[R-sig-eco] NMDS vegan

[stephen sefick]

highlight all of the cells in the data matrix and in the edit menu (?)
you should find "find and replace".
HTH,

Stephen

On Tue, Oct 26, 2010 at 1:30 PM, Soumi Ray <soumiray74 at gmail.com> wrote:
> 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 at 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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-- 
Stephen Sefick
____________________________________
| Auburn University                                   |
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| sas0025 at auburn.edu                             |
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