On Thu, May 15, 2008 at 9:22 AM, Luis Cayuela <[EMAIL PROTECTED]> wrote: > Hi everybody,
> I am trying to fit a model with the lmer function for mixed effects. I have > an experimental design consisting of 5 field plots. Each plot is divided in > 12 subplots where the influence of three factors on the growing of tree > seedlings is tested: (1) seed (1 = presence; 0 = absence); (2) seedling > species (oak holm vs. pine); (3) treatment (three different treatments). In > each of these subplots we planted 13 seedlings. Therefore I would have a > model with three fixed factors and one random factor (a block?). If I´m not > wrong the model would be as follows: > model2 <- lmer(Growing ~ Seed + Species + Treatment +(Seed + Species + > Treatment|Block), data) That's unlikely. This specification would fit 5 fixed effects parameters and 5, possibly correlated, random effects for each level of the Block factor. This would require estimating a total of 15 variance-covariance parameters for the random effects from the 5 blocks. Can you indicate how many random effects you expect to obtain and how many variance-covariance parameters would be involved? For example, a model with a simple random effect would be expressed as lmer(Growing ~ Seed + Species + Treatment + (1|Block), data) and would involve estimating the 5 fixed effects and one variance for the random effects. > My first question is: if the three fixed factors occur within-subjects > (considering the plot as a subject), is the model correctly defined (assuming > no interactions)? Should I specify the model in some other way? > > > > I second problem I had is that the factors are not crossed because some of > the seedling died during the experiment. This means that some factors are > nested. Specifically Species is nested within Seed and Block would be nested > within Treatment. I have tried to use the %in% specification for nested > designs but it does not work. > > > > model2 <- lmer(Growing ~ Seed + Species%in%Seed + Treatment +(Seed + Species > + Treatment|Block%in%Treatment), data) > > > > I get the following error: > > > > Error en lmer(Growing ~ Seed + Species %in% Seed + Treatment + : .. > > Leading minor of order 5 in downdated X'X is not positive definite > > > > I would appreciate some help to fit this model. > > > Thanks to everybody, > > Luis > > Luis Cayuela > Departamento de Ecología > Universidad de Alcalá > Crta. de Barcelona km. 33,600 > E-28871 Alcalá de Henares > Madrid > España > Tlf: (+0034) 918856407 > Fax: (+0034) 918854929 > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
