[R] Abundance data ordination in R

Gavin Simpson gavin.simpson at ucl.ac.uk
Mon Apr 2 09:42:44 CEST 2007

On Sun, 2007-04-01 at 09:20 -0700, Milton Cezar Ribeiro wrote:
> Dear R-gurus
> I have a data.frame with abundance data for species and sites which looks like:
> mydf<-data.frame(
>  sp1=sample(0:10,5,replace=T),
>  sp2=sample(0:20,5,replace=T),
>  sp3=sample(0:4,5,replace=T),
>  sp4=sample(0:2,5,replace=T))
> rownames(mydf)<-paste("sites",1:5,sep="")
> I would like make an ordination analysis of these data and my worries
> is about the "zeros" (absence of species) into the matrix. Up to I
> read (Gotelli - A primir of ecological statistics, 2004), when I have
> abundance data I cant compute Euclidian Distances because the zeros
> have the meaning of absence of the species and not as zero counting.
> Gotelli suggests one make "principal coordinates analysis". I would
> like to here from you what you think about and what is the best
> packages and functions to I compute my distance matrices and do my
> ordination analysis. Can I considere zero as NA on my data.frame? Is
> there a good PDF book available about Multivariate Analysis for
> abundance data available on the web?

In addition to the other suggestions, there is a Task View on CRAN for
the topic of Environmetrics. This has a section describing the various
ordination techniques available in R as well as functions to calculate
distance/dissimilarity matrices:



> Kind regards
> Miltinho
> Brazil
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Gavin Simpson                     [t] +44 (0)20 7679 0522
ECRC                              [f] +44 (0)20 7679 0565
UCL Department of Geography
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