Elaine:

You would do better posting this on the R-sig-ecology list, I believe. THE
r-help list is mostly for general R programming questions, while the
ecology list readers will have expertise more closely related to your
specific issues.


Cheers,
Bert


On Fri, Sep 6, 2013 at 3:25 PM, Elaine Kuo <elaine.kuo.tw@gmail.com> wrote:

> Dear List,
>
>
>
> This is Elaine, a postgraduate studying in bird distributions in East Asia.
>
>
>
> I want to calculate Simpson dissimilarity index,
>
> based on a presence/absence matrix of bird species in islands in East Asia.
>
> (matrix row: 36 islands/matrix column: species ID)
>
> (R package vegan to make NMDS and R package betapart)
>
>
>
> In most papers using vegan for NMDS and betapart for dissimilarity index,
>
> the dissimilarity index is generated by grid data in continents.
>
> The calculation of this index is done by comparing species presence/absence
> between a pair of grids adjacent to each other.
>
>
>
> However, in my case, the dissimilarity index needs to be generated per
> island,
>
> and it is difficult for islands to find continuous landmass nearby.
>
> I would like ask if the calculation of dissimilarity index using metaMDS
> and beta.pair in continents can work as well as in islands.
>
> If so, please kindly advice how the mechanisim behind the code generates
> the dissimilarity index for island.
>
> (Does it compare species presence/absence between a pair of island?
>
> Should the two islands be specifically located or close to each other?)
>
>
>
> Thank you
>
> Elaine
>
>
>
> Code
>
> # NMDS
>
>   library(MASS)
>
>   library(vegan)
>
>   island.NMDS  <-  metaMDS(island,k=2, distfun  =  betadiver,  distance  =
> "sim",trymax=100,zerodist="add")
>
>   plot(island.NMDS,  type  =  "n")
>
>
>
> #Simpson Dissimilarity Index
>
> library(betapart)
>
>   island.dist<-beta.pair(island, index.family="sor")
>
>   class(island.dist)
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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.
>



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

	[[alternative HTML version deleted]]

