[R] matrix for diversity functions?
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:
> 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
>  0.7242788 0.7485246 0.7298712 0.9012085 1.0366280 0.9470281
>  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.
> Manju V. Sharma
> Gardenwood East 3.1, Division of Biology,
> Imperial College London, Silwood Park Campus
> Ascot SL5 7PY
> Tel (O): 0044 207 5942360
> (R): 0044 207 8520808
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Size: 197 bytes
Desc: This is a digitally signed message part
More information about the R-help