[R] How to obtain the coefficients from a summary of aov ?

Wed Apr 21 20:47:25 CEST 2010

Slight addition below;

On 2010-04-21 10:51, David Winsemius wrote:
>
> On Apr 21, 2010, at 12:36 PM, David Winsemius wrote:
>
>>
>> On Apr 21, 2010, at 12:09 PM, Andrea Bernasconi DG wrote:
>>
>>> Thank you David,
>>>
>>> but how to get the value of 0.015939 present in s.npk.aov, and not
>>> given by s.npk.aov$coef["block","Pr(>F)"] ?
>>
>> ??? That's not a coefficient. It's a p-value.
>
>  > str(s.npk.aov)
> List of 1
> $ :Classes ‘anova’ and 'data.frame': 8 obs. of 5 variables:
> ..$ Df : num [1:8] 5 1 1 1 1 1 1 12
> ..$ Sum Sq : num [1:8] 343.3 189.3 8.4 95.2 21.3 ...
> ..$ Mean Sq: num [1:8] 68.7 189.3 8.4 95.2 21.3 ...
> ..$ F value: num [1:8] 4.447 12.259 0.544 6.166 1.378 ...
> ..$ Pr(>F) : num [1:8] 0.01594 0.00437 0.4749 0.0288 0.26317 ...
> - attr(*, "class")= chr [1:2] "summary.aov" "listof"
>
> So the p-values are the inside the first element
>
>  > s.npk.aov[[1]][1,5]
> [1] 0.01593879
>
> Or.... experimenting a bit ..
>
>  > s.npk.aov[[1]]['Pr(>F)']
> Pr(>F)
> block 0.01594 *
> N 0.00437 **
> P 0.47490
> K 0.02880 *
> N:P 0.26317
> N:K 0.16865
> P:K 0.86275
> Residuals
> ---
> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>  > s.npk.aov[[1]]['Pr(>F)'][[1]]
> [1] 0.015938790 0.004371812 0.474904093 0.028795054 0.263165283
> 0.168647879 0.862752086
> [8] NA
>  > s.npk.aov[[1]]['Pr(>F)'][[1]][1]
> [1] 0.01593879

or, if you prefer:

  s.npk.aov[[1]]['block', 'Pr(>F)']
#[1] 0.01593879

  -Peter Ehlers

>
>
>
>>>
>>> On the other, the procedure to extract coefficients from a summary of
>>> lm or aov should be the same.
>>
>> I think one generally extracts the coefficients from the model, rather
>> than from summary(model):
>>
>> > coef(npk.aov)
>> (Intercept) block2 block3 block4 block5 block6 N1
>> 51.8250000 3.4250000 6.7500000 -3.9000000 -3.5000000 2.3250000 9.8500000
>> P1 K1 N1:P1 N1:K1 P1:K1
>> 0.4166667 -1.9166667 -3.7666667 -4.7000000 0.5666667
>>
>> > coef(npk.lm)
>> (Intercept) block2 block3 block4 block5 block6 N1
>> 51.8250000 3.4250000 6.7500000 -3.9000000 -3.5000000 2.3250000 9.8500000
>> P1 K1 N1:P1 N1:K1 P1:K1 N1:P1:K1
>> 0.4166667 -1.9166667 -3.7666667 -4.7000000 0.5666667 NA
>>
>>
>>
>>>
>>> Andrea
>>>
>>> On 21 Apr, 2010, at 3:20 PM, David Winsemius wrote:
>>>
>>>>
>>>> On Apr 21, 2010, at 8:37 AM, Andrea Bernasconi DG wrote:
>>>>
>>>>> Dear Madame, Dear Sir,
>>>>>
>>>>> I am able to obtain the coefficients from a 'summary' of 'lm', but
>>>>> NOT from a 'summary' of 'aov'.
>>>>> The following example shows my steps.
>>>>>
>>>>> ## Initialize
>>>>> rm(list = ls()) # remove (almost) everything in the working
>>>>> environment
>>>>
>>>> @#$%^&*() DON'T DO THAT.... luckily I left off the "l" when I copied
>>>> and pasted but otherwise this would have trashed my workspace.
>>>>
>>>>> utils::data(npk, package="MASS") # get data
>>>>> model <- yield ~ block + N*P*K
>>>>>
>>>>> ## Using lm
>>>>> npk.lm <- lm(model, npk)
>>>>> ( s.npk.lm <- summary(npk.lm) )
>>>>>
>>>>> ...
>>>>> Estimate Std. Error t value Pr(>|t|)
>>>>> (Intercept) 54.8750 0.8021 68.415 < 2e-16 ***
>>>>> block1 1.7125 1.3893 1.233 0.24131
>>>>> block2 1.6792 0.8021 2.093 0.05822 .
>>>>> block3 -1.8229 0.5672 -3.214 0.00744 **
>>>>> ...
>>>>>
>>>>> s.npk.lm$coef["block1","Pr(>|t|)"] # this works
>>>>> [1] 0.2413061
>>>>>
>>>>> ## Using aov
>>>>> npk.aov <- aov(model, npk)
>>>>
>>>> str(npk.aov)
>>>>
>>>>> npk.aov$coefficients
>>>> (Intercept) block2 block3 block4 block5 block6 N1
>>>> 51.8250000 3.4250000 6.7500000 -3.9000000 -3.5000000 2.3250000
>>>> 9.8500000
>>>> P1 K1 N1:P1 N1:K1 P1:K1 N1:P1:K1
>>>> 0.4166667 -1.9166667 -3.7666667 -4.7000000 0.5666667 NA
>>>>
>>>> Or reading the help pages one might have tried, although I will
>>>> admit that the differences in parametrization confounded my efforts
>>>> at describing a linear combination of those results to create the
>>>> simpler result offered above:
>>>>
>>>> ?model.tables
>>>>> model.tables(npk.aov, "effects")
>>>> Tables of effects
>>>>
>>>> block
>>>> block
>>>> 1 2 3 4 5 6
>>>> -0.850 2.575 5.900 -4.750 -4.350 1.475
>>>>
>>>> N
>>>> N
>>>> 0 1
>>>> -2.8083 2.8083
>>>>
>>>> P
>>>> P
>>>> 0 1
>>>> 0.5917 -0.5917
>>>>
>>>> K
>>>> K
>>>> 0 1
>>>> 1.9917 -1.9917
>>>>
>>>> N:P
>>>> P
>>>> N 0 1
>>>> 0 -0.9417 0.9417
>>>> 1 0.9417 -0.9417
>>>>
>>>> N:K
>>>> K
>>>> N 0 1
>>>> 0 -1.175 1.175
>>>> 1 1.175 -1.175
>>>>
>>>> P:K
>>>> K
>>>> P 0 1
>>>> 0 0.14167 -0.14167
>>>> 1 -0.14167 0.14167
>>>>
>>>>>
>>>>> ( s.npk.aov <- summary(npk.aov) )
>>>>>
>>>>> ...
>>>>> Df Sum Sq Mean Sq F value Pr(>F)
>>>>> block 5 343.29 68.659 4.4467 0.015939 *
>>>>> N 1 189.28 189.282 12.2587 0.004372 **
>>>>> P 1 8.40 8.402 0.5441 0.474904
>>>>> ...
>>>>>
>>>>> s.npk.aov$coef["block","Pr(>F)"] # this does NOT works
>>>>>
>>>>> ...
>>>>> NULL
>>>>> ...
>>>>>
>>>>> How to obtain the coefficients from a 'summary' of 'aov' ?
>>>>>
>>>>> In advance, I thank you very much for your eventual answer.
>>>>>
>>>>> Sincerely, Andrea Bernasconi
>>>>>
>>>>> mobile: +41 79 621 74 07
>>>>> URL:
>>>>> http://web.me.com/andrea.bernasconi.dg/Andrea_Bernasconi_DG_home_page/HOME.html
>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>
>>>> David Winsemius, MD
>>>> West Hartford, CT
>>>>
>>>
>>> mobile: +41 79 621 74 07
>>>
>>>
>>>
>>>
>>>
>>>
>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>> ______________________________________________
>> 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.
>
> David Winsemius, MD
> West Hartford, CT
>
> ______________________________________________
> 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.
>
>

-- 
Peter Ehlers
University of Calgary