Greetings to all, This is my model: aov.fit<-aov(Y~A+B+C+D+E+A:C+A:E) In summary(aov.fit) all F values are comptuted by eg MS(A)/MS(Residuals). This is not correct (or what I want), except for F(B) and F(A:E). I suppose P values are not correct either. Is it possible with aov to define the way F computations will be done? I 'd like them to be like this: F(A)=MS(A)/MS(E), F(C)=MS(C)/MS(E), F(D)=MS(D)/MS(E), F(E)=MS(E)/MS(A:E), F(A:C)=MS(A:C)/MS(A:E) thanks
Howdy, In the past, I've just run the ANOVA as normal, and then just grabbed the appropriate MS for the estimation of F ratios. Eg, this will get you the MS in your anova object: summary(obj.aov)[[1]][3] or summary(obj.aov)$Mean And if you want a specific MS, summary(obj.aov)[[1]][[1,3]] or summary(obj.aov)[[1]]$Mean[1] Then you can just put whichever MS over whichever other MS, estimate your F-ratios, with something like: Ffact<- summary(obj.aov)[[1]]$Mean[1]/summary(obj.aov)[[1]]$Mean[3] estimate the p-values with: pFfact<-1-pf(Ffact, summary(obj.aov)[[1]]$Df[1], summary(obj.aov)[[1]]$Df[3]) and you're off to the races. You can also specify error strata in the aov() model, but then all you get is the MS and you have to estimate your F-ratios anyway (though the indexing is a little different). E.g., if you had a nested anova, you could specify it as: ex.aov<-aov(Fixed ~ Nested + Error(Nested/Fixed)) At least this way, the summary() doesn't give you the wrong F-ratios, so you aren't temped to interpret them incorrectly (as you would in the previous example). HTH, Mike Galanidis Alexandros wrote:> Greetings to all, > > This is my model: aov.fit<-aov(Y~A+B+C+D+E+A:C+A:E) > > In summary(aov.fit) all F values are comptuted by eg MS(A)/MS(Residuals). This is not correct (or what I want), except for F(B) and F(A:E). I suppose P values are not correct either. > > Is it possible with aov to define the way F computations will be done? I 'd like them to be like this: F(A)=MS(A)/MS(E), F(C)=MS(C)/MS(E), F(D)=MS(D)/MS(E), F(E)=MS(E)/MS(A:E), F(A:C)=MS(A:C)/MS(A:E) > > thanks > ______________________________________________ > R-help at 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. > >
Please look at the Error term in ?aov On Wed, Mar 17, 2010 at 4:25 AM, Galanidis Alexandros <agal@env.aegean.gr>wrote:> Greetings to all, > > This is my model: aov.fit<-aov(Y~A+B+C+D+E+A:C+A:E) > > In summary(aov.fit) all F values are comptuted by eg MS(A)/MS(Residuals). > This is not correct (or what I want), except for F(B) and F(A:E). I suppose > P values are not correct either. > > Is it possible with aov to define the way F computations will be done? I 'd > like them to be like this: F(A)=MS(A)/MS(E), F(C)=MS(C)/MS(E), > F(D)=MS(D)/MS(E), F(E)=MS(E)/MS(A:E), F(A:C)=MS(A:C)/MS(A:E) >For your example, it looks like mydata.aov <- aov(Y ~ A+B+C+D + Error(E/A), data=mydata) might be what you need. It isn't possible to be sure of the correct statement for your example without seeing the actual treatment plan. The standard split-plot design is specified with splplot <- data.frame(y=rnorm(72), blocks=factor(rep(1:6, each=12)), plots=factor(rep(rep(1:3, each=4), 6)), subplots=factor(rep(1:4, 18)), A=factor(rep(c(3,1,2, 3,1,2, 2,3,1, 3,2,1, 2,1,3, 1,2,3), each=4)), B=factor( c(4, 3, 2, 1, 1, 2, 4, 3, 1, 2, 3, 4, 3, 1, 2, 4, 4, 1, 2, 3, 2, 1, 3, 4, 2, 3, 4, 1, 4, 2, 3, 1, 1, 4, 2, 3, 3, 4, 1, 2, 1, 3, 4, 2, 2, 3, 4, 1, 4, 1, 3, 2, 3, 4, 1, 2, 3, 4, 2, 1, 3, 1, 4, 2, 4, 3, 1, 2, 1, 2, 3, 4))) splplot.aov <- aov(y ~ A*B + Error(blocks/plots/subplots), data=splplot) summary(splplot.aov)> summary(splplot.aov)Error: blocks Df Sum Sq Mean Sq F value Pr(>F) Residuals 5 2.0231 0.40463 Error: blocks:plots Df Sum Sq Mean Sq F value Pr(>F) A 2 0.2876 0.1438 0.1135 0.8938 Residuals 10 12.6646 1.2665 Error: blocks:plots:subplots Df Sum Sq Mean Sq F value Pr(>F) B 3 2.814 0.93797 0.8987 0.4493 A:B 6 3.358 0.55964 0.5362 0.7778 Residuals 45 46.965 1.04367>As you see, the correct F tests are automatically determined and displayed. Rich [[alternative HTML version deleted]]