On Sat, 2008-03-15 at 12:48 -0500, daniel jupiter wrote:
> Hi all,
>
> I apologize for what might be a silly question.
>
> I am interested in doing a one way anova.
> This is not too hard in and of itself, either with anova, aov or oneway.test
> .
>
> However, I need to
> 1) get pvalues,
if obj is the result of anova, aov, oneway.test, then
str(obj) ## for anova
str(summary(obj)) ## for aov
str(obj) ## for oneway.test
to find the names of the elements of obj that contain the p-values of
the various tests/models. In the first two you are looking for the
component "Pr(>F)" and the latter is obvious ("p.value")
For summary(aov) objects, the result is a list so this gets the p-value
you need:
obj[[1]]$`Pr(>F)` or obj[[1]][,5]]
for anova then this:
obj$`Pr(>F)` or obj[,5]
note the quoting of the component name using backticks.
For oneway.test
obj$p.value
> 2) do a posthoc analysis with Tukey HSD,
?TukeyHSD for the results of aov
> 3) and have (sometimes) an unbalanced design.
See ?lme in package nlme
>
> I just can't seem to put all the pieces together.
>
> Any suggestions?
I'm not sure what the problem is here - you don't say. All of what I say
above is documented in the relevant help pages for the various functions
and using str() is a basic tenet of using R and looking at returned
objects.
Ok, you might have needed help with getting the p-values for some of
those tests/models, but 2) and 3) are answered on ?aov
For what you describe, stick with aov for balanced designs if you want
to do TukeyHSD as there is a method for aov objects (otherwise) you'll
need to refit the model.
For unbalanced designs, check out lme and for that you may need to
get/borrow the book by Pinhiero and Bates, reference details of which
are given in item [7] on:
http://www.r-project.org/doc/bib/R-books.html
>
> Thanks in advance,
>
> Dan.
>
HTH
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
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