Thank you very much Jari.

Is the Raup--Crick dissimilarity metric the only option for a 
presence/absence data in "vegdist" or using binary = T could I use any 
other dissimilarity metric?

Best,

Manuel

On 27/03/2011 09:07 a.m., Jari Oksanen wrote:
> On 26/03/11 17:35 PM, "Manuel Spínola"<mspinola10@gmail.com>  wrote:
>
>> Dear list members,
>>
>> I got an error message working with Raup--Crick distance in metaMDS.
>>
>>> flora.mds = metaMDS(indicadora, distance = "raup", trace = FALSE, zerodist
>> = "ignore")
>> Error in isoMDS(dist, k = k, trace = isotrace) :
>>    zero or negative distance between objects 1 and 2
>> In addition: Warning message:
>> In distfun(comm, method = distance, ...) :
>>    data have empty species which influence the results im method raup
>>
> Manuel,
>
> As I read it, the error message comes from isoMDS() that does not accept
> zero distances, and you have decided to ignore this (by setting zerodist =
> "ignore"). Either you or isoMDS must give up, and I think it is easier for
> you: try setting 'zerodist = "add"', and confess that isoMDS() wins your
> dispute.
>
> Another message you got is from vegdist() which only tells you that empty
> species (= that do not occur in your data) will influence your data. That is
> only informational, and not an error.
>
> Cheers, Jari Oksanen
>
>
>


-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
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