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NA error in envfit

8 messages · Mitchell, Kendra, stephen sefick, Eduard Szöcs +2 more

Original
stephen sefick
# 
Kendra,

Something is wrong in X or P; find out what the foreign function call is 
  and then you may be able to track down the offending data problem. 
Maybe a logarithm somewhere? This is probably not much help; I don't 
have much experience with envfit.

Stephen
On 12/03/2013 07:06 PM, Mitchell, Kendra wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jari Oksanen
    

    

      
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Hello,

I think I saw something like this in autumn (northern hemisphere) when a variable had constant values with no variation, and envfit did not know how to scale the arrow. 

We fixed this in the development version of vegan in R-Forge on September 29. Unfortunately R-Forge is again dysfunctional and cannot build the package, but if you are able to do that yourself you can try to see if the problem is fixed there. The same files are also in github, but you need to build the package yourself there too. I'm working with a minor release of vegan (2.0-10) which may be published on Monday 9 Dec, but there are no guarantees that it will have this envfit fix or be released like planned (you know, the best laid plans of mice and men...) 

It may be easiest to see if a constant "variable" is the culprit, and remove that if needed. If this is not the case, we need more info and a *reproducible* example. We haven't got any now, and I cannot reproduce your problem.

Cheers, Jari Oksanen

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Eduard Szöcs
    

    

      
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Hai,

building and installing from github is quite easy with the devtools
package (thanks to Hadley!):

# install devtools
install.packages('devtools')
require(devtools)

# install vegan from github
install_github('vegan', 'jarioksa')


Cheers,

Eduard Sz?cs

        
On 12/05/2013 02:07 PM, Jari Oksanen wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Hadley Wickham
    

    

      
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BTW I recommend using this form:

install_github('jarioksa/vegan')

Hadley

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jari Oksanen
    

    

      
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It is easy if you have C and Fortran compilers plus unix tools. I assume most people do not have those. Then 'easy' is quite different a concept.

Cheers, Jari Oksanen
---- alkuper?inen viesti ----
L?hett?j?: Hadley Wickham
L?hetetty:  05.12.2013, 16:19
Vastaanottaja: Eduard Sz?cs
Kopio: r-sig-ecology at r-project.org
Aihe: Re: [R-sig-eco] NA error in envfit

            

      
      
      
    

        
BTW I recommend using this form:

install_github('jarioksa/vegan')

Hadley

--
http://had.co.nz/

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      Mitchell, Kendra
    

    

      
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Thanks, makes sense to remove a variable that has no variation and it fixed the issue.  And that is much easier than building and installing from source.


--
Kendra Maas Mitchell, Ph.D.
Post Doctoral Research Fellow
University of British Columbia
604-822-5646

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hadley Wickham
    

    

      
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It's not that hard:

* windows: just go to http://cran.r-project.org/bin/windows/Rtools/,
then download and run the installer.
* mac: download xcode from the app store and gfortran from
http://cran.r-project.org/bin/macosx/tools/
* linux: you're on linux, you can figure it out yourself ;)

Hadley

        
On Thu, Dec 5, 2013 at 9:04 AM, Jari Oksanen <jari.oksanen at oulu.fi> wrote: