Philippe Hensel
2010-Nov-17 22:28 UTC
[R] Trouble with mixed model anova (incl. random block)
Dear R community, I have slightly unbalanced survey/land elevation data (over 7,000 data points, grouped according to 60 transects, 30 in each of two treatments). Observations in both treatments are taken simultaneously, and the surveying of all 60 transects took 22 days. Comparisons among treatments have to be restricted to the same days the two treatments were sampled. I think the following model would be appropriate (at least at a first cut): Elevation Day (Random block) Treatment (Fixed) Day x Treatment (Random, error for Treatment) Transect (Day, Treatment) (Random) Point (Transect, Day, Treatment) (Random - residual error) Question: What are good candidates for algorithms to test this nested error anova? I have been trying lme() and lmer(), but I am confused as to how I should code for the nested error structure. I have tried: lme(Elevation ~ Treatment, random = ~Day | Transect, data) lmer(Elevation ~ Treatment + (1|Day / Transect), data) I am not yet very familiar with the R output, so it is hard for me to figure out if I have written the model statements correctly. How do I code for Day x Transect to make sure that it is being used as the error term for evaluating the fixed Treatment effect? How do I code for Transect(Day, Treatment)? In the anova output for the lme function, I get a highly significant intercept, but a non-significant Treatment effect (p=0.34). In the anova output for the lmer function, I get a significant Treatment effect (p = 0.03). How can I reconcile these two? The log-likelihoods are similar: 15183 (lme) and 15189 (lmer). Values of AIC and BIC are also similar between the two models. Before I go any further and compare to an intercept-only model (no Treatment effects), I wanted to make sure I chose the correct path and interpret correctly. Thank you in advance for any assistance. Yours, -Philippe -- Philippe Hensel, PhD Physical Scientist NOAA National Geodetic Survey 1315 East-West Hwy. Silver Spring MD 20910 (301) 713 3198 ext. 137