The problems on BIO-ENV procedure by [R]

Shun Tsuobi,

   isoMDS (and routines based on it) will not allow zero 
dissimilarity, which implies perfect replicates.  One alternative is 
to remove one of the replicates, but that may have unsatisfactory 
effect on further analyses.  Alternatively, if you are sure you want 
to keep the duplicate plots you can change the zero to a small value

d[d==0] <- 0.0001

and run the isoMDS on the resulting revised dissimilarity matrix.

Undoubtedly someone from the vegan group will respond to your second 
question.

Dave Roberts

On 12/05/2011 01:28 AM, ???? wrote:

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