[R-sig-eco] The problems on BIO-ENV procedure by [R]
坪井 隼
tsuboi-shun-gw at ynu.ac.jp
Mon Dec 5 09:28:12 CET 2011
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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