# How to Code Random Nested Variables within Two-way Fixed Model in lmer or lme

4 messages
Open this post in threaded view
|

## How to Code Random Nested Variables within Two-way Fixed Model in lmer or lme

 Hi All, I am frustrated by mixed-effects model! I have searched the web for hours, and found lots on the nested anova, but nothing useful on my specific case, which is: a random factor (C) is nested within one of the fixed-factors (A), and a second fixed factor (B) is crossed with the first fixed factor: C/A A B A x B My question: I have a functioning model using the aov command (see below), and I would now would like to recode it, using a more flexible command such as lme or lmer. Once I have the equivalent syntax down, I would ideally like to re-run my analysis using "family = poisson", as CO is actually count data. I have a dataset including a response variable CO, measured once per Week (for 11 weeks) at 13 Locations. The 13 Locations are divided into 2 habitat types (Control and Treatment). Thus: CO is a continuous response variable, Week is a fixed categorical factor, Habitat is a fixed categorical factor, and Location is a random categorical factor nested within Habitat. Here is my model in R: mCO = aov(CO ~ Week * Habitat + Error(Location/Week)) summary(mCO) And the output: Error: Location            Df Sum Sq Mean Sq F value   Pr(>F)   Habitat     1 182566   182566   8.6519 0.01341 * Residuals 11 232115    21101                     Error: Location:Week               Df Sum Sq Mean Sq F value     Pr(>F)     Week          10 596431    59643 11.0534    7.5e-13 *** Week:Habitat 10 196349    19635   3.6389 0.0003251 *** Residuals    110 593551     5396                       Given that this is a mixed model, I believe the appropriate error terms are as follows: For the F test of Habitat, the denominator MS is that for location/habitat; For the F test of Week, the denominator MS is the residual; and For the F test of Habitat x Week, the denominator MS is the residual. My tinkering with lmer and lme have not produced results similar to the above For example, m. = lmer(CO ~ Week * Habitat + (1|Habitat/Location)) anova(m.) produces: Analysis of Variance Table                Df Sum Sq Mean Sq F value Week           10 596431    59643 11.0534 Habitat        1   28652    28652   5.3100 Week:Habitat 10 196349    19635   3.6389 Any coding advice would be greatly appreciated! Thanks for your consideration, Dave Robichaud         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
Open this post in threaded view
|