Re: [R] Running an ANOVA with a BY
Or with plyr there's a more flexible approach:
res.aov - dlply(warpbreaks, .(tension), function(x) aov(breaks ~ wool, data=x))
# aov results are stored in a list, you can directly extract what you want with
l*ply
l_ply(res.aov, function(x) print(summary(x)))
ldply(res.aov, function(x) data.frame( fitted(x)))
ldply(res.aov, coefficients)
HTH,
Xavier
- Mail Original -
De: Tobias Verbeke tobias.verb...@gmail.com
À: baxterj j...@vt.edu
Cc: r-help@r-project.org
Envoyé: Lundi 28 Septembre 2009 22h55:34 GMT +01:00 Amsterdam / Berlin / Berne
/ Rome / Stockholm / Vienne
Objet: Re: [R] Running an ANOVA with a BY
baxterj wrote:
I downloaded the package and got it to work with the coding:
model - function(df) {aov(values ~ WellID, data = twelldata)}
Hmm.. I guess you mean to use 'data = df' instead of 'data = twelldata'
ANOVA1way - dlply(twelldata, .(Analyte), model)
print(ANOVA1way)
This gives me degrees of freedom and sum of squares for each anova per
analyte. However, I cant get the summary(ANOVA1way) to work so that I can
get p-values, etc... How can I do this?
You need to extend your model function:
- extract the bits you want
- construct a result data frame
- return it
and use a ddply
For example (non-tested):
model - function(df) {
lmObj - lm(values ~ WellID, data = df)
summaryLmObj - summary(lmObj)
res - data.frame(intercept = coef(lmObj)[1],
adjr2 = summaryLmObj$adj.r.squared) # extract and insert anything
return(res)
}
(ANOVA1way - ddply(twelldata, .(Analyte), model))
HTH,
Tobias
Tobias Verbeke-2 wrote:
baxterj wrote:
I have a simple 1 way anova coded like
summary(ANOVA1way - aov(Value ~ WellID, data = welldata))
How can I use the BY function to do this ANOVA for each group using
another
variable in the dataset?? I tried coding it like this, but it doesn't
seem
to work.
summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~
WellID,
data = welldata)))
In SAS I would code it like this:
Proc sort data=welldata; by analyte; run;
Proc glm data=welldata;
by analyte;
class wellid;
model value = wellid;
run;
Look at the plyr package for a general solution to
this type of problems:
http://cran.r-project.org/web/packages/plyr/index.html
and its introductory guide on the package home page:
http://had.co.nz/plyr/
HTH,
Tobias
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running an ANOVA with a BY
On Sep 28, 2009, at 11:39 AM, baxterj wrote: I have a simple 1 way anova coded like summary(ANOVA1way - aov(Value ~ WellID, data = welldata)) How can I use the BY function to do this ANOVA for each group using another variable in the dataset?? I tried coding it like this, but it doesn't seem to work. Since you have not offered a reproducible example, we are left to choose our own. Checking the help page for by we see that a problem extremely similar to yours is already solved. I choose not to attach() the data for well-understood reasons: anova.LMH - by(warpbreaks, warpbreaks$tension, function(x) aov(breaks ~ wool, data=x) ) summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~ WellID, data = welldata))) In SAS I would code it like this: Proc sort data=welldata; by analyte; run; Proc glm data=welldata; by analyte; class wellid; model value = wellid; run; David Winsemius, MD Heritage Laboratories 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.
Re: [R] Running an ANOVA with a BY
baxterj wrote: I have a simple 1 way anova coded like summary(ANOVA1way - aov(Value ~ WellID, data = welldata)) How can I use the BY function to do this ANOVA for each group using another variable in the dataset?? I tried coding it like this, but it doesn't seem to work. summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~ WellID, data = welldata))) In SAS I would code it like this: Proc sort data=welldata; by analyte; run; Proc glm data=welldata; by analyte; class wellid; model value = wellid; run; Any suggestions??? Given you have asked two questions on translating SAS idioms to R, you might be a candidate for Bob Muenchen's book which some people have previously recommended: [3] Robert A. Muenchen. R for SAS and SPSS Users. Springer Series in Statistics and Computing. Springer, 2009. ISBN: 978-0-387-09417-5. [ bib | Discount Info | Publisher Info ] This book demonstrates which of the add-on packages are most like SAS and SPSS and compares them to R's built-in functions. It steps through over 30 programs written in all three packages, comparing and contrasting the packages' differing approaches. The programs and practice datasets are available for download. David Scott -- _ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics __ 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.
Re: [R] Running an ANOVA with a BY
I downloaded the package and got it to work with the coding:
model - function(df) {aov(values ~ WellID, data = twelldata)}
ANOVA1way - dlply(twelldata, .(Analyte), model)
print(ANOVA1way)
This gives me degrees of freedom and sum of squares for each anova per
analyte. However, I cant get the summary(ANOVA1way) to work so that I can
get p-values, etc... How can I do this?
Jodi
Tobias Verbeke-2 wrote:
baxterj wrote:
I have a simple 1 way anova coded like
summary(ANOVA1way - aov(Value ~ WellID, data = welldata))
How can I use the BY function to do this ANOVA for each group using
another
variable in the dataset?? I tried coding it like this, but it doesn't
seem
to work.
summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~
WellID,
data = welldata)))
In SAS I would code it like this:
Proc sort data=welldata; by analyte; run;
Proc glm data=welldata;
by analyte;
class wellid;
model value = wellid;
run;
Look at the plyr package for a general solution to
this type of problems:
http://cran.r-project.org/web/packages/plyr/index.html
and its introductory guide on the package home page:
http://had.co.nz/plyr/
HTH,
Tobias
__
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.
--
View this message in context:
http://www.nabble.com/Running-an-ANOVA-with-a-BY-tp25645413p25650273.html
Sent from the R help mailing list archive at Nabble.com.
__
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.
Re: [R] Running an ANOVA with a BY
baxterj wrote:
I downloaded the package and got it to work with the coding:
model - function(df) {aov(values ~ WellID, data = twelldata)}
Hmm.. I guess you mean to use 'data = df' instead of 'data = twelldata'
ANOVA1way - dlply(twelldata, .(Analyte), model)
print(ANOVA1way)
This gives me degrees of freedom and sum of squares for each anova per
analyte. However, I cant get the summary(ANOVA1way) to work so that I can
get p-values, etc... How can I do this?
You need to extend your model function:
- extract the bits you want
- construct a result data frame
- return it
and use a ddply
For example (non-tested):
model - function(df) {
lmObj - lm(values ~ WellID, data = df)
summaryLmObj - summary(lmObj)
res - data.frame(intercept = coef(lmObj)[1],
adjr2 = summaryLmObj$adj.r.squared) # extract and insert anything
return(res)
}
(ANOVA1way - ddply(twelldata, .(Analyte), model))
HTH,
Tobias
Tobias Verbeke-2 wrote:
baxterj wrote:
I have a simple 1 way anova coded like
summary(ANOVA1way - aov(Value ~ WellID, data = welldata))
How can I use the BY function to do this ANOVA for each group using
another
variable in the dataset?? I tried coding it like this, but it doesn't
seem
to work.
summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~
WellID,
data = welldata)))
In SAS I would code it like this:
Proc sort data=welldata; by analyte; run;
Proc glm data=welldata;
by analyte;
class wellid;
model value = wellid;
run;
Look at the plyr package for a general solution to
this type of problems:
http://cran.r-project.org/web/packages/plyr/index.html
and its introductory guide on the package home page:
http://had.co.nz/plyr/
HTH,
Tobias
__
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.
__
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.
[R] Running an ANOVA with a BY
I have a simple 1 way anova coded like summary(ANOVA1way - aov(Value ~ WellID, data = welldata)) How can I use the BY function to do this ANOVA for each group using another variable in the dataset?? I tried coding it like this, but it doesn't seem to work. summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~ WellID, data = welldata))) In SAS I would code it like this: Proc sort data=welldata; by analyte; run; Proc glm data=welldata; by analyte; class wellid; model value = wellid; run; Any suggestions??? -- View this message in context: http://www.nabble.com/Running-an-ANOVA-with-a-BY-tp25645413p25645413.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Running an ANOVA with a BY
baxterj wrote: I have a simple 1 way anova coded like summary(ANOVA1way - aov(Value ~ WellID, data = welldata)) How can I use the BY function to do this ANOVA for each group using another variable in the dataset?? I tried coding it like this, but it doesn't seem to work. summary(ANOVA1way - by(welldata, Analyte, function(x) aov(Value ~ WellID, data = welldata))) In SAS I would code it like this: Proc sort data=welldata; by analyte; run; Proc glm data=welldata; by analyte; class wellid; model value = wellid; run; Look at the plyr package for a general solution to this type of problems: http://cran.r-project.org/web/packages/plyr/index.html and its introductory guide on the package home page: http://had.co.nz/plyr/ HTH, Tobias __ 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.
