[R] anova p value extraction

[Abhijit Dasgupta]

What works, amazingly, is
summary(pb)$"Pr(>F)" [note the quotes]

Abhijit

On Wed, 07 May 2008 18:17:09 -0700
"H. Paul Benton" <hpbenton at scripps.edu> wrote:

> Yea the anova object seems to be odd. It's not S4 so that's why I tried originally the attr() funtion but....
> 
> summary(pb)$Pr(>F)
> 
> Error: unexpected '>' in "summary(pb)$Pr(>"
> > summary(pb)$Pr
> 
> NULL
> > summary(pb)@Pr(>F)
> 
> Error: unexpected '>' in "summary(pb)@Pr(>"
> > summary(pb)@Pr(F)
> 
> Error: no slot of name "Pr" for this object of class "summary.aov"
> In addition: Warning message:
> trying to get slot "Pr" from an object (class "summary.aov") that is
> not an S4 object
> >
> 
> Research Programmer & Technician
> The Scripps Research Institute
> Mass Spectrometry Core Facility
>   o The
>  /
> o Scripps
>  \
>   o Research
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> 
> 
> 
> markleeds at verizon.net wrote:
> >  Hi: it's probably the Pr(> F) element so just access it by
> >
> > sum<-summary(whatever).
> >
> > then sum$Pr(>F) will probably work. But make sure that's it because 
> > usually the name is pval or pvalue etc so I'm
> > surprised about the weird name.
> >
> >
> >
> >
> > On Wed, May 7, 2008 at  8:47 PM, Paul Benton wrote:
> >
> >> hello all,
> >>
> >> Quick question, how do I get the p value out of the anova?
> >>
> >> Thanks,
> >>
> >> Paul
> >>
> >>> pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> >>> summary(pb)
> >>             Df     Sum Sq    Mean Sq F value  Pr(>F)
> >> grF          3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
> >> Residuals   14 3.0783e+10 2.1988e+09
> >> ---
> >> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> >>> str(summary(pb))
> >> List of 1
> >>  $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
> >>   ..$ Df     : num [1:2] 3 14
> >>   ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
> >>   ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
> >>   ..$ F value: num [1:2] 4.22   NA
> >>   ..$ Pr(>F) : num [1:2] 0.0253     NA
> >>  - attr(*, "class")= chr [1:2] "summary.aov" "listof"
> >>> attr(summary(pb), "Pr(>F)")
> >> NULL
> >>
> >> ______________________________________________
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> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Abhijit Dasgupta