[R-sig-eco] FW: Functional Diversity help!

[Holland, Jeffrey D]

Dear Mark,
     Gower does seem to the correct dissimilarity metric based upon your variables.  This will return a dissimilarity matrix that I believe you can use to calculate the functional diversity indices, by base code and likely by FD package as well.  Using this matrix will ensure that you are actually calculating the indices based upon the functional differences of the actual replicates, and will give you a continuous dissimilarity measure.  However, I am unsure why you want to insert PCoA into this before using FD?  This will output a reduced dimensionality object with replicate scores on the PCo axes---is this what you are after?  In any case, you will not get a number to replace the classes of your categorical data---you will get a dissimilarity measure between all pairs of replicates.
     Hope this helps,
Jeff Holland

-----Original Message-----
From: R-sig-ecology <r-sig-ecology-bounces using r-project.org> On Behalf Of Mark Thomas
Sent: Friday, August 10, 2018 7:07 AM
To: r-sig-ecology using r-project.org
Subject: [R-sig-eco] Functional Diversity help!

Dear r-sig-ecology,
Please forgive me if this question has already been answered, I have perused the web and due to me being fairly new to R, I have had trouble interpreting the answers.

I wish to calculate the functional diversity indices (Functional Richness, divergence, evenness, Rao-quadratic).

My dataset consists of 14 species, 25 sites, and 8 categorical traits.

I have been using the FD package but from what I have read I need to convert the categorical data using the gowdist function and then run pcoa to generate continuous data?

However, when I run the gowdist and pcoa I thought I'd get a number to replace the categorical data so I could then run the dbFD function in the FD package to calculate the FD indices, but this isn't happening, and I am not sure how to take the output from the pcoa and run in dbFD.

Any help would be greatly appreciated (apologies for the beginner question) thanks

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