[R] [R-sig-eco] reception of (Vegan) envfit analysis by manuscript reviewers

[Jari Oksanen]

On 10/05/2012, at 11:45 AM, Gavin Simpson wrote:

> On Wed, 2012-05-09 at 15:51 -0600, Matt Bakker wrote:
>> I'm getting lots of grief from reviewers about figures generated with
>> the envfit function in the Vegan package. Has anyone else struggled to
>> effectively explain this analysis? If so, can you share any helpful
>> tips?
>> 
>> The most recent comment I've gotten back: "What this shows is which
>> NMDS axis separates the communities, not the relationship between the
>> edaphic factor and the Bray-Curtis distance."
> 
> Without further context for that quote and your manuscript to see how
> you are using the method it is difficult to say whether you are doing
> something silly or the reviewer is bone-headed.
> 
> I've had similar comments from reviewers about my use of the ordisurf()
> function. In each case it was the reviewers' failure to understand the
> methods applied that was the cause of the confusion.
> 
> As you provide little or no context I'll explain what envfit() does etc.
> 
> The idea goes back a long way (!) and is in my 1995 edition of Jongman
> et al Data Analysis in Community and Landscape Ecology (Cambridge
> University Press) though most likely was in 1987 version too. See
> Section 5.4 of the Ordination chapter by Ter Braak in that book.
> 
> The idea is to find the direction (in the k-dimensional ordination
> space) that has maximal correlation with an external variable.


Hello,

The method was indeed in the first edition of ter Braak's book. However, the idea is much older. The vegan implementation was based on an unpublished report from the Bell Labs from 1970s (or earlier). In this Bell Labs memorandum the method was specifically suggested for NMDS. Vegan uses different algorithm, but the method is the same. The early history in vegan can be traced in  ORDNEWS correspondence from 2001 or so, but it is so old that I cannot find that message via this computer any longer.

Then about Bray-Curtis. The referee may be correct when writing that the fitted vectors are not directly related to Bray-Curtis. You fit the vectors to the NMDS ordination, and that is a non-linear mapping from Bray-Curtis to the metric ordination space.  There are two points here: non-linearity and stress. Because of these, it is not strictly about B-C. Of course, the referee is wrong when writing about NMDS axes: the fitted vector has nothing to do with axes (unless you rotate your axis parallel to the fitted vector which you can do). The NMDS is based on Bray-Curtis, but it is not the same, and the vector fitting is based on NMDS. So why not write that is about NMDS? Why to insist on Bray-Curtis which is only in the background?

Cheers, Jari Oksanen

-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland