Hello: I am using R mainly on windows XP, version 2.5. I´m a biologist, with a medium level statistics background. I have a problem stating a two-way factorial design where both factors are random. I´m using the lmer() function implemented in the Matrix package version 0.99.
My design is as follows: Two species were randomly selected from a total of 4 species. This species are present in five different populations, again selected at random. Five trees per species were selected randomly in each population and fruit number was estimated. The main question is to estimate variance components for species, population and their interaction. Since both species are present in each population, I figured they are not nested, but are crossed. There is no fixed factor. I conducted a normal aov() to estimate variance components manually via EMS approximation: fm1 <- aov(fruto~pop*spp, data=p1) to test the significance of the variance components I did: fm2 <- aov(fruto~pop+spp+Error(pop:spp), data=p1) Manually, the variance component for the interaction is negative, therefore I turned to lmer() to try to get a better estimate as well as confidence intervals. After invoking the Matrix library, I typed: fm3 <- lmer(fruto~(1|pop) + (1|spp) + (1|pop:spp), data=p1) During calculations I get an error which indicates that the variance components for pop and pop:spp are almost zero. The summary output presents variance components that do not resemble the manually estimated values (eg. sigma_pop = 3650 vs sigma_pop(reml) = 7840). If I conduct the analysis in SAS, with GLM and the random option, I get correct estimates of variance components. After reading a couple of help files, it looks like I need a fixed component, which I don´t know how to code (dummy coding?). My specific questions are: 1. Is my lmer formula correct? If not, how should it be stated? 2. Should I use another formula or command to estimate the interaction component? 3. Do I have to create a fixed factor in order to correctly use lmer()? I know I should have consulted Pinhero´s book, but I´m currently in Costa Rica, and the book is taking a long time to get here. Thanks in advance for all your help. I´m new in the mailing list, and I hope I´ve made myself clear enough. thanks Eric Fuchs Universidad de Costa Rica -- Eric J. Fuchs Biologo http://e.j.fuchs.googlepages.com/ __________________________________________ lex parsimoniae: entia non sunt multiplicanda praeter necessitatem ______________________________________________ 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.
