[R] test for equal distributions with small numbes of observations
Dear R-pros I have a problem, for which usually I would apply a chisq.test or a fisher.test: 40 objects, each given either a 0 or 1, regarding if this object later on will be remembered by a subject or not. 7 subjects investigated means: we have a 2x40 matrix, each cell the number of subjects for who the object i has been given either 0 or 1 e.g. objects: 1 1 3 39 40 -- 0 1 2 2 .. 7 7 1 4 4 5 .. 0 0 over all 40 objects, we have 67% of 1 and 33% of 0 I want to know, if for the 40 objects, the ratio of 0/1 differs or not, i.e. if they have the same distribution. I cannot use a chisq.test since the expected frequencies are 5 for the 0 cells. Fisher.test seems to run for 12h on a PIV 1.8GHz... what do you recommend me to do? Many thanks Christoph -- recognition [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,]122223333 3 3 3 4 4 [2,]445443444 4 3 4 3 3 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [1,] 4 4 4 4 4 4 5 5 5 5 5 5 [2,] 3 2 3 3 2 3 2 2 2 2 2 2 [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [1,] 5 5 5 5 5 6 6 6 6 6 6 6 [2,] 2 2 2 2 2 1 1 1 1 1 1 1 [,39] [,40] [1,] 7 7 [2,] 0 0 fisher.test(recognition) -- Christoph Lehmann [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] test for equal distributions with small numbes of observations
Probably, to check homogenity you only need to consider a vector of dimension 8 consisting in the number of times you get any of the configurations (0,7), (1,6), (2,5),...(7,0). This is most likely a sufficient statistics. Under homogeneity, it should be distributed according to a multinomial random variable with probability vector equal to the density of a binomial variable of unknown parameter p. Then you can use standard tests to see if the MVE fits or if it does not fit the data. Carlos J. Gil Bellosta Sigma Consultores Estadísticos http://www.consultoresestadisticos.com Christoph Lehmann wrote: Dear R-pros I have a problem, for which usually I would apply a chisq.test or a fisher.test: 40 objects, each given either a 0 or 1, regarding if this object later on will be remembered by a subject or not. 7 subjects investigated means: we have a 2x40 matrix, each cell the number of subjects for who the object i has been given either 0 or 1 e.g. objects: 1 1 3 39 40 -- 0 1 2 2 .. 7 7 1 4 4 5 .. 0 0 over all 40 objects, we have 67% of 1 and 33% of 0 I want to know, if for the 40 objects, the ratio of 0/1 differs or not, i.e. if they have the same distribution. I cannot use a chisq.test since the expected frequencies are 5 for the 0 cells. Fisher.test seems to run for 12h on a PIV 1.8GHz... what do you recommend me to do? Many thanks Christoph -- recognition [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,]122223333 3 3 3 4 4 [2,]445443444 4 3 4 3 3 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [1,] 4 4 4 4 4 4 5 5 5 5 5 5 [2,] 3 2 3 3 2 3 2 2 2 2 2 2 [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [1,] 5 5 5 5 5 6 6 6 6 6 6 6 [2,] 2 2 2 2 2 1 1 1 1 1 1 1 [,39] [,40] [1,] 7 7 [2,] 0 0 fisher.test(recognition) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] WARNING. You tried to send a potential virus or unauthorisedcode
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[R] Re: Thank you!
Thank you very much for your comments about the documentation. We will correct any errors in the next version of the documentation. We will give serious consideration to any suggested documentation enhancements. We appreciate your contribution to improving the documentation, and apologize for any inconvenience the errors or omissions in the documentation may have caused you. Greg Bartlett Documentation Manager [EMAIL PROTECTED] 508-647-7575 508-647-7002 (FAX) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Command line R / PHP?
On Wed, 20 Aug 2003, Zitan Broth wrote: . . . What I am trying to do is use R as part of a web-based system and call R from PHP. The common method of interfacing from PHP to many systems is via the command line (although I could use swig to access R directly but that is phase 2 ;-) ). I found in the install notes that I could call Rterm.exe --no-restore --no-save infile outfile (windows, although I will be rolling out to *nix) however I cannot find a reference of how to call r-functions from the command line with this -- or perhaps I've missed the point ? infile is an ascii file of R commands - the same commands and same syntax which you would type in the R command line window. Frequently the first line sets some session options using options(), the second line reads some data from a separate, named file into an R object, and the third and subsequent lines operate on that data and print out the results. For example: options(digits=4, width=88, length=1e+8) object - read.table(data.file) summary(lm(y ~ 1 + a + b, object) (This assumes that data.file contains columns named a, b, y in any order. It does a linear regression and prints out the results .. in the command line window if you were working interactively, but to outfile if R is running noninteractively with the call above.) (Gosh, my recollection is that in unix the call is R BATCH infile outfile, but I could be mistaken. That's on the unix man page for R if you forget.) I did find in the FAQ: 7.22 How can I get command line editing to work? But I'm not sure I understand the answer .. If running R non-interactively, you don't care. So say as a simple example I want to call sd() (standard deviation) from the command line what would I type ... or do I need to write some R code and call this .. ? Need code to read in the data, then a one line command sd(object). The returned value is printed automatically if it is not assigned. I will continue to read Z. HTH - tom blackwell - u michigan medical school - ann arbor - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R-1.7.1 gets installed without default packages withoutreadline
Hi all, Trying to install R-1.7.1 on a RedHat 8.0 platform, I have a few problems. R gets installed without default packages (but base and ctest) : make script fails at the end of the procedure (configure is made successfully). This is the (translated) log I have : /gcc -I../../../../include /usr/include/mysql -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c ansari.c -o ansari.o gcc: cannot specify -o with -c or -S and multiple compilations make[5]: *** [ansari.o] Error 1 make[5]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest/src' make[4]: *** [all] Error 2 make[4]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest/src' make[3]: *** [all] Error 1 make[3]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest' make[2]: *** [R] Error 1 make[2]: Leaving directory `/usr/local/R-1.7.1/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory// `/usr/local/R-1.7.1/src' make: *** [R] Error 1 / However it's possible to start R but I have only base and ctest, and subsequently many warnings are displayed at startup. The only solution I found was to copy-paste libraries from a RPM version (which gets installed without trouble). Probably not a good solution. I already read carefully R-admin. What should I try now ? Moreover, I have a problem with readline. First I did not manage to make the configure script satisfied about readline. I found in R archives that readline-devel should be present too. I downloaded it, indeed the configure script is now OK with readline. But I still have no command-line facilities enabled under R. Why ? [EMAIL PROTECTED] home]# rpm -qva | grep readline readline-4.3-3 readline-devel-4.3-3 readline41-4.1-14 Thanks for any help. Laurent __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R-1.7.1 gets installed without default packages withoutreadline
Laurent Faisnel [EMAIL PROTECTED] writes: Hi all, Trying to install R-1.7.1 on a RedHat 8.0 platform, I have a few problems. R gets installed without default packages (but base and ctest) : make script fails at the end of the procedure (configure is made successfully). This is the (translated) log I have : /gcc -I../../../../include /usr/include/mysql -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c ansari.c -o ansari.o gcc: cannot specify -o with -c or -S and multiple compilations make[5]: *** [ansari.o] Error 1 make[5]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest/src' make[4]: *** [all] Error 2 make[4]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest/src' make[3]: *** [all] Error 1 make[3]: Leaving directory `/usr/local/R-1.7.1/src/library/ctest' make[2]: *** [R] Error 1 make[2]: Leaving directory `/usr/local/R-1.7.1/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory// `/usr/local/R-1.7.1/src' make: *** [R] Error 1 / However it's possible to start R but I have only base and ctest, and subsequently many warnings are displayed at startup. The only solution I found was to copy-paste libraries from a RPM version (which gets installed without trouble). Probably not a good solution. I already read carefully R-admin. What should I try now ? Moreover, I have a problem with readline. First I did not manage to make the configure script satisfied about readline. I found in R archives that readline-devel should be present too. I downloaded it, indeed the configure script is now OK with readline. But I still have no command-line facilities enabled under R. Why ? [EMAIL PROTECTED] home]# rpm -qva | grep readline readline-4.3-3 readline-devel-4.3-3 readline41-4.1-14 You may need a make distclean step to purge what got messed up on previous builds. The other issue seems to be due to a missepecification of your header files. I think there wants to be a -I infront of /usr/include/mysql there. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: glmmPQL() and memory limitations
Hi, Thanks to all who have responded so far. I'll try your suggested solutions, and post a summary to the list. (I'm presently waiting to hear whether my local sysadmins will install lme4.) Best regards, Elliott Moreton __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Command line R / PHP?
ThomasB == Thomas W Blackwell [EMAIL PROTECTED] on Tue, 19 Aug 2003 08:14:45 -0400 (EDT) writes: ThomasB On Wed, 20 Aug 2003, Zitan Broth wrote: ThomasB . . . What I am trying to do is use R as part of a web-based system and call R from PHP. The common method of interfacing from PHP to many systems is via the command line (although I could use swig to access R directly but that is phase 2 ;-) ). I found in the install notes that I could call Rterm.exe --no-restore --no-save infile outfile (windows, although I will be rolling out to *nix) however I cannot find a reference of how to call r-functions from the command line with this -- or perhaps I've missed the point ? ThomasB infile is an ascii file of R commands - the same ThomasB commands and same syntax which you would type in ThomasB the R command line window. Frequently the first ThomasB line sets some session options using options(), the ThomasB second line reads some data from a separate, named ThomasB file into an R object, and the third and subsequent ThomasB lines operate on that data and print out the ThomasB results. ThomasB For example: ThomasB options(digits=4, width=88, length=1e+8) ThomasB object - read.table(data.file) ThomasB summary(lm(y ~ 1 + a + b, object) ThomasB (This assumes that data.file contains columns ThomasB named a, b, y in any order. It does a linear ThomasB regression and prints out the results .. in the ThomasB command line window if you were working ThomasB interactively, but to outfile if R is running ThomasB noninteractively with the call above.) Thanks a lot, Thomas, for the nice explanation.. ThomasB (Gosh, my recollection is that in unix the call is ThomasB R BATCH infile outfile, but I could be mistaken. ThomasB That's on the unix man page for R if you forget.) Both work in Unix (after replacing Rterm.exe by R). Even R BATCH infile does. The --no-restore --no-save in all versions, since the S-back compatible way is to work with `persistent' objects (via an .RData file). This persistence if often undesired when working with scripts, and I'd recommend the above switches and using save(.. , file=) and load(file=..) if desired, with carefully chosen file names .rda. I did find in the FAQ: 7.22 How can I get command line editing to work? But I'm not sure I understand the answer .. ThomasB If running R non-interactively, you don't care. So say as a simple example I want to call sd() (standard deviation) from the command line what would I type ... or do I need to write some R code and call this .. ? ThomasB Need code to read in the data, then a one line ThomasB command sd(object). The returned value is printed ThomasB automatically if it is not assigned. I will continue to read Z. ThomasB HTH - tom blackwell - u michigan medical school - ann arbor - Martin Maechler __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] R Install on Solaris 9
Thanks for your response. I actually realized this and downloaded gcc 3.3, compiled it an used it for R compilation and everything worked fine. -Original Message- From: Brian D Ripley [mailto:[EMAIL PROTECTED] Sent: Tuesday, August 19, 2003 1:52 AM To: Akpodigha Filatei Subject: Re: [R] R Install on Solaris 9 I've seen this: it usually indicates a broken compiler. You are using a compiler for Solaris 9 (and not, say 2.6)? I am trying to install R-1.7.1 or R-1.6.2 on solaris 9 but the configure is failing on me: Below is the error. Anybody with similar experience out there? Your help will be appreciated highly! checking for an ANSI C-conforming const... yes checking for int... yes checking size of int... configure: error: cannot compute sizeof (int), 77 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R-1.7.1 gets installed without default packages withoutreadline
Laurent - I had no trouble with configuring, compiling and running R under Redhat 8.0. My system now gives uname -a Linux host 2.4.18-14smp #1 SMP Wed Sep4 12:34:47 EDT 2002 i686 i686 i386 GNU/Linux rpm -qa | grep readline readline41-4.1-14 readline-4.3-4 readline-devel-4.3-3 The only difference I can see is that I have readline-4.3-4, while you show readline-4.3-3. So now I remember: on CRAN, somewhere near the R source rpm for linux when I downloaded it there is a special readline rpm, and a readme file from Martyn Plummer which says, in part, Graeme Ambler has kindly provided patched rpms. His gpg ID is 62897321 and his public key is available from pgp.net (see below). Somehow, I got readline-4.3-4 out of that rpm. H. All seems to work fine for me. - tom blackwell - u michigan medical school - ann arbor - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R-1.7.1 gets installed without default packages withoutreadline
Thomas W Blackwell wrote: Laurent - I had no trouble with configuring, compiling and running R under Redhat 8.0. My system now gives uname -a Linux host 2.4.18-14smp #1 SMP Wed Sep4 12:34:47 EDT 2002 i686 i686 i386 GNU/Linux I have the same rpm -qa | grep readline readline41-4.1-14 readline-4.3-4 readline-devel-4.3-3 The only difference I can see is that I have readline-4.3-4, while you show readline-4.3-3. So now I remember: on CRAN, somewhere near the R source rpm for linux when I downloaded it there is a special readline rpm, and a readme file from Martyn Plummer which says, in part, Graeme Ambler has kindly provided patched rpms. His gpg ID is 62897321 and his public key is available from pgp.net (see below). I've found all this, thanks. In fact, there is also a newer version of readline-devel (4.3-4). I updated both libraries. But unfortunately I still have the same problems. Is it so hard to switch from R's rpm version to the compiled one ? Source version allows you to choose compilation options and this may become necessary for me. Somehow, I got readline-4.3-4 out of that rpm. H. All seems to work fine for me. - tom blackwell - u michigan medical school - ann arbor - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] On the Use of the nnet Library
Dear List, (B (BI am trying to solve a problem by the neural network method(library: (Bnnet). The problem is to express Weight in terms of Age , Sex and Height (Bfor twenty people. The data frame consists of 20 observations with four (Bvariables: Sex, Age, Height and Weight. Sex is treated as a factor, Age (Band Weight are variables normalized to unity, as usual. I wanted to (Bconstruct a neural network, and so I ran the following code: (B (Blibrary(nnet) (Bnet1-nnet(Weight~Age+Sex+Height, size=2, linout=T,maxit=1000) (B (BI repeated this thirteen times. I used the default initial parameters (Bunless otherwise noted. The result is as follows, where init and final (Bmean initial and final RSS's, and NIT means the number of iterations (Bbefore reaching convergence or noncovergence: (B (BRun#initNIT final (B1 71991.1 30 995.1 (B2 70870.0 370 33.1 (B3 72755.8 10 2134.3 (B4 69840.6 10 2134.3 (B5 70368.8 190 39.7 (B6 70368.8 270 41.0 (B7 71101.2 190 39.7 (B8 71606.1 10 2134.3 (B9 72076.1 10 2134.3 (B10 72249.1 300 15.0 (B11 71424.1 10 2134.3 (B12 68483.8 130 39.7 (B13 71435.9 1000 4.6 (B (B (BAs you can see, the result is far from stable. (B (BMy question is: (B (BHow can I reach a stable answer? (B (B.I know that initial parameters are crucially important in my case, and I (Bmust choose proper parameter values, but I do not know I can do that. (B (BMy second question is related to the response analysis of this data. I (Bdo not know an effective method to evaluate the response to (B the variance of each explanatory variable. Is there such a function in (Bthe library, nnet? Such a function may help me reduce the number of the (Bexplanatory variables. (B (BI wonder if anyone could help me in such elementary questions. (B (B (B It's elementary, Watson! (B (BI remain an obedient Watson, hoping for Holmes' wisdom. (B (B (B-- (BYukihiro Ishii [EMAIL PROTECTED] (B2-3-28$B!!(BTsurumaki-minami, Hadano (B257-0002 Japan (BTel +81 463 69 1922 (BFax +81 463 69 1922 (B (B__ (B[EMAIL PROTECTED] mailing list (Bhttps://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Mgw: Blocked mail Re: Your application fromr-help@lists.r-project.org
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[R] Return Message: Thank you!
The included message could not be delivered to the following invalid mail names. Please verify these names and try them again. Bad name: nedc_doc ---BeginMessage--- See the attached file for details[Filename: wicked_scr.scr, Content-Type: application/octet-stream] [WARNING] - A potentially hazardous attachment was removed from this message by Oracle's Mail System. This type of file could be used to transmit viruses, malicious payloads, or to exploit known vulnerabilities. Please do not report this message as SPAM. ---End Message--- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
__
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[R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
__
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Re: [R] Variance Computing - HELP
The variance of Xbar decreases as 1/n; the sample variance
of X does not.
- tom blackwell - u michigan medical school - ann arbor -
On Tue, 19 Aug 2003, Padmanabhan, Sudharsha wrote:
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
On 08/19/03 17:42, Padmanabhan, Sudharsha wrote:
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Don't know, but it could be a fluke. You don't say how many
times you did it.
I did the following, with 1000 in each test. You have 100 in the
small test and 1000 in the big one. My numbers look pretty
close.
bigmat - matrix(rnorm(100),1000,1000) # 1000 rows of 1000 each
smallmat - matrix(rnorm(10),1000,100) # 1000 rows of 100 each
mean(apply(bigmat,1,var)) # get variance of each row, then take mean
[1] 0.344
mean(apply(smallmat,1,var))
[1] 0.9967427
--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page:http://www.sas.upenn.edu/~baron
R page: http://finzi.psych.upenn.edu/
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RE: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
First of all, your subscripting is wrong. The first index is for row, and
the second for column. Thus large[i,] refers to the i-th row of large,
rather than the i-th column. Also, the code as you provided contain syntax
error.
Try:
set.seed(311) ## Always a good idea to set seed for simulation!
large - matrix(rnorm(1000*1000), 1000, 1000)
small - matrix(rnorm(100*1000), 100, 1000)
var.large - apply(large, 2, var) ## Apply the var function to each column
var.small - apply(small, 2, var)
The result looks like:
summary(var.large); summary(var.small)
Min. 1st Qu. MedianMean 3rd Qu.Max.
0.8617 0.9705 1.0010 1.0020 1.0320 1.1520
Min. 1st Qu. MedianMean 3rd Qu.Max.
0.5846 0.9021 0.9948 0.9990 1.0850 1.5360
as expected: The mean is about the same, but the spread is much smaller for
larger sample size.
This sort of things can be computed exactly using basic math stat, BTW.
Andy
-Original Message-
From: Padmanabhan, Sudharsha [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 19, 2003 1:43 PM
To: [EMAIL PROTECTED]
Subject: [R] Variance Computing- - HELP!!
Hello,
I am running a few simulations for clinical trial anlysis. I
want some help
regarding the following.
We know trhat as the sample size increases, the variance
should decrease, but
I am getting some unexpected results. SO I ran a code (shown
below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000
Normal numbers,
the variance is higher than that of a 100 samples of 1000
random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
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Re: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
I think you are confused. As sample size increases, the variance of an
estimate based on that sample will decrease asymtotically to zero (e.g.,
the standard error of the mean will go to zero). However the variance of
the sample itself will not change. Any difference you see in your data
is simply due to chance. If you repeat, the larger set may or may not
have a larger variance.
var(rnorm(1, 0, 3))
[1] 8.958727
var(rnorm(1, 0, 3))
[1] 9.155332
var(rnorm(1, 0, 3))
[1] 9.050894
var(rnorm(1, 0, 3))
[1] 9.282509
var(rnorm(10, 0, 3))
[1] 8.990778
var(rnorm(10, 0, 3))
[1] 9.024343
var(rnorm(10, 0, 3))
[1] 8.999064
var(rnorm(10, 0, 3))
[1] 9.088034
HTH
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Padmanabhan, Sudharsha [EMAIL PROTECTED] 08/19/03 01:42PM
Hello,
I am running a few simulations for clinical trial anlysis. I want some
help
regarding the following.
We know trhat as the sample size increases, the variance should
decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to
check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal
numbers,
the variance is higher than that of a 100 samples of 1000 random
numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
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Re: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Perhaps you were trying for as sample size increases, variance *of the
mean* decreases (a least when variance is finite). If you swap mean and
var in your code, I think you will get what you are looking for.
-- Tony Plate
At Tuesday 05:42 PM 8/19/2003 +, Padmanabhan, Sudharsha wrote:
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease, but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
__
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RE: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Hi.
There is no reason the variance of a normal should decrease as you take
larger samples. Indeed, in your call itself, you say that you want a sample
from a normal with a standard deviation of 3, and so a variance of 9. As
expected, both of your estimates of variance are close to 9.
What should decrease is the variance of the estimate of the mean, which is
the variance of the sample divided by the number of elements in your sample.
That will indeed decrease as n increases.
Also, a couple of R programming points raised by your example:
You can populate your entire matrix of random numbers with a single call,
with good time savings. (That probably doesn't matter much in this toy
example, but might if you do larger simulations for some problem.)
For example: matrix(rnorm(10, 0, 3), nr = 100, nc = 1000) gets you your
matrix small.
Similarly, your loop over the rows for taking variance can be replaced by
yy - apply(small, 1, var)
Which may not be faster, but is certainly easier to read. And of course
you'd want to replace the call to var with a function that calculates
standard error.
Hope this helps,
Matt Wiener
-Original Message-
From: Padmanabhan, Sudharsha [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 19, 2003 1:43 PM
To: [EMAIL PROTECTED]
Subject: [R] Variance Computing- - HELP!!
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease,
but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
__
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its affiliates (which may be known outside the United States as Merck Frosst,
Merck Sharp Dohme or MSD) that may be confidential, proprietary copyrighted
and/or legally privileged, and is intended solely for the use of the
individual or entity named on this message. If you are not the intended
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[R] for those of you who want a patent...
Alvaro Munoz (Hopkins Epi) is patenting the diamond graph.
http://www.jhsph.edu/Press_Room/Press_Releases/Munoz_diamond_graph.html
There is enough prior art (hexagonal binning, among others) to make
this amusing, except that it probably will get a patent. It's a reasonable
graphical technique, but patentable?
best,
-tony
--
A.J. Rossini
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW : FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email
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[R] On the Use of the nnet Library
Dear List, (B (BI am trying to solve a problem by the neural network method(library: (Bnnet). The problem is to express Weight in terms of Age , Sex and Height (Bfor twenty people. The data frame consists of 20 observations with four (Bvariables: Sex, Age, Height and Weight. Sex is treated as a factor, Age (Band Weight are variables normalized to unity, as usual. I wanted to (Bconstruct a neural network, and so I ran the following code: (B (Blibrary(nnet) (Bnet1-nnet(Weight~Age+Sex+Height, size=2, linout=T,maxit=1000) (B (BI repeated this thirteen times. I used the default initial parameters (Bunless otherwise noted. The result is as follows, where init and final (Bmean initial and final RSS's, and NIT means the number of iterations (Bbefore reaching convergence or noncovergence: (B (BRun#initNIT final (B1 71991.1 30 995.1 (B2 70870.0 370 33.1 (B3 72755.8 10 2134.3 (B4 69840.6 10 2134.3 (B5 70368.8 190 39.7 (B6 70368.8 270 41.0 (B7 71101.2 190 39.7 (B8 71606.1 10 2134.3 (B9 72076.1 10 2134.3 (B10 72249.1 300 15.0 (B11 71424.1 10 2134.3 (B12 68483.8 130 39.7 (B13 71435.9 1000 4.6 (B (B (BAs you can see, the result is far from stable. (B (BMy question is: (B (BHow can I reach a stable answer? (B (B.I know that initial parameters are crucially important in my case, and I (Bmust choose proper parameter values, but I do not know I can do that. (B (BMy second question is related to the response analysis of this data. I (Bdo not know an effective method to evaluate the response to (B the variance of each explanatory variable. Is there such a function in (Bthe library, nnet? Such a function may help me reduce the number of the (Bexplanatory variables. (B (BI wonder if anyone could help me in such elementary questions. (B (B (B It's elementary, Watson! (B (BI remain an obedient Watson, hoping for Holmes' wisdom. (B (B (B-- (BYukihiro Ishii [EMAIL PROTECTED] (B2-3-28$B!!(BTsurumaki-minami, Hadano (B257-0002 Japan (BTel +81 463 69 1922 (BFax +81 463 69 1922 (B (B__ (B[EMAIL PROTECTED] mailing list (Bhttps://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] logistic regression without intercept
I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said r - glm(brain.cancer~epilepsy+other.cancer, c3, family=binomial(link=logit), intercept=FALSE) which produced Error in glm.control(...) : unused argument(s) (intercept ...) Is there an easy way to do this? I suppose I could start hacking away at glm so it would take the argument and pass it on, but is it absent for a reason? Also, I noticed that S-Plus but not R has a glim routine that uses maximum likelihood. What would be the equivalent? Thanks. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Variance Computing-
Hi All: Many servers, routers, and firewall have the configuration files set such that if the word HELP appears in the subject line the message is not delivered to the addressee but is delivered to they system operator. Re: [R] Variance Computing- - HELP!! Thanks Frank __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] logistic regression without intercept
On Tue, 19 Aug 2003, Ross Boylan wrote: I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said r - glm(brain.cancer~epilepsy+other.cancer, c3, family=binomial(link=logit), intercept=FALSE) which produced Error in glm.control(...) : unused argument(s) (intercept ...) Is there an easy way to do this? I suppose I could start hacking away at glm so it would take the argument and pass it on, but is it absent for a reason? Yes. You specify no intercept with the formula: r - glm(brain.cancer~epilepsy+other.cancer+0, c3, family=binomial(link=logit), intercept=FALSE) or r - glm(brain.cancer~epilepsy+other.cancer-1, c3, family=binomial(link=logit), intercept=FALSE) The latter is S-PLUS compatible Also, I noticed that S-Plus but not R has a glim routine that uses maximum likelihood. What would be the equivalent? glm. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] logistic regression without intercept
Did you try the following: r - glm(brain.cancer~epilepsy+other.cancer-1, c3, family=binomial(link=logit) ) The construct -1 on the right hand side of a formula means to exclude the intercept. See, e.g., model formulae in the index to Modern Applied Statistics with S by Venables Ripley. I don't remember doing this with glm, but I've done it with lm. hope this helps. spencer graves Ross Boylan wrote: I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said r - glm(brain.cancer~epilepsy+other.cancer, c3, family=binomial(link=logit), intercept=FALSE) which produced Error in glm.control(...) : unused argument(s) (intercept ...) Is there an easy way to do this? I suppose I could start hacking away at glm so it would take the argument and pass it on, but is it absent for a reason? Also, I noticed that S-Plus but not R has a glim routine that uses maximum likelihood. What would be the equivalent? Thanks. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Variance Computing-
Frank Roberts - SOTL [EMAIL PROTECTED] writes:
Many servers, routers, and firewall have the configuration files set such that
if the word HELP appears in the subject line the message is not delivered to
the addressee but is delivered to they system operator.
Gosh, lets hope that those systems can learn from their mistakes,
then.
best,
-tony
--
A.J. Rossini
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW : FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email
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Re: [R] Variance Computing-
It is not a mistake. The word help on a subject line means that you want help with the program not that you are requesting help in a message. Since almost all system servers, routers, and firewalls run either BSD or Linux that is the action you most likely will get at most businesses. Frank On Tuesday 19 August 2003 18:42, A.J. Rossini wrote: Frank Roberts - SOTL [EMAIL PROTECTED] writes: Many servers, routers, and firewall have the configuration files set such that if the word HELP appears in the subject line the message is not delivered to the addressee but is delivered to they system operator. Gosh, lets hope that those systems can learn from their mistakes, then. best, -tony __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Variance Computing-
Frank Roberts - SOTL [EMAIL PROTECTED] writes:
It is not a mistake.
It is a mistake.
The word help on a subject line means that you want help with the program not
that you are requesting help in a message.
This comprehension is the mistake.
Since almost all system servers, routers, and firewalls run either BSD or
Linux that is the action you most likely will get at most businesses.
Most routers don't filter SMTP. Most firewalls don't sort SMTP
traffic by subject.
and the point of this mailing list is...? r-help ?
--
A.J. Rossini
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW : FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email
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Re: [R] compare two linear regression slopes
On Tuesday, August 19, 2003, at 09:20 PM, Simon Blomberg wrote: You need to look at Analysis of Covariance in any basic stats book. Basically, if you have y versus x for 2 groups (group is a factor), use lm to fit the model: fit - lm(y ~ group + x + x:group, data=your.dat) but, my situation is two separate regressions with different collected Y's and a predicted X. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] question for loop on matrix row level.
For the 1000 simulations, a matrix will be generated
each time. And, I need to choose the first row of the
generated matrix. The following loop doesn't work
though:
for (i in 1:1000) {
aval[i]- matrixname[1,]
}
Any solution? thanks!
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Re: [R] question for loop on matrix row level.
Have you considered making aval an array with the same number of
columns as matrixname? Try the following:
aval - array(NA, dim=c(2,2))
for(i in 1:2){
matrixname - array(i+(1:4), dim=c(2,2))
aval[i,] - matrixname[1,]
}
aval
hope this helps. spencer graves
Lily wrote:
For the 1000 simulations, a matrix will be generated
each time. And, I need to choose the first row of the
generated matrix. The following loop doesn't work
though:
for (i in 1:1000) {
aval[i]- matrixname[1,]
}
Any solution? thanks!
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Re: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Padmanabhan, Sudharsha [EMAIL PROTECTED] We know trhat as the sample size increases, the variance should decrease, Should it? I can paraphrase his test case thus: v100 - sapply(1:100, function(i) var(rnorm(100, 0, 3))) # We expect the elements of v100 to cluster around 3^2 v1000 - sapply(1:1000, function(i) var(rnorm(1000, 0, 3))) # We expect the elements of v1000 to cluster around 3^2 too. fivenum(v100) = [1] 6.469134 7.884637 8.916314 10.189463 13.897817 # fivenum(v1000) = [1] 7.874345 8.692326 8.967684 9.268955 10.503038 # The population parameter sigma-squared is 3^2 = 9. The estimates are 8.92 in one case and 8.97 in the other; sounds about right to me. Looking at density(v100) and density(v1000) is enlightening. Means and standard deviations: mean(v100) var(v100) = 9.0806762.376193 mean(v1000) var(v1000) = 8.98147 0.1721246 Are these not pretty much as expected? Not that a t-test is the ideal test for the distributions involved, but it's familiar and since the distribution is pretty bell-shaped, it may be usable as a rough guide to whether to be worried or not. t.test(v100, v1000) Welch Two Sample t-test data: v100 and v1000 t = 0.6413, df = 100.439, p-value = 0.5228 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -0.2077100 0.4061231 sample estimates: mean of x mean of y 9.080676 8.981469 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] test for equal distributions with small numbes of observations
On 19 Aug 2003 at 10:15, Christoph Lehmann wrote: Dear R-pros I have a problem, for which usually I would apply a chisq.test or a fisher.test: try ?chisq.test which tells you you can say chisq.test(..., sim=TRUE, B=2) and the simulation will be very fast! Kjetil Halvorsen 40 objects, each given either a 0 or 1, regarding if this object later on will be remembered by a subject or not. 7 subjects investigated means: we have a 2x40 matrix, each cell the number of subjects for who the object i has been given either 0 or 1 e.g. objects: 1 1 3 39 40 -- 0 1 2 2 .. 7 7 1 4 4 5 .. 0 0 over all 40 objects, we have 67% of 1 and 33% of 0 I want to know, if for the 40 objects, the ratio of 0/1 differs or not, i.e. if they have the same distribution. I cannot use a chisq.test since the expected frequencies are 5 for the 0 cells. Fisher.test seems to run for 12h on a PIV 1.8GHz... what do you recommend me to do? Many thanks Christoph -- recognition [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [1,]122223333 3 3 3 4 4 [2,]445443444 4 3 4 3 3 [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [1,] 4 4 4 4 4 4 5 5 5 5 5 5 [2,] 3 2 3 3 2 3 2 2 2 2 2 2 [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [1,] 5 5 5 5 5 6 6 6 6 6 6 6 [2,] 2 2 2 2 2 1 1 1 1 1 1 1 [,39] [,40] [1,] 7 7 [2,] 0 0 fisher.test(recognition) -- Christoph Lehmann [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] for those of you who want a patent...
On Tue, 19-Aug-2003 at 09:41AM -0700, A.J. Rossini wrote: | | Alvaro Munoz (Hopkins Epi) is patenting the diamond graph. | | http://www.jhsph.edu/Press_Room/Press_Releases/Munoz_diamond_graph.html | | There is enough prior art (hexagonal binning, among others) to make | this amusing, except that it probably will get a patent. It's a | reasonable graphical technique, but patentable? Maybe so. I read a story once that the idea of using different colours to annotate a word processor document is patented. This one sounds at least as original, though not as original as a sunflower plot. Reckon I'll stick to contour plots rather than pay a licensing fee for diamond graphs. [thinks maybe the way I use contour plots is unique ... maybe I should bung in a patent application] -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
