One comment: in the models I am considering some predictor variables also
vary anually:
occupancy_ij ~ predictor1_ij + predictor2_i + (1|territoryID_i) +
(1|year_j)
On Mon, Jun 22, 2009 at 5:37 PM, Andrew J Tyre wrote:
> Toni,
>
> I assume that your predictor variables vary by territory, and that your
> random effect is applied to the intercept, like this
>
> occupancy_ij ~ predictor1_i + predictor2_i + (1|territoryID_i) +
> (1|year_j)
>
> in that case, the territoryID random effect is "competing" to explain
> variation in occupancy between territories with predictors1 and 2. Hence
> the failure to converge.
>
> A better question to ask yourself is this: is the probability that a
> territory is occupied this year different depending on whether the
> territory was occupied last year? If yes, then you have AUTOCORRELATION,
> and that has to be handled differently - a random effect on territoryID
> influences the probability of the territory being occupied, as do the
> predictor variables, but that model still assumes that occupancy is
> independent from year to year. I do not know how to accomadate
> autocorrelation in a binomial model in lmer; in general, it isn't
> something that is easy to do.
>
> 1) You cannot use the estimates from lmer if it hasn't converged, in my
> opinion.
>
> 2) not sure ... looking forward to an answer from greater gurus.
>
> hth,
>
> Drew Tyre
>
> School of Natural Resources
> University of Nebraska-Lincoln
> 416 Hardin Hall, East Campus
> 3310 Holdrege Street
> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
> fax: +1 402 472 2946
> email: atyre2@unl.edu
> http://snr.unl.edu/tyre
> http://aminpractice.blogspot.com
>
>
>
> Toni Hernandez-Matias
> Sent by: r-sig-mixed-models-bounces@r-project.org
> 06/22/2009 09:54 AM
>
> To
> R-SIG-Mixed-Models@r-project.org
> cc
>
> Subject
> [R-sig-ME] problems with 'false convergence' in lmer
>
>
>
>
>
>
> Dear all,
>
> I am analyzing a data set with the 'lmer' function (lme4_0.999375-28).
> The dependent variable is binary: occupation status of a breeding site by
> a
> bird species (territory ocupied vs. non-ocupied).
> There are clustered observations: observations of the same territory for
> several years and observations of different territories in the same year.
> So
> I considered two random factors: territory identity and year.
> I considered several predictors which are standardized.
> I am using aic values to obtain the final model.
>
> The problem is that the program generates the warning message in most of
> the
> fitted models:
> In mer_finalize(ans) : false convergence (8)
>
> This probably happens because many territories are either occupied or
> non-occupied for many or all years in the study. [there are no problems
> when
> I include the random factor year in the formula, and I do not include the
> random factor territory identity]
>
> I added the option 'verbose=TRUE', and I found that the printed value of
> deviance does not match with that saved by the model object (I extract it
> using 'attr(summary(nameofthemodel),"AIC")$AIC').
>
> My questions are:
>
> (1) are the results (estimated parameters and se) of the fitted model
> correct? Can I use them?
>
> (2) how can I extract the deviance value of the printed table given by the
> 'verbose' option? I mean extract, as a R object. I need this because I am
> performing a large set of models and I consider those with better aic.
>
> Thank you very much in advance,
>
>
> Toni Hernandez
>
> --
> *********************************************************
>
> Antonio Hernandez Matias
>
> Departament de Biologia Animal (Vertebrats)
> Facultat de Biologia
> Universitat de Barcelona
>
> ***********************************************************
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-mixed-models@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
>
--
*********************************************************
Antonio Hernandez Matias
Departament de Biologia Animal (Vertebrats)
Facultat de Biologia
Universitat de Barcelona
Av. Diagonal, 645
Barcelona 08028
Spain
Telephone: +34-934035857
FAX: +34-934035740
e-mail: ahernandezmatias@ub.edu
***********************************************************
[[alternative HTML version deleted]]