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Daniel Stahl

2007-Aug-14 13:11 UTC

[R] Problem with "by": does not work with ttest (but with lme)

Hello,

I would like to do a large number of e.g. 1000 paired ttest using the
by-function. But instead of using only the data within the 1000 groups, R
caclulates 1000 times the ttest for the full data set(The same happens with
Wilcoxon test). However, the by-function works fine with the lme function.
Did I just miss something or is it really not working? If not, is there any
other possibility to avoid loops?
Thanks 
Daniel

Here is the R help example for "by" 
 require(stats)
 attach(warpbreaks)
 by(warpbreaks, tension, function(x) lm(breaks ~ wool, data = x))
*->works great
by(warpbreaks,tension,function(x)t.test(breaks ~ wool,data=warpbreaks,paired =
TRUE))
*Same output for each level of tension:

tension: L

	Paired t-test

data:  breaks by wool
t = 1.9956, df = 26, p-value = 0.05656
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-0.1735803 11.7291358
sample estimates:
mean of the differences
                5.777778

------------------------------------------------------------------------

tension: M

	Paired t-test

data:  breaks by wool
t = 1.9956, df = 26, p-value = 0.05656
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-0.1735803 11.7291358
sample estimates:
mean of the differences
                5.777778

------------------------------------------------------------------------

tension: H

	Paired t-test

data:  breaks by wool
t = 1.9956, df = 26, p-value = 0.05656
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-0.1735803 11.7291358
sample estimates:
mean of the differences
                5.777778







--

Petr PIKAL

2007-Aug-14 13:35 UTC

head link

[R] Odp: Problem with "by": does not work with ttest (but with lme)

Hi

r-help-bounces at stat.math.ethz.ch napsal dne 14.08.2007 15:11:11:
> Hello,
> 
> I would like to do a large number of e.g. 1000 paired ttest using the 
by-> function. But instead of using only the data within the 1000 groups, R 
> caclulates 1000 times the ttest for the full data set(The same happens 
with > Wilcoxon test). However, the by-function works fine with the lme 
function.> Did I just miss something or is it really not working? If not, is there 
any > other possibility to avoid loops? 
> Thanks 
> Daniel
> 
> Here is the R help example for "by" 
>  require(stats)
>  attach(warpbreaks)
>  by(warpbreaks, tension, function(x) lm(breaks ~ wool, data = x))
> *->works great
> by(warpbreaks,tension,function(x)t.test(breaks ~ wool,data=warpbreaks,paired = TRUE))

What about

by(warpbreaks,tension,function(x)t.test(breaks ~ wool,data=x,paired = 
TRUE))

Regards
Petr

> *Same output for each level of tension:
> 
> tension: L
> 
>    Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> ------------------------------------------------------------------------
> 
> tension: M
> 
>    Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> ------------------------------------------------------------------------
> 
> tension: H
> 
>    Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> 
> 
> 
> 
> 
> 
> --
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.

Chuck Cleland

2007-Aug-14 13:43 UTC

head link

[R] Problem with "by": does not work with ttest (but with lme)

Daniel Stahl wrote:> Hello,
> 
> I would like to do a large number of e.g. 1000 paired ttest using the
by-function. But instead of using only the data within the 1000 groups, R
caclulates 1000 times the ttest for the full data set(The same happens with
Wilcoxon test). However, the by-function works fine with the lme function.
> Did I just miss something or is it really not working? If not, is there any
other possibility to avoid loops?
> Thanks 
> Daniel
> 
> Here is the R help example for "by" 
>  require(stats)
>  attach(warpbreaks)
>  by(warpbreaks, tension, function(x) lm(breaks ~ wool, data = x))
> *->works great
> by(warpbreaks,tension,function(x)t.test(breaks ~
wool,data=warpbreaks,paired = TRUE))
> *Same output for each level of tension:
> 
> tension: L
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> ------------------------------------------------------------------------
> 
> tension: M
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> ------------------------------------------------------------------------
> 
> tension: H
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
  Try something like this:

library(MASS)
df <- mvrnorm(30, mu=c(-1,1), Sigma = diag(2))
df <- as.data.frame(df)
df$GROUP <- rep(1:3, each=10)

df.uni <- reshape(df, varying = list(c("V1","V2")),
v.names="Y",
direction="long")

by(df.uni, df.uni$GROUP, function(x)t.test(Y ~ time,
                                           data = x, paired = TRUE))

df.uni$GROUP: 1

        Paired t-test

data:  Y by time
t = -4.3719, df = 9, p-value = 0.001792
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -3.249894 -1.033530
sample estimates:
mean of the differences
              -2.141712

---------------------------------------------------------------------------------------------------------------------------

df.uni$GROUP: 2

        Paired t-test

data:  Y by time
t = -6.4125, df = 9, p-value = 0.0001234
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -3.277425 -1.568074
sample estimates:
mean of the differences
              -2.422749

---------------------------------------------------------------------------------------------------------------------------

df.uni$GROUP: 3

        Paired t-test

data:  Y by time
t = -4.4918, df = 9, p-value = 0.001507
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -3.581428 -1.182313
sample estimates:
mean of the differences
              -2.381871
> --
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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. 
-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894

Dieter Menne

2007-Aug-14 14:57 UTC

head link

[R] Problem with

Daniel Stahl <daniel_stahl <at> operamail.com> writes:
> 
> I would like to do a large number of e.g. 1000 paired ttest using theby-function.

Technical stuff aside: do you really want to do 1000 paired t-tests?
Followed by a *** pick-nic?

Mmm...

Dieter

Greg Snow

2007-Aug-14 15:42 UTC

head link

[R] Problem with "by": does not work with ttest (but with lme)

I think at least part of your problem is that in the lm example you use
data=x (correct), but in the t.test example you use data=warpbreaks, so
in that case it is uing the full data set, not just the portion passed
by the 'by' function.  Try the t.test example again with data=x and see
what happens.

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at intermountainmail.org
(801) 408-8111
 
 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Daniel Stahl
> Sent: Tuesday, August 14, 2007 7:11 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Problem with "by": does not work with ttest (but 
> with lme)
> 
> Hello,
> 
> I would like to do a large number of e.g. 1000 paired ttest 
> using the by-function. But instead of using only the data 
> within the 1000 groups, R caclulates 1000 times the ttest for 
> the full data set(The same happens with Wilcoxon test). 
> However, the by-function works fine with the lme function.
> Did I just miss something or is it really not working? If 
> not, is there any other possibility to avoid loops? 
> Thanks
> Daniel
> 
> Here is the R help example for "by" 
>  require(stats)
>  attach(warpbreaks)
>  by(warpbreaks, tension, function(x) lm(breaks ~ wool, data = 
> x)) *->works great 
> by(warpbreaks,tension,function(x)t.test(breaks ~ 
> wool,data=warpbreaks,paired = TRUE)) *Same output for each 
> level of tension:
> 
> tension: L
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> --------------------------------------------------------------
> ----------
> 
> tension: M
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> --------------------------------------------------------------
> ----------
> 
> tension: H
> 
> 	Paired t-test
> 
> data:  breaks by wool
> t = 1.9956, df = 26, p-value = 0.05656
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.1735803 11.7291358
> sample estimates:
> mean of the differences
>                 5.777778
> 
> 
> 
> 
> 
> 
> 
> --
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
>

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