This post https://stat.ethz.ch/pipermail/r-sig-mixed-models/2009q1/001819.html may help you understand why the standard p-values in some cases are not the right thing to do and what one alternative is.
On Tue, Feb 14, 2012 at 3:36 PM, Xiang Gao <xianggao2...@gmail.com> wrote: > Hi > > I am working on a Nested one-way ANOVA. I don't know how to implement > R code to test the significance of the random factor > > My R code so far can only test the fixed factor : > > anova(lme(PCB~Area,random=~1|Sites, data = PCBdata)) > numDF denDF F-value p-value > (Intercept) 1 12 1841.7845 <.0001 > Area 1 4 4.9846 0.0894 > > > Here is my data and my hand calculation. > >> PCBdata > Area Sites PCB > 1 A 1 18 > 2 A 1 16 > 3 A 1 16 > 4 A 2 19 > 5 A 2 20 > 6 A 2 19 > 7 A 3 18 > 8 A 3 18 > 9 A 3 20 > 10 B 4 21 > 11 B 4 20 > 12 B 4 18 > 13 B 5 19 > 14 B 5 20 > 15 B 5 21 > 16 B 6 19 > 17 B 6 23 > 18 B 6 21 > > By hand calculation, the result should be: > Source SS DF MS > Areas 18.00 1 18.00 > Sites 14.44 4 3.61 > Error 20.67 12 1.72 > Total 53.11 17 --- > > > MSareas/MSsites = 4.99 --- matching the R output > MSsites/MSE = 2.10 > Conclusion is that Neither of Areas nor Sites make differences. > > > My R code so far can only test the fixed effect : > > anova(lme(PCB~Area,random=~1|Sites, data = PCBdata)) > numDF denDF F-value p-value > (Intercept) 1 12 1841.7845 <.0001 > Area 1 4 4.9846 0.0894 > > > > -- > Xiang Gao, Ph.D. > Department of Biology > University of North Texas > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
