[R-sig-eco] The problems on BIO-ENV procedure by [R]

[坪井 隼]

Dear Madam / Sir,

I have two questions for the use of the “R” program for the ecological 
research. I am studying the relationship between the community 
structures of environmental microbes and some environmental conditions. 
For this objective, I have known that the BIOENV procedure, which was 
developed by Clarke & Ainsworth (1993), is available on the “R” software.
  

Fist question; 
I attempted the use of the procedure to analyze the relationship between 
the variation of the microbial community structures and the 
environmental factors. However, I can not analyze the relationship based 
on isoMDS function. The isoMDS was inacceptable for my dataset. The 
command for the BIOENV procedure, which I programmed, and the error 
massage I gained was as follow; 

> library(MASS)
> library(vegan) 
> communitydat<-read.table("C:/Documents and Settings/shuntsuboi/desktop
/bray.txt", head- er=T)
> environdat<-read.csv("C:/Documents and Settings shuntsuboi/desktop/ev.
csv",header=T)
> env<-environdat[,c("variablesA","variablesB.","variablesC","variablesD
","variablesE")]
> d <- vegdist(communitydat, "bray")
> isoMDS(d)
error   isoMDS(d) : zero or negative distance between objects 1 and 2

As mentioned above, I can not run the program because the error, which 
is “isoMDS(d) : zero or negative distance between objects 1 and 2”, 
occurred. What are the ways to solve this problem ? On isoMDS function, 
what are the ways that the zero distance of “Bray-Curtis distance” is 
acceptable in the function ?

Second question; 
	Based on the command as above, I ran the metaMDS function. However, 
although I could automatically describe the two dimensional ordination 
plot figure, I could not gain the X and Y value of the respective plots. 
Then, the error massage was shown as follow; 
“In ordiplot(x, choices = choices, type = type, display = display,  :
Species scores not available”
 
What are the ways to solve this problem ?

Sincerely yours, 
Shun Tsuboi