Skip to content

error message using glmmadmb

8 messages · RH Gibson, School Biological Sciences, Ben Bolker

Original
Ben Bolker
# 
I figured out the problem.

  I almost always use glmmadmb with the data= argument, putting my data
into a data frame rather than having my variables attach()ed (almost
always a bad idea) or floating around in the global workspace.  If you
do this:

mydata <- data.frame(spdiv,nsn,ara,rap,Insect.type,fsize,Site)
glmmadmb(spdiv~(nsn+ara+rap)*Insect.type+fsize+(1|Site),family="nbinom")

it ought to work.  However, it *should* work the way you specified -- I
will work on fixing the bug.

  thanks
    Ben Bolker
On 12-03-01 09:19 AM, RH Gibson, School Biological Sciences wrote:
Ben Bolker
# 
Ben Bolker <bbolker at ...> writes:

 [snip]
This should be fixed now (i.e. in glmmADMB 0.7.2.7).
  It's still a good idea to use the data= argument.
3 days later
RH Gibson, School Biological Sciences
# 
Thank you, I will let you know how I get on!
--On 01 March 2012 18:10 +0000 Ben Bolker <bbolker at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        
----------------------
RH Gibson, School Biological Sciences
Rachel.Gibson at bristol.ac.uk

  
  


  


      

    

    

      
      

        


  

        

      RH Gibson, School Biological Sciences
    

    

      
      #
    

  


  

      
Updated to latest version and now having new problems:

m3<- 
glmmadmb(x~nsn*Insect.type+ara*Insect.type+rap*Insect.type+fsize+offset(logTotal.grains)+(1|Site),data=data1, 
zeroInflation=TRUE, family="binomial")
Error in glmmadmb(x ~ nsn * Insect.type + ara * Insect.type + rap * 
Insect.type +  :
  The function maximizer failed (couldn't find STD file)
In addition: Warning message:
running command 'C:\WINDOWS\system32\cmd.exe /c "C:/Program 
Files/R/R-2.14.2/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500 
-maxph 5 -noinit -shess' had status 1


Can you help with this?

Many thanks, Rachel.

        
--On 01 March 2012 18:10 +0000 Ben Bolker <bbolker at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

        
----------------------
RH Gibson, School Biological Sciences
Rachel.Gibson at bristol.ac.uk

  
  


  


      

    

    

      
      

        


  

        

      Ben Bolker
    

    

      
      #
    

  


  

      
On 12-03-05 06:00 AM, RH Gibson, School Biological Sciences wrote:

            

      
      
      
    

        
This now means that the optimization failed for some reason.
  There are many reasons this can happen, mostly having to do with
too-sparse or unusual data.  Without knowing anything about your data,
the one thing that pops out is you are using a binomial family with
zeroInflation=TRUE.  If your response is a matrix of successes and
failures, that's unusual but plausible; if your response is a single 0/1
vector, then it doesn't make sense to use zero-inflation.  (If your
response is anything else it's odd too, although that probably would
have been caught earlier.)
  Try working through the troubleshooting steps under ?admbControl (and
running with verbose=TRUE to see exactly what AD Model Builder reports
as the problem).

  Ben Bolker

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      RH Gibson, School Biological Sciences
    

    

      
      #
    

  


  

      
That would make sense as I am able to fit a zero-inflated negative binomial 
model, but not just the binomial. I have tried poisson too, but this gave 
me the same error message as trying to fit the binomial.

The y variable is a count, offset by a sample total. There is 
overdispersion and a lot of zeros in the data. Does using the zero-inflated 
negative binomial make sense here?

Thanks.

        
--On 05 March 2012 08:25 -0500 Ben Bolker <bbolker at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
----------------------
RH Gibson, School Biological Sciences
Rachel.Gibson at bristol.ac.uk

  
  


  


      

    

    

      
      

        


  

        

      Ben Bolker
    

    

      
      #
    

  


  

      
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

        
On 12-03-05 08:52 AM, RH Gibson, School Biological Sciences wrote:

            

      
      
      
    

        
It very rarely makes sense to use the binomial and the negative
binomial to fit the same set of data; the binomial has a fixed
(typically known) upper limit, the Poisson and NB do not.  (The
exception to this is that people will sometimes use Poisson/NB models
when the upper limit is known but the observed frequency is very low
- -- this is especially common e.g. in epidemiology.)  ZINB, or plain
old NB, probably make the most sense.

  It's more interesting that you get an error message with the
Poisson, which may indicate some glmmADMB instability.  What are the
results of summary(data1)?  How many sites do you have?

  Ben Bolker

            

      
      
      
    

        
logTotal.grains)+(1|Site),data=data1, zeroInflation=TRUE,

            

      
      
      
    

        
")

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iQEcBAEBAgAGBQJPVMwkAAoJED2whTVMEyK9uVIIAIWj65sTlLNJWgOXsI1xZNaQ
pFD7dAOCotHlcFfDhulOZwuvcMwS5jnN459GMURSuyriQDrW1itQyqZ2y6EGpBuh
wj3OHG9vYBSUenkPBe+lBN5uXD62JPyKmfzp7djHs6zPeIWOGoxVXMTLHDBgmfky
kas5eOq91b/N88DpeL+duYAqjo+rtgD/h1kjMlELUwQXC3M3aeA1k78Lxx+Bahye
hsbTFJm/7cc7moBv9SpgO//qDJDqhKUa4z01XljibHl9J57m76/TY2M8/sFrOBDB
ig3h4Yc6ajoaSegaTn1NmzaISMMdTWVi1RWI4PL5Uu/SqLLxt4sloXuXMoF+4fY=
=xOtC
-----END PGP SIGNATURE-----

  
  


  


      

    

    

      
      

        


  

        

      RH Gibson, School Biological Sciences
    

    

      
      #
    

  


  

      
here is what happens when I tried the poisson:

            

      
      
      
    

        
m7<-glmmadmb(x~nsn*Insect.type+ara*Insect.type+offset(logTotal.grains)+(1|Site),data=data1, 
zeroInflation=TRUE, family="poisson")
Warning message:
In glmmadmb(x ~ nsn * Insect.type + ara * Insect.type + 
offset(logTotal.grains) +  :
  Convergence failed:log-likelihood of gradient= -223.949

I will email you the summary(data1) output separately.

I have 8 sites only.

Thanks for all the help.

        
--On 05 March 2012 09:22 -0500 Ben Bolker <bbolker at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
----------------------
RH Gibson, School Biological Sciences
Rachel.Gibson at bristol.ac.uk