Hi Chris, You don't need to code categorical predictors with dummy variables. As long as they are factors, the function knows what to do (same for glmer and most others). I don't know if that would cause a problem, but it's possible that it could be wasting space. If that doesn't solve the problem, try writing to the mixed models list. Mollie
On 12 Jan 2012, at 11:54 AM, Christopher Rota wrote: > Hi Mollie, > > The variables 'BrnLight' through 'RedHit' represent categorical variables > describing tree condition. They are coded as dummy variables, and one tree > condition category (Green) is omitted from model specification and > interpreted as the intercept. The season (Autumn, Spring, Winter) and year > (Yr01, etc.) variables are coded in an identical manner. DBH and Start.Time > are of course continuous variables. > > On 1/12/2012 10:44 AM, Mollie Brooks wrote: >> On 12 Jan 2012, at 11:31 AM, Christopher Rota wrote: >> >>> Hi Mollie, >>> >>> Here is my code: >>> >>> fit<- glmmadmb(formula=count~BrnLight + BrnMod + BrnMPB + BrnSev + GrnHit + >>> GryHit + RedHit + Autumn + Spring + Winter + Yr01 + Yr12 + Yr23 + Yr34 + >>> Yr45 + Est.DBH.in + Start.Time + (1|Color.Combo) + (1|Observers), >>> data=beh.data, family='nbinom') >>> >> This looks ok, but I wonder, did you separate out levels of the categorical >> fixed effects? i.e. are BrnLight + BrnMod + BrnMPB + BrnSev levels of Brn, >> GrnHit + GryHit + RedHit levels of Hit, Autumn + Spring + Winter levels of >> season, and Yr01 + Yr12 + Yr23 + Yr34 + Yr45 levels of Yr ? >> >>> Thanks for the prompt response, >>> >>> Chris >>> >>> On 1/12/2012 10:27 AM, Mollie Brooks wrote: >>>> Hi Chris, >>>> I am using this function on a dataset larger than this, so I don't think >>>> that's the problem, but I could be wrong. >>>> Often, this error indicates that the model was mis-specified. Could you >>>> send the call to glmmadmb? >>>> thanks, >>>> Mollie >>>> >>>> Mollie Brooks >>>> Ph.D. Candidate >>>> NSF IGERT Fellow >>>> Biology Department >>>> University of Florida >>>> mbro...@ufl.edu >>>> http://people.biology.ufl.edu/mbrooks >>>> >>>> >>>> >>>> >>>> On 12 Jan 2012, at 11:18 AM, Christopher Rota wrote: >>>> >>>>> Dear R Users, >>>>> >>>>> I am running into some trouble when using glmmADMB version 0.7.1 and am >>>>> hoping someone in the R community may have some insight. >>>>> >>>>> I am trying to fit a rather large negative binomial mixed-effects model. >>>>> I have 3980 observations (counts of foraging attempts). My 'global' >>>>> model has 17 fixed effects and 2 random effects. Fixed effects consist >>>>> of both continuous and categorical variables. Each categorical variable >>>>> has at least 22 observations, most have considerably more. One random >>>>> effect is an 'observer' effect consisting of 11 different observers. >>>>> Each observer made at least 29 observations, but most made considerably >>>>> more. The other random effect in an 'individual bird' effect consisting >>>>> of 78 individual birds. There are at least 20 observations made on each >>>>> bird. >>>>> >>>>> This global model runs for about 10 minutes, then fails with the >>>>> following message: >>>>> Memory allocation error -- Perhaps you are trying to allocate too much >>>>> memory in your program >>>>> >>>>> When I monitor my computer performance with Windows Task Manager while >>>>> the model is running, I can watch Physical Memory Usage slowly tick up. >>>>> All of that increased memory use is attributed to glmmadmb.exe. I will >>>>> watch memory use for this program tick up to about 1.7GB, and that is >>>>> when the model fails. I am using a computer with a Windows Vista 32-bit >>>>> operating system with 4GB RAM. Is the problem simply that I do not have >>>>> enough memory on my computer to run this model? If indeed the problem is >>>>> a shortage of memory, is there any way to make glmmadmb.exe use memory >>>>> differently, or do I need to use a more powerful computer? >>>>> >>>>> Thank you for any insight. >>>>> >>>>> Chris Rota >>>>> >>>>> -- >>>>> Christopher Rota >>>>> Ph.D. Student >>>>> >>>>> University of Missouri >>>>> Fisheries and Wildlife Science >>>>> 302 Anheuser-Busch Natural Resources Building >>>>> Columbia, MO 65211 >>>>> >>>>> Office: 303O Anheuser-Busch Natural Resources Buildling >>>>> Email: ctr...@mail.missouri.edu >>>>> Phone: 573-239-6975 >>>>> Website: http://www.biosci.missouri.edu/avianecology/rota/index.html >>>>> Calendar: >>>>> http://www.google.com/calendar/embed?src=christopher.rota%40gmail.com&ctz=America/Chicago >>>>> >>>>> _______________________________________________ >>>>> R-sig-ecology mailing list >>>>> R-sig-ecology@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>>>> >>> -- >>> Christopher Rota >>> Ph.D. Student >>> >>> University of Missouri >>> Fisheries and Wildlife Science >>> 302 Anheuser-Busch Natural Resources Building >>> Columbia, MO 65211 >>> >>> Office: 303O Anheuser-Busch Natural Resources Buildling >>> Email: ctr...@mail.missouri.edu >>> Phone: 573-239-6975 >>> Website: http://www.biosci.missouri.edu/avianecology/rota/index.html >>> Calendar: >>> http://www.google.com/calendar/embed?src=christopher.rota%40gmail.com&ctz=America/Chicago >>> >>> >>> >> > > -- > Christopher Rota > Ph.D. Student > > University of Missouri > Fisheries and Wildlife Science > 302 Anheuser-Busch Natural Resources Building > Columbia, MO 65211 > > Office: 303O Anheuser-Busch Natural Resources Buildling > Email: ctr...@mail.missouri.edu > Phone: 573-239-6975 > Website: http://www.biosci.missouri.edu/avianecology/rota/index.html > Calendar: > http://www.google.com/calendar/embed?src=christopher.rota%40gmail.com&ctz=America/Chicago > > > _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
