Re: [R] matrix for diversity functions?

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Tue, 18 Nov 2008 19:08:43 +0000

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 data.

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

G

>
> 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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______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Received on Tue 18 Nov 2008 - 19:11:43 GMT

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