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

[Eduard Szöcs]

Regarding your second question:

Did you run metaMDS on the dissimilarity matrix? - Than metaMDS and 
ordiplot have no information about the species.
Try running metaMDS on your community matrix and specify the distance 
argument.


Hope this helps,

Szöcs Eduard


On 12/05/2011 06:57 PM, Dave Roberts wrote:
> 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, 坪井　隼 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
>>
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>