[R-sig-eco] Dissimilarity measure for rank data

[Hanna Tuomisto]

Hi Tania,

Even though there is no perfect answer: don't use the combination Hellinger transformation + Bray-Curtis distance. The appropriate combination is Hellinger transformation + Euclidean distance, which gives you Hellinger distances (this is an asymmetric dissimilarity measure, which does not suffer from the double-zero problem that plagues the Euclidean distance). Bray-Curtis distance is in itself asymmetric, and it can be used directly both on regular abundance data and on ranked data.

Cheers,
Hanna Tuomisto


On 8 Jun 2017, at 14:45, Sarah Goslee wrote:

> Hi Tania,
> 
> That's not really an R question, and there's no one perfect answer.
> Googling "distance metric for ordinal data" turns up some discussions of
> the pros and cons of the various options.
> 
> You need to choose the one best able to address your hypothesis. You might
> get better ideas on a statistics forum, rather than an R-specific list.
> 
> Sarah
> 
> On Thu, Jun 8, 2017 at 6:54 AM Tania Bird <taniabird at gmail.com> wrote:
> 
>> I have species data that I would like to use for ordination. With
>> regular abundance data I would apply a Hellinger Transformation and
>> then use the Bray-Curtis distance.
>> 
>> Since the data are ranked (0 to 5) I will not transform it. But what
>> dissimilarity measure should I use instead of Bray-Curtis?
>> 
>> Thanks
>> 
>> 
>> Tania Bird MSc
>> "There is a sufficiency in the world for man's need but not for man's
>> greed" ~ Mahatma Gandhi
>> 
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> 
> -- 
> Sarah Goslee
> http://www.stringpage.com
> http://www.sarahgoslee.com
> http://www.functionaldiversity.org
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology