I am using the FD package in program R to estimate the indices of functional diversity. The package help file describes how functional richness (FRic) is calculated from continuous traits, but it gives only a vague description of the calculation when the traits are binary. So, I am seeking a resource that describes how FRic is calculated from binary traits. Any help would be appreciated.
Dan
Dan
Check out this paper. I'm not if it is of help to you.
http://adn.biol.umontreal.ca/~numericalecology/Reprints/Laliberte_Legendre_Ecology_2010.pdf
Anesh
Hi Dan,
Usually, when the traits are not continuous and quantitative (i.e. categorical), the computation of such indices of functional diversity requires an intermediate step, where a distance matrix between species is built (using Gower's distance for instance) on the basis of the table of traits. This results in a matrix (No.species x No.species) reflecting the degree of difference between species according to their respective traits. Then, this matrix is synthetized using PCoA to make the computation possible (i.e. number of traits needs to be lower than the number of species).
More details can be found in Villéger et al. (2008) for instance (Figure 5 gives a good overview)
I'm not 100% sure that this is true for binary traits, but I can't see why it would be wrong unless you do not have a sufficient number of traits to be able to differentiate well the species.
Hope it helps.
Anthony
Article New multidimensional functional diversity indices for a mult...
Dan
Check out this paper. I'm not if it is of help to you.
http://adn.biol.umontreal.ca/~numericalecology/Reprints/Laliberte_Legendre_Ecology_2010.pdf
Anesh
Hi Dan
I hope these papers may also help you with binary traits:
How many dimensions are needed to accurately assess functional diversity? A pragmatic approach for assessing the quality of functional spaces. http://onlinelibrary.wiley.com/doi/10.1111/geb.12299/full
Functional diversity (FD), species richness and community composition.
http://onlinelibrary.wiley.com/wol1/doi/10.1046/j.1461-0248.2002.00339.x/full
Regards
Jose
Hi I understand that this is bumping up old post, but just want this link to be on the record for anybody who reached this thread: http://villeger.sebastien.free.fr/Rscripts.html
These are R codes kindly provided by Villeger, including FRic.
http://villeger.sebastien.free.fr/Rscripts.html
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