[R-sig-ME] glmmADMB fails to fit poisson data
Ben Bolker
bbolker at gmail.com
Sat Jun 11 02:29:11 CEST 2016
* I can appreciate your frustration that glmmADMB doesn't work
out of the box on what seems initially to be a simple problem,
and I appreciate that you are being reasonably diplomatic about
it (not everyone is), but ... it is surprisingly hard to make
a general-purpose solve that works for every data set. glm()
works so well because it uses special-purpose algorithms for
a particular class of models that's narrower than what glmmADMB
can do.
* The particular problem is that for Poisson responses with
very large means, the coefficient of variation of the data
also becomes very small. That means that values that are a little
bit off the mean become very unlikely, so unlikely that they
underflow (the probabilities become numerically zero). I can
get your example to work if I set the starting value close enough:
set.seed(101)
d <- data.frame(x=rpois(100, lambda=8000))
library(glmmADMB)
glmmadmb(x~1, family="poisson", data=d)
glmmadmb(x~1, family="poisson", data=d,
start=list(fixed=log(7500))) ## works
... it does, however, fail with fixed=log(7000).
* the "mysterious" poiss_prob_bound (which *is* documented in
?admbControl, so it may be obscure but it's not completely mysterious ...)
was added to fix a problem that another user was having with
another data set ... if you
file.show(system.file("tpl","glmmadmb.tpl",package="glmmADMB"))
and dig around, you'll find that glmmADMB bumps up the probability of
a Poisson by 1e-6 or 1e-10 (in different optimization phases) to prevent
a value of exactly zero. There *is* probably a better way to do this -
there are approximations of the Poisson that work very well in such
small ranges, and they could be used instead - but there is also
a reasonably unending number of such edge cases, and not that many
person-hours to deal with them.
* You could try the glmmTMB package, which is a more modern
eventually-replacement for glmmADMB, and which seems
to work on this particular problem -- but be warned that it's
in development, so you may find holes!
devtools::install_github("glmmTMB/glmmTMB",sub="glmmTMB")
library(glmmTMB)
glmmTMB(x~1, family="poisson", data=d)
* if you have a reproducible example of 'dramatic stop that
does not reach the top level and so cannot be caught with
tryCatch' that would be useful. Maybe we can help resolve
that (more general) problem.
* Andrew Gelman has stated a principle called the "folk theorem of
statistical computing": When you have computational problems, often
there’s a problem with your model.
http://andrewgelman.com/2008/05/13/the_folk_theore/
In this case, I think the issue is that in real life (unless you're
in a field like particle physics), Poisson models are generally
not great models for processes with large means -- the coefficient
of variation is way too small to be realistic. This works with
a negative binomial ...
set.seed(101)
d2 <- data.frame(x=rnbinom(100, mu=8000, size=2))
glmmadmb(x~1,data=d2,family="nbinom")
(I can appreciate that you may have started with a neg binom
and come to the Poisson in part as a way of trying to simplify
your problem so you could diagnose it ...)
cheers
Ben Bolker
> While this is a “solution”, I would expect this kind of fit to work
> “off-the-box” (it certainly does with the standard glm function). Can
> someone comment on this. I am not an expert on GLMs and needed
> something that would fit ZINB + random effects (admittedly the deep
> end of GLMs) and was excited to find glmmADMB, but using it has proven
> rather frustrating because it often fails (with a dramatic stop that
> does not reach the top level and so cannot be caught with tryCatch,
> nonetheless) and after I found the above example, I am not so sure it
> is always for a good reason.
> Thanks,
> Vladimir
>
>
>
> Session:
>
>> sessionInfo()
On 16-06-09 07:48 PM, Vladimir Trifonov wrote:
> Hi,
>
> Why is the following “trivial” model fit failing? After all, we are
> fitting a Poisson GLM on a Poisson data.
>
> --------
>> glmmadmb(rpois(100, lambda=8000)~1, family="poisson")
> Hessian is 0 in row 1
> This means that the derivative if probably identically 0 for this
parameter
> Error in matrix inverse -- matrix singular in inv(dmatrix)
> Estimated covariance matrix may not be positive definite
> 1e+20
> Estimated covariance matrix may not be positive definite
> 1e+20
>
> GLMM's in R powered by AD Model Builder:
>
> Family: poisson
> link = log
>
> I tried varying the number of samples (100 above), the mean (8000
above) and this fails. Here is another attempt (with a different
kind of fail)
>> glmmadmb(rpois(100, lambda=50)~1, family="poisson")
> Parameters were estimated, but standard errors were not: the most
likely problem is that the curvature at MLE was zero or negative
> Error in glmmadmb(rpois(100, lambda = 50) ~ 1, family = "poisson") :
> The function maximizer failed (couldn't find parameter file)
Troubleshooting steps include (1) run with 'save.dir' set and inspect
output files; (2) change run parameters: see '?admbControl';(3) re-run
with debug=TRUE for more information on failure mode
> In addition: Warning message:
> running command './glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had
status 1
> --------
> After some trial and error, the only thing I found that “works” (with
a warning about the covariance matrix) consistently is to set a
“mysterious” poiss_prob_bound = FALSE
>
> --------
>> glmmadmb(rpois(100, lambda=50)~1, family="poisson",
admb.opts=admbControl(poiss_prob_bound=FALSE))
> Estimated covariance matrix may not be positive definite
> 0.020141
> Estimated covariance matrix may not be positive definite
> 0.020141
>
> GLMM's in R powered by AD Model Builder:
>
> Family: poisson
> link = log
>
> Fixed effects:
> Log-likelihood: -327.749
> AIC: 657.498
> Formula: rpois(100, lambda = 50) ~ 1
> (Intercept)
> 3.904998
>
> Number of observations: total=100
> --------
>
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