[R-sig-eco] Error with "raup" distance, in metaMDS

[Brian Inouye]

There are other dissimilarity metrics that could also be used, each with 
different assumptions of course.
Raup-Crick is a reasonable choice of distance metric, but I'm not sure 
if the current version of vegdist() has been updated to reflect 
discussion in Chase et al 2011 in Ecosphere 
(http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1).

-Brian

On 3/28/2011 12:00 PM,"Manuel Spínola"<mspinola10 at gmail.com>  wrote:
> 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
> <snip>
> On 27/03/2011 09:07 a.m., Jari Oksanen wrote:
>> 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