new version of lme4 - Log-Likelihood of model returned as "-Inf"
It looks like the proximal problem here is that you have non-integer responses in the Poisson distribution. I haven't dug in to figure out why this should cause a problem; having non-integer responses in a nominally Poisson response breaks the nominal statistical model, but normal GLMs can manage anyway, and there's *probably* no reason that the internal lme4 code couldn't be made a bit more flexible. Where do your non-integer responses come from? I would also comment offhand that trying to fit a random effect of (1|BatID/PlantID) seems rather optimistic; you have a total of 26 observations (after removing NAs), and 121 Bat:Plant combinations, so very few of the combinations are actually measured, and are measured at most twice ... the BatID:PlantID interaction is going to translate _almost_ to an observation-level random effect. When I fit without the single non-integer response, I get a zero variance estimate for the Bat:Plant interaction ... Ben Bolker
On 14-02-13 09:46 PM, juwb08 at hampshire.edu wrote:
Hi Ben Bolker,
I tried running the code with lme4 version 1.1-4, and receive a model
that I can print, but it still lacks the LogLikelihood. When I call
summary on that model I get a new error message.
"
Error in diag(vcov(object, use.hessian = use.hessian)) :
error in evaluating the argument 'x' in selecting a method for
function 'diag': Error in if (nonSymm > stopTol)
stop(sprintf("calculated variance-covariance matrix is non-symmetric
(tol=%f)", :
missing value where TRUE/FALSE needed
"
I had not received any error message with lme4 version 1.0-5 when
calling summary() on that model. Still lost about the -Inf as the
LogLikelihood.
cheers
Justin Baldwin
Quoting Ben Bolker <bbolker at gmail.com>:
Still haven't seen the data set ... cheers Ben Bolker On 14-02-12 06:14 PM, juwb08 at hampshire.edu wrote:
... the dataset failed to attach, so here it is. Sorry! Quoting juwb08 at hampshire.edu:
Hi All, I was working with Poisson glmms in lme4 last year in 2013 using Windows XP, lme4 version 0.999375-16 (2008-06-23) and R version 2.15.1 (2012-06-22), evaluating a set of candidate models with AIC to select the best ones. This worked well until I updated lme4 and R last month. I now updated to R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" and lme4 version 1.0-5 (2013-10-24), still Windows XP, and am running the same models again on the same data, and lme4 now returns "-Inf" for the log likelihood, so it can't calculate AIC. Using the previous versions, I got stable values for Log-Likelihoods and calculated AICs with them. Attached is a sample of the dataset and the code I am using. How can I get a Log-Likelihood estimate with the current versions of lme4 and R? Thanks in advance. Justin Baldwin Hampshire College, MA, USA
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