant modalités d'application de la directive 2007/2/CE du Parlement européen et du Conseil en ce qui concerne l'interopérabilité des séries et des services de données géographiques 2010-12-08 publication See the referenced specification