[R] R Error: System is computationally singular

[David Winsemius]

On May 24, 2012, at 3:41 PM, Nathan Svoboda wrote:

> Re: [R] R Error: System is computationally singular
> Hi David,
>
> My apologies, I am not sure if this makes a big difference in your  
> assessment of the problem, but the results I just sent were only  
> from a portion (1/15) of the data. The dataset is rather large and  
> the computer I am currently using to set up the models is limited in  
> its capabilities to analyze large datasets. When I run the code you  
> provided on a larger portion of the data (1/2) this is the output I  
> receive:
>
>  LCOVER
> LOCS       1       2       3       4       5       6       7       9
>    0 1692196  630659  550623 6140352  180896  255512  785929   63756
>    1     141      30      48     279       9      14      36       1
>    2      17       4       5      14       3       3       4       1
>    3       0       0       0       3       0       0       1       0
>    5       2       0       0       0       0       0       0       0

I do not see linear dependence (aka computational singularity) in that  
data, but if there are no LOCS values of 4, an missing levels has been  
reported as a show-stopper with zinf models with pscl in the past.  
There could also easily emerge linear dependence if you tabulated the  
entire data set. If level 4 had 3 at level 4 of LCOVER or 1 at level 7  
then there would be linear dependence.

Marc Schwartz, a smarter guy than I,  has already suggested to you  
that your Poisson error structure might not be a good description of  
the data.


>
> Thanks again for your time and assistance,
>
> Nate
>
> Nathan Svoboda
> Graduate Research Assistant
> Mississippi State University
>
>
> From: David Winsemius [mailto:dwinsemius at comcast.net]
> Sent: Thu 5/24/2012 1:54 PM
> To: Nathan Svoboda
> Cc: r-help at r-project.org
> Subject: Re: [R] R Error: System is computationally singular
>
>
> On May 24, 2012, at 1:57 PM, Nathan Svoboda wrote:
>
> > Greetings,
> >
> > I am trying to fit a zero-inflated Poisson model using zeroinfl()
> > from the
> > pscl library. I have 5 covariates (4 continuous, 1 categorical); the
> > categorical variable has 7 levels.  I have had success fitting
> > models that
> > contain only the continuous covariates; however, when I add the
> > categorical
> > variable to any of the models (or if I run it by itself) I get the
> > following
> > error:
> >
> > Error in solve.default(as.matrix(fit$hessian)) :
> >
> >  system is computationally singular: reciprocal condition number =
> > 3.46934e-20
> >
> > The code I am using is:
> >
> > library(pscl)
> > f1 <- formula(LOCS ~ as.factor(LCOVER) + D_ROADS + D_WATER +  
> D_EDGE +
> > D_GRASS)
> > ZIP1 <- zeroinfl(f1, dist="poisson", link = "logit", data = FAWNS)
> >
> > There is no correlation between my covariates. Also, I tried
> > reducing my
> > categorical covariate to 3 levels and still receive the same error.
> > Can
> > anyone suggest why I may be getting this error when I add the
> > categorical
> > covariate?
> >
>
> What does this show:
>
> with( FAWNS, table(LOCS, LCOVER) )
>
> --
> David Winsemius, MD
> West Hartford, CT
>
>

David Winsemius, MD
West Hartford, CT