1. mFD: an R package to compute and illustrate the multiple facets of functional diversity
- Author
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Magneville, Camille, Loiseau, Nicolas, Albouy, Camille, Casajus, Nicolas, Claverie, Thomas, Escalas, Arthur, Leprieur, Fabien, Maire, Eva, Mouillot, David, Villéger, Sébastien, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), Centre Universitaire de Formation et de Recherche de Mayotte (CUFR), Lancaster Environment Centre, Lancaster University, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), and ANR-17-CE32-0003,EXOFISHMED,Poissons herbivores exotiques dans les écosystèmes méditerranéens : causes biologiques et conséquences écologiques d'une invasion en cours(2017)
- Subjects
0106 biological sciences ,Functional entities ,beta-diversity ,Entropy ,[SDE.MCG]Environmental Sciences/Global Changes ,Framework ,Trait ,Functional space ,010603 evolutionary biology ,01 natural sciences ,Hill numbers ,03 medical and health sciences ,[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems ,functional entities ,functional traits ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Ecology ,Reveals ,functional space ,Beta-diversity ,Biodiversity ,15. Life on land ,Alpha-diversity ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Functional traits ,alpha-diversity - Abstract
WOS:000729415000001; International audience; Functional diversity (FD), the diversity of organism attributes that relates to their interactions with the abiotic and biotic environment, has been increasingly used for the last two decades in ecology, biogeography and conservation. Yet, FD has many facets and their estimations are not standardized nor embedded in a single tool. mFD (multifaceted functional diversity) is an R package that uses matrices of species assemblages and species trait values as building blocks to compute most FD indices. mFD is firstly based on two functions allowing the user to summarize trait and assemblage data. Then it calculates trait-based distances between species pairs, informs the user whether species have to be clustered into functional entities and finally computes multidimensional functional space. To let the user choose the most appropriate functional space for computing multidimensional functional diversity indices, two mFD functions allow assessing and illustrating the quality of each functional space. Next, mFD provides 6 core functions to calculate 16 existing FD indices based on trait-based distances, functional entities or species position in a functional space. The mFD package also provides graphical functions based on the ggplot library to illustrate FD values through customizable and high-resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. To facilitate the use of mFD framework, we built an associated website hosting five tutorials illustrating the use of all the functions step by step.
- Published
- 2021
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