[R] matrix for diversity functions?

Gavin Simpson gavin.simpson at ucl.ac.uk
Tue Nov 18 20:08:43 CET 2008

On Tue, 2008-11-18 at 16:27 +0000, Sharma, Manju wrote:
> Hi, 
> I have a small simple data frame (attached) -  to compare diversity of
> insects encountered in disturbed and unditurbed site.  What i have is
> the count of insects -  the total number of times they were encountered
> over 30 monitoring slots.
> Can someone please check for me to make sure how the 'community data
> matrix' for the diversity function needs to be oriented so that i'm
> comparing the right sets.

Is this vegan::diversity ? If so, then it doesn't do what you are trying
to do, nor does the help for diversity() say that it can do this.

A community data matrix, as the example in ?diversity shows, is an n by
m matrix of n samples and m species (n are the rows, m are the columns)
containing counts/observations/proportions etc on the m species in each
of the n samples.

You need data on the species themselves, not counts of things in two or
more different types of samples.

> I know that community data matrices mustn't carry characters that aren't
> numbers. I replaced my sps. names sp1, sp2, sp3, etc., with just 1, 2,
> 3.... but not sure what I can replace 'dist' and 'undist' with! 
> I try this to start with -- 
> insects.div<-diversity(insects, index="shannon")  
> > insects.div
> [1] 0.7242788 0.7485246 0.7298712 0.9012085 1.0366280 0.9470281
> 1.0466542
> [8] 1.0133127 0.6450332
> & thats not what i want. Any advice on the matrix format or commands
> would be big help! 

If you want to use vegan::diversity() then you'll need some different

Alternatively, If you an try to explain what you want to do maybe we can
point you in the right direction.


> Cheers,
> Manju V. Sharma
> Gardenwood East 3.1, Division of Biology, 
> Imperial College London, Silwood Park Campus
> Ascot SL5 7PY
> UK
> Tel (O): 0044 207 5942360
>       (R): 0044 207 8520808 
> ______________________________________________
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 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
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 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk

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