mFD: an R package to compute and illustrate the multiple facets of functional diversity

Magneville, C. and Loiseau, N. and Albouy, C. and Casajus, N. and Claverie, T. and Escalas, A. and Leprieur, F. and Maire, E. and Mouillot, D. and Villéger, S. (2022) mFD: an R package to compute and illustrate the multiple facets of functional diversity. Ecography, 2022 (1). ISSN 0906-7590

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Abstract

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.

Item Type:
Journal Article
Journal or Publication Title:
Ecography
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1100/1105
Subjects:
ID Code:
164195
Deposited By:
Deposited On:
10 Jan 2022 10:15
Refereed?:
Yes
Published?:
Published
Last Modified:
22 Nov 2022 10:58