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-boun...@r-project.org> On Behalf Of Mark
Thomas
Sent: Friday, August 10, 2018 7:07 AM
To: r-sig-ecology@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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