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
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@r-project.org mailing list
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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@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@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.
