[R-sig-eco] Quantifying functional trait diversity through Gower distance and pcoa

Frank Dziock frank.dziock at tu-berlin.de
Tue Nov 16 17:34:02 CET 2010


Hi Chris,

1. an easy way to calculate Functional Diversity when you only have 
categorical trait data is to calculate Functional Richness as the number 
of unique trait combinations. This is what the FD package does for you 
automatically.

2. Laliberte & Legendre 2010 have extended the framework by Villeger et 
al 2008 in order to calculate FD from categorical traits doing exactly 
the thing you have in mind, i.e calculating distance matrices with Gower 
distance and PCoA. But they have included all that in their FD package, 
so you dont have to do that programming on your own. Their paper and 
their FD package will help you in choosing and calculating the proper 
index for your question. Also think about choosing the right trait 
weights, if your traits have different numbers of categories.

Best wishes from rainy Potsdam,

Frank Dziock


Laliberté, E. & P. Legendre (2010): A distance-based framework for 
measuring functional diversity from multiple traits. - Ecology, 91(1), 
2010, pp. 299–305

Villeger et al (2008): NEW MULTIDIMENSIONAL FUNCTIONAL DIVERSITY INDICES
FOR A MULTIFACETED FRAMEWORK IN FUNCTIONAL ECOLOGY. - Ecology, 89(8), 
2008, pp. 2290–2301


Am 16.11.2010 16:24, schrieb Phil Novack-Gottshall:
> Dear Chris,
>
> You might consider the FD library, which allows measurement of a range
> of functional diversity metrics, and includes functions for Gower
> distance (and, within other functions, PCoA, using, I believe, the
> dudi.pco function from the ade4 library). A benefit of the library's
> functions is control over the number of dimensions to include.
>
> Laliberté, E., and B. Shipley. 2010. FD: Measuring functional diversity
> (FD) from multiple traits, and other tools for functional ecology,
> Version 1.0-9.
>
> Cheers,
> Phil
>
> On 11/16/2010 9:08 AM, chris mcowen wrote:
>> Dear List,
>>
>> I am relatively new to this area of ecology and R, coming from a
>> phylogenetic background. I am looking to quantify functional trait
>> diversity in in order to plot global functional trait diversity
>> hotspots. My trait data are categorical and all indicies of functional
>> diversity require continuous data.
>>
>> My approach was to generate a distance matrix based on the Gower
>> method - i have done this with vegdist- and then i was planning on
>> running a pcoa on these to generate the continuous data to use in the
>> calculation of functional diversity indicies.
>>
>> I have two questions:-
>>
>> First, does this make sense, i appreciate i will loose information
>> this way.
>>
>> Second, I have looked at vegan but can not see a way to run a pcoa on
>> the output from a vegdist analysis, is this possible and once again
>> does this make sense?
>>
>> Any help would be greatly appreciated,
>>
>> Chris
>>
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>>
>>
>>
>

-- 

Prof. Dr. Frank Dziock
Animal Ecologist and Head of Department (Juniorprofessor)

Department of Biodiversity Dynamics
Technische Universitaet Berlin
Sekr. AB 1
Rothenburgstr. 12
D - 12165 Berlin
Germany

Tel: 030 – 314 71368

Secretary Gisela Falk
gisela.falk at tu-berlin.de
Tel: 030 - 314 71350
Fax: 030 – 314 71355

http://www.biodiv.tu-berlin.de/


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