glmm question
I think you would be better off to start with a mixed effects model with a random effect for site and a fixed effect for year. All a random effect is doing is to model the correlation between responses allowing for other variables, in other words the residuals, by conditioning on a variable that is unobserved. For the years there are only 3 so it is just as easy or easier to model them using a known variable, the actual year. It is also difficult to think of them as a random sample of years. Now for the sites you would expect the same, that the 3 measurements within a site, representing the 3 years would be correlated. Now it is reasonable to model them using a random effect, as otherwise there would need to be a fixed effect for each site, a large number of parameters. It is possible that this random effect has variance zero then the model reverts to a standard glm.
On 14 May 2015 at 22:55, Joaqu?n Aldabe <joaquin.aldabe at gmail.com> wrote:
Thanks a lot Ken for your response. I had decided to use mix model with random effects because I have repeated measures in each field (one per year). If I perform a glm, how can I manage the pseudoreplication? (repeated counts on the same field) I have one data per field per year. So, no hierarchical or nested structure of the data. Can I use field as a random effect anyway? Thanks a lot for your help. Cheers, Joaqu?n. 2015-05-13 19:17 GMT-03:00 Ken Beath <ken.beath at mq.edu.au>: Having a random effect with only 3 levels is not recommended, it usually
gives problems fitting. There are also some philosophical questions about its use as a random effect. A random effect for field is reasonable, but you may be fitting too many parameters. With only 57 observations it is easy to overfit the models, and a standard linear model may be all that is necessary. On 14 May 2015 at 07:15, Joaqu?n Aldabe <joaquin.aldabe at gmail.com> wrote:
Hello, this is Joaqu?n Aldabe from Uruguay. I?m trying to model shorebird counts (Buff breasted Sandpiper, BBSA) with glmm (using lme4 package), using continuous variables (grass height, field area, forest cover) and one factor variable (presence/absence of other shorebird species: American Golden Plover, AMGP). I sampled 19 fields during three years in December. I?m interested in identifying predictors correlated with BBSA counts. I used Year as a random effect as I?m not interested in Year as a fix effect and because fields were counted three times (pseudoreplication). The model doesn?t converge, and the output showed that the factorial variable has not a significant effect. This is weird as in every field I observed the Buff breasted Sandpiper I also observed the other species. When I take AMGP out, the model runs ok. This is the model I?m trying to run: mysub3.3<-glmer(BBSA~Grass_height+Field_area+Field_enclosure_700m+Grass_height*Field_enclosure_700m+fAMGP+(1|fYear),family="poisson", data=mysub3.2) continuous variables were scaled. I can send de data frame if somebody is interested. Thanks in advanced for helping me on my master thesis. Cheers, Joaqu?n. -- *Joaqu?n Aldabe* *Grupo Biodiversidad, Ambiente y Sociedad* Centro Universitario de la Regi?n Este, Universidad de la Rep?blica Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha *Departamento de Conservaci?n* Aves Uruguay BirdLife International Canelones 1164, Montevideo https://sites.google.com/site/joaquin.aldabe <https://sites.google.com/site/perfilprofesionaljoaquinaldabe> [[alternative HTML version deleted]]
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-- *Ken Beath* Lecturer Statistics Department MACQUARIE UNIVERSITY NSW 2109, Australia Phone: +61 (0)2 9850 8516 Building E4A, room 526 http://stat.mq.edu.au/our_staff/staff_-_alphabetical/staff/beath,_ken/ CRICOS Provider No 00002J This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Faculty of Science, Department of Statistics or Macquarie University.
-- *Joaqu?n Aldabe* *Grupo Biodiversidad, Ambiente y Sociedad* Centro Universitario de la Regi?n Este, Universidad de la Rep?blica Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha *Departamento de Conservaci?n* Aves Uruguay BirdLife International Canelones 1164, Montevideo https://sites.google.com/site/joaquin.aldabe <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
*Ken Beath* Lecturer Statistics Department MACQUARIE UNIVERSITY NSW 2109, Australia Phone: +61 (0)2 9850 8516 Building E4A, room 526 http://stat.mq.edu.au/our_staff/staff_-_alphabetical/staff/beath,_ken/ CRICOS Provider No 00002J This message is intended for the addressee named and may...{{dropped:9}}