[R] Abundance data ordination in R

Sarah Goslee sarah.goslee at gmail.com
Sun Apr 1 19:12:11 CEST 2007


There's a very good ordination web page by Mike Palmer aimed at
ecologists (and since you have a species x site matrix, I'm assuming
that describes you) at http://ordination.okstate.edu/

My recommendation is generally nonmetric multidimensional scaling
(principal coordinates analysis is a metric scaling ordination), with a
dissimilarity metric that doesn't consider joint absences, for example
Bray-Curtis/Sorensen. Treating absent species as missing data is
not a good idea, because while it may not be possible to say
that they are truly missing from that site (depending on taxa and
sampling methods), you at least know they aren't common at that
site. Ecological data are messy enough without discarding information!

There are several R packages that may be helpful, including
ecodist and vegan.


On 4/1/07, Milton Cezar Ribeiro <milton_ruser at yahoo.com.br> 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 can´t 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?
> Kind regards
> Miltinho
> Brazil

Sarah Goslee

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