R help - Sep 2013 - Fwd: calculating dissimilarity index of islands (vegan and betapart)

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]]

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]]