Dear Prof. Bates, Thank you for your reply. I did actually check the book at pages 89-92, but I have to say I found it a bit "cryptic", if not downright confusing, for a genetist like me. Any day of the week.
To use the example in the book, I cannot see why MACHINE is inner to WORKER. Or where the Pi = sum of df for the term estimatet at level i... To me it's just a two way anova with one random effect + one interaction. My df correspond to those in the book, but I calculated them in the "bog standard" way of 2 df for 3 machines, 5 df for 6 workers and 2 * 5 = 10 df for the interaction...oh well... I attach the datasest (I did a sample with replace = TRUE, should have thought of this earlier...). I hope thing would be clearer. It is obvious that if I consider day a "factor", as I have just one datapoint per day per line within regime, I end up using all my degrees of freedom: 2 df for 3 regimes 6 df for line within regime 8 df for day (9 days, day as factor) 16 df for regime * day 48 df for line * day total 80 df, with 0 df remaining for the error. A bit of a problem I daresay, but I did not collect the data! BUT I did calculate my anova considering day as a continuous variable, 2 df for 3 regimes 6 df for line within regime 1 df for day (day as a number) 2 df for regime * day 6 df for line * day total 17 df, with 63 df remaining for the error. I still do not get why the interaction term Regime*Day is not tested on the interaction Line-in-regime*Day... In my analysis LME is clumping Error and Line-in-regime*Day together, judging by the df I was talking about in my previuos email. To me it should be just another "bog standard" situation...But if I were smart enough to be a statistician I would not be here doing genetics ;) Regards, Federico Calboli Day Line Regime Matings 2 501 es 0.4 4 501 es 0.32989691 9 501 es 0.48484848 11 501 es 0.72727273 16 501 es 0.34042553 18 501 es 0.56470588 25 501 es 0.37509377 30 501 es 0.22222222 32 501 es 0.77777778 2 502 es 0.57142857 4 502 es 1.06666667 9 502 es 0.16 11 502 es 0.4 16 502 es 0.4 18 502 es 0.33333333 25 502 es 0.80808081 30 502 es 0.48 32 502 es 0.25531915 2 503 es 0 4 503 es 0.72727273 9 503 es 0.3 11 503 es 0.77777778 16 503 es 0.34042553 18 503 es 1.06666667 25 503 es 0.32989691 30 503 es 1.24444444 32 503 es 0.19153725 2 fb1 fb 0.72727273 4 fb1 fb 0.42105263 9 fb1 fb 0.32989691 11 fb1 fb 0.32323232 16 fb1 fb 0.37509377 18 fb1 fb 0.51612903 25 fb1 fb 0.4 30 fb1 fb 0.24742268 32 fb1 fb 0.24742268 2 fb2 fb 1.33333333 4 fb2 fb 0.25263158 9 fb2 fb 0.66666667 11 fb2 fb 1.06666667 16 fb2 fb 0.97959184 18 fb2 fb 0.42105263 25 fb2 fb 0.57142857 30 fb2 fb 1.15555556 32 fb2 fb 0.80808081 2 fb3 fb 0.18952106 4 fb3 fb 0.66666667 9 fb3 fb 1.22033898 11 fb3 fb 0.35955056 16 fb3 fb 1.68421053 18 fb3 fb 0.57461174 25 fb3 fb 0.93506493 30 fb3 fb 0.80808081 32 fb3 fb 0.57461174 2 mb1 mb 0.22222222 4 mb1 mb 0.3902439 9 mb1 mb 0.42105263 11 mb1 mb 0.48484848 16 mb1 mb 0.55555556 18 mb1 mb 1.68421053 25 mb1 mb 0.4 30 mb1 mb 0.16 32 mb1 mb 0.09523809 2 mb2 mb 0.77777778 4 mb2 mb 0.68817204 9 mb2 mb 0.25263158 11 mb2 mb 1.33333333 16 mb2 mb 0.5 18 mb2 mb 0.37509377 25 mb2 mb 0.16494845 30 mb2 mb 2.46153846 32 mb2 mb 0.47058824 2 mb3 mb 1.06666667 4 mb3 mb 0.5 9 mb3 mb 0.5 11 mb3 mb 0.38095238 16 mb3 mb 0.26373626 18 mb3 mb 0.87912088 25 mb3 mb 0.55555556 30 mb3 mb 0.74418605 32 mb3 mb 1.33333333 > >I think your calculation is based on using only within-strata >information whereas lme uses both within-strata and between-strata >information for estimates of effects. > >The way that we calculate denominator degrees of freedom is described >on pp. 90-91 of Pinheiro and Bates (2000). For each term in the >fixed-effects we determine the innermost level of the random effects >at which is it changing. Because Regime is constant for each Line it >has the fewest degrees of freedom but Day is changing within Line so >terms in Day have more degrees of freedom. Is this what you intended? > >I must admit I am having difficulty understanding the structure of the >experiment but it is still Monday morning for me so perhaps that is >not surprising. ========================= Federico C.F. Calboli Department of Biology University College London Room 327 Darwin Building Gower Street London WClE 6BT Tel: (+44) 020 7679 4395 Fax (+44) 020 7679 7096 [EMAIL PROTECTED] ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
