Hi all,
It worked when I replaced the blanks (missing) in my spreadsheet as NA and
saved it as csv.
Stephen, my data is in excel spreadsheet, I have no clue how to replace all
the blank cells in the huge dataset as NA.

Thank for the help.

Soumi

On Mon, Oct 25, 2010 at 2:10 PM, Soumi Ray <soumiray74@gmail.com> wrote:

> Hi listers,
>
> I am trying to run NMDS in vegan package. I have a species dataset - with
> columns as species and rows as variables. All my data are 0/1
> (presence/absence). My data has missing values. I saved my data in txt file
> and the missing values are blank spaces. I am using the syntax:
> <nmds <-read.table ('nmds.txt', header=T, rows.names=1, sep="\t")
> <nmds.mds.alt <- metaMDS (nmds, distance="bray", k=2, autotransform=FALSE)
>
> But it is showing me the error:
> Error in distfun(comm, method = distance, ...) :
>   NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> In distfun(comm, method = distance, ...) :
>   you have empty rows: their dissimilarities may be meaningless in method
> bray
>
> Could anyone kindly let me know where am I going wrong? I admit i am new to
> R, trying to self tutor myself.
>
> Thank you,
>
> Regards,
>
> Soumi
>

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