Hank Stevens wrote:
d> HI Ben and Spencer, | Thank you very much for your help. | | 1. The QQ plots look normal, but highlight the lack of balance (from one | to dozens of reps per treatment combo). | 2. The MCMC sample traces look (in my limited experience) without | peculiarities, and the densityplots are all quite symmetrical and | normal-ish. | 3. Simulations (lmer::simulate) of the null hypothesis indicate that | F-stats as large (or larger) than my observed F-stats are VERY unlikely, | under the null hypothesis. | | As I learn anything else useful, I will be happy to share. | Cheers, | Hank | ~ #3 pretty much seals it for me -- since that is really what the F test is trying to test. ~ It's a little hard to reconcile #2 and #3, though ... I would think you could move on at this point, but just for laughs -- are you using mcmcpvalue on a single contrast, or multiple parameters? If the former, does it seem to agree with the results of HPDinterval() or quantile()? If the latter, is there something about the _combinations_ of parameters that is wonky? ~ Don't forget my earlier comment about whether what you are testing (p-values of main effects in the presence of interactions) actually makes sense ... ~ cheers ~ Ben