Hi, I am trying to do an analysis of variance for an unbalanced design. As a toy example, I use a dataset presented by K. Hinkelmann and O. Kempthorne in "Design and Anaylysis of Experiments" (p353-356). This example is very similar to my own dataset, with one difference: it is balanced. Thus it is possible to do an anaylsis using both: (1) anova, and (2) lmer. Furthermore, I can compare my results with the results presented in the book (the book uses SAS). In short:> using anova, I can reproduce the results presented in the book. > using lmer, I fail to reproduce the resultsHowever, for my "real" analysis, I need lmer - what do I do wrong? The example uses as randomized complete block desigh (RCBD) with a nested blocking structure and subsampling. response: height (of some trees) covariates: HSF (type of the trees) nested covariates: loc (location) block (block is nested in location) # the data (file: pine.txt) looks like this: loc block HSF height 1 1 1 210 1 1 1 221 1 1 2 252 1 1 2 260 1 1 3 197 1 1 3 190 1 2 1 222 1 2 1 214 1 2 2 265 1 2 2 271 1 2 3 201 1 2 3 210 1 3 1 220 1 3 1 225 1 3 2 271 1 3 2 277 1 3 3 205 1 3 3 204 1 4 1 224 1 4 1 231 1 4 2 270 1 4 2 283 1 4 3 211 1 4 3 216 2 1 1 178 2 1 1 175 2 1 2 191 2 1 2 193 2 1 3 182 2 1 3 179 2 2 1 180 2 2 1 184 2 2 2 198 2 2 2 201 2 2 3 183 2 2 3 190 2 3 1 189 2 3 1 183 2 3 2 200 2 3 2 195 2 3 3 197 2 3 3 205 2 4 1 184 2 4 1 192 2 4 2 197 2 4 2 204 2 4 3 192 2 4 3 190 # # using anova..... # m.aov = aov( height ~ HSF*loc + Error(loc/block + HSF:loc/block), data=d ) summary( m.aov ) # # I get: # Error: loc Df Sum Sq Mean Sq loc 1 20336 20336 Error: loc:block Df Sum Sq Mean Sq F value Pr(>F) Residuals 6 1462.33 243.72 Error: loc:HSF Df Sum Sq Mean Sq HSF 2 12170.7 6085.3 HSF:loc 2 6511.2 3255.6 Error: loc:block:HSF Df Sum Sq Mean Sq F value Pr(>F) Residuals 12 301.167 25.097 Error: Within Df Sum Sq Mean Sq F value Pr(>F) Residuals 24 529.00 22.04 # # however, using lmer.... # m.lmer = lmer( height ~ HSF*loc + HSF*(loc|block), data=d ) anova( m.lmer ) # # I get: # Analysis of Variance Table Df Sum Sq Mean Sq HSF 2 12170.7 6085.3 loc 1 1924.6 1924.6 HSF:loc 2 6511.2 3255.6 # # what is wrong # Thanks for your help, Lars