[R-sig-eco] Fwd: Reply: Functional Diversity help! (Holland, Jeffrey D)

[Mark Thomas]

> Dear Jeff,

> thank you for your email and advice. I found a previous thread from 2010 which mentioned that as a workaround when using categorical data and calculating FD indices: 
> 
> https://stat.ethz.ch/pipermail/r-sig-ecology/2010-November/001642.html
> 
> Within the thread, it doesn't give all the steps to take i.e. 
> 
> library(FD)
> df<-gowdist(traits)
> df<-dudi.pco(df)
> df_traits<-df$tab (not sure if this is correct but gives me a df with numbers for all eight traits)
> 
> As I am not sure how to take the result from the gowdis and then use it with the dbFD function in the FD package, or even after I use the dudi.pco. 
> 
> I have tried many ways and I don't really have an example to base it on, so I am not totally sure if what I have done is correct. 
> 
> Thanks
> Mark
> 
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> Subject: R-sig-ecology Digest, Vol 125, Issue 2
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> Today's Topics:
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>    1. Functional Diversity help! (Mark Thomas)
>    2. FW:  Functional Diversity help! (Holland, Jeffrey D)
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> Message: 1
> Date: Fri, 10 Aug 2018 12:06:50 +0100
> From: Mark Thomas <travelmark85 using gmail.com>
> To: r-sig-ecology using r-project.org
> Subject: [R-sig-eco] Functional Diversity help!
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> 
> 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
> 
>         [[alternative HTML version deleted]]
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 10 Aug 2018 12:37:36 +0000
> From: "Holland, Jeffrey D" <jdhollan using purdue.edu>
> To: "r-sig-ecology using r-project.org" <r-sig-ecology using r-project.org>
> Subject: [R-sig-eco] FW:  Functional Diversity help!
> Message-ID: <cc68207f0f7743f085c31d148ab78492 using wppexc08.purdue.lcl>
> Content-Type: text/plain; charset="us-ascii"
> 
> 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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