[R] anova p value extraction

[Gavin Simpson]

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
 - attr(*, "heading")= chr  "Analysis of Variance Table\n" "Response: sr"
> tmp$`Pr(>F)`
[1] 0.0004921955 0.0611254598 0.3593550848 0.0424711387           NA
> tmp$"Pr(>F)"
[1] 0.0004921955 0.0611254598 0.3593550848 0.0424711387           NA
> tmp[,5]
[1] 0.0004921955 0.0611254598 0.3593550848 0.0424711387           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
> >> 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.
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
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