Re: [R] anova p value extraction

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Thu, 08 May 2008 14:44:09 +0100

quote the variable name or index the results from anova as a dataframe using [. Someone (Prof. Ripley IIRC, apologies if I got this wrong) once told me that backticks ` are the preferred, portable way of doing this, but in this case " quotes work as well.

> example(anova.lm) ## produces fit
> tmp <- anova(fit)
> str(tmp) ## notice the Classes line below

Classes ‘anova’ and 'data.frame':       5 obs. of  5 variables:
 $ Df     : int  1 1 1 1 45
 $ Sum Sq : num  204.1  53.3  12.4  63.1 650.7
 $ Mean Sq: num  204.1  53.3  12.4  63.1  14.5
 $ F value: num  14.116  3.689  0.858  4.360     NA
 $ Pr(>F) : num  0.000492 0.061125 0.359355 0.042471       NA

##drop the last entry corresponding to the row for Residuals:
> tmp[1:4,5]

[1] 0.0004921955 0.0611254598 0.3593550848 0.0424711387

This has nothing to do with S3 or S4, just knowing how to reference non-standard (probably not the correct terminology) names.

HTH G

On Wed, 2008-05-07 at 18:17 -0700, H. Paul Benton 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)$Pr
>
> NULL
> > summary(pb)@Pr(>F)
>
> Error: unexpected '>' in "summary(pb)@Pr(>"
> > summary(pb)@Pr(F)
>
> Error: no slot of name "Pr" for this object of class "summary.aov"
> In addition: Warning message:
> trying to get slot "Pr" from an object (class "summary.aov") that is
> not an S4 object
> >
>
> Research Programmer & Technician
> The Scripps Research Institute
> Mass Spectrometry Core Facility
> o The
> /
> o Scripps
> \
> o Research
> /
> o Institute
>
>
>
> markleeds_at_verizon.net wrote:
> > Hi: it's probably the Pr(> F) element so just access it by
> >
> > sum<-summary(whatever).
> >
> > then sum$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
> >>
> >> ______________________________________________
> >> R-help_at_r-project.org mailing list
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> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
> [[alternative HTML version deleted]]
>
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Received on Thu 08 May 2008 - 13:47:37 GMT

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