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:dwinsem...@comcast.net]
Sent: Thu 5/24/2012 1:54 PM
To: Nathan Svoboda
Cc: r-help@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
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