Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
kernlab's ksvm method freeze
14 messages · Heiko Strathmann, Uwe Ligges, David Winsemius +3 more
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
I just tried ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", cross=10, C=2) several times on both workspaces and both returned some results after a couple of seconds under the same versions (R version 2.10.0 and kernlab 0.9-9.) under Windows XP. There mist be something else going on... Best wishes, Uwe Ligges
Heiko Strathmann wrote:
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
______________________________________________ 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.
Hello uwe, Thanks for trying out. the freeze happens after about 10 to 20 iterations. Did you try as many? Am Sonntag, den 29.11.2009, 17:22 +0100 schrieb Uwe Ligges:
I just tried ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", cross=10, C=2) several times on both workspaces and both returned some results after a couple of seconds under the same versions (R version 2.10.0 and kernlab 0.9-9.) under Windows XP. There mist be something else going on... Best wishes, Uwe Ligges Heiko Strathmann wrote:
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
______________________________________________ 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.
Heiko Strathmann wrote:
Hello uwe, Thanks for trying out. the freeze happens after about 10 to 20 iterations. Did you try as many?
I just tried again:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(100, ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc", C=2))
and everything is still fine (same on Linux).
Uwe Ligges
Am Sonntag, den 29.11.2009, 17:22 +0100 schrieb Uwe Ligges:
I just tried ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", cross=10, C=2) several times on both workspaces and both returned some results after a couple of seconds under the same versions (R version 2.10.0 and kernlab 0.9-9.) under Windows XP. There mist be something else going on... Best wishes, Uwe Ligges Heiko Strathmann wrote:
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
______________________________________________ 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.
No "freezes" on a Mac using Ligges' 100 replication script. Tried it twice. They took around a minute each time. -- David.
David On Nov 29, 2009, at 1:28 PM, Heiko Strathmann wrote: > Hello uwe, > Thanks for trying out. > the freeze happens after about 10 to 20 iterations. Did you try as > many? > > Am Sonntag, den 29.11.2009, 17:22 +0100 schrieb Uwe Ligges: >> I just tried >> >> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", >> cross=10, C=2) >> >> several times on both workspaces and both returned some results >> after a >> couple of seconds under the same versions (R version 2.10.0 and >> kernlab >> 0.9-9.) under Windows XP. >> >> There mist be something else going on... >> >> Best wishes, >> Uwe Ligges >> >> >> >> >> >> Heiko Strathmann wrote: >>> Hello again, >>> >>> the freeze seems to depend on the kernel matrix. >>> With another kernel matrix of similiar size, gernerated with the >>> same >>> kernel, but on another dataset, there is no freeze. >>> >>> I have put a workspace with the working matrix and one with the >>> freezing >>> matrix online for testing (see old email) >>> http://www-stud.uni-due.de/~sfhestra/ >>> >>> In my eyes this behavior is really strange, and i have no clue, >>> what to >>> do to solve this. >>> >>> Regards, >>> Heiko Strathmann >>> >>> Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann: >>>> Hello, >>>> >>>> I am using kernlab to do some binary classification on aminoacid >>>> strings. >>>> >>>> I am using a custom kernel, so i use the kernel="matrix" option >>>> of the >>>> ksvm method. >>>> >>>> My (normalized) kernel matrix is of size 1309*1309, my results >>>> vector >>>> has the same length. >>>> >>>> I am using C-svc. >>>> >>>> My kernlab call is something similiar to this: >>>> >>>> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", >>>> cross=10, C=2) >>>> >>>> To this point, everything works fine. >>>> >>>> But now, i want to do a search for a good C Parameter, so I call >>>> the >>>> ksvm method multiple times in a loop, with changing parameters. >>>> This loop freezes after a few iterations. >>>> >>>> >>>> The following simple example also freezes after few iterations (the >>>> number varies). See that the ksvm call is always the same in every >>>> iteration: >>>> >>>> for (i in c(1:20)) { >>>> print(i) >>>> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, >>>> type="C-svc", >>>> cross=10, C=2) >>>> } >>>> >>>> >>>> Does anybody have an idea what causes this? I am new to R and >>>> kernlab, >>>> perhaps i missed something? >>>> >>>> I put my workspace online, which contains the kernel matrix and the >>>> training labels. Simply load workspace, kernlab library and paste >>>> the >>>> example code to reproduce: >>>> http://www-stud.uni-due.de/~sfhestra/ >>>> >>>> I am using R version 2.10.0 and kernlab 0.9-9. >>>> >>>> Thanks for your help! >>>> >>>> Regards, >>>> Heiko Strathmann >>>> >>>> >>> >>> ______________________________________________ >>> 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. > > ______________________________________________ > 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 Heritage Laboratories West Hartford, CT
I tried out the code you wrote, it also works for me, but it lacks a
parameter i use in my code.
The problem (at this computer) seems to be this "cross"-parameter of
ksvm - if I, for example, add the parameter cross=10, i get the old
problem:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(10, ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", C=2, cross=10))
gets me a frozen R process, CTRL-C does not work anymore, and the only thing left is to kill it.
(for cross < 4, the thing still works)
(I also just reinstalled my Ubuntu and R)
Heiko Strathmann
Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe Ligges:
Heiko Strathmann wrote:
Hello uwe, Thanks for trying out. the freeze happens after about 10 to 20 iterations. Did you try as many?
I just tried again:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(100, ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc", C=2))
and everything is still fine (same on Linux).
Uwe Ligges
Am Sonntag, den 29.11.2009, 17:22 +0100 schrieb Uwe Ligges:
I just tried ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", cross=10, C=2) several times on both workspaces and both returned some results after a couple of seconds under the same versions (R version 2.10.0 and kernlab 0.9-9.) under Windows XP. There mist be something else going on... Best wishes, Uwe Ligges Heiko Strathmann wrote:
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
______________________________________________ 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.
My apologies, that must have been a copy&paste error and the essential argument got lost. I can reproduce it now under R-2.10.0 both Windows and Linux. Please report your findings to the package maintainer who might be able to debug this under Linux (probably easier than under Windows). Best, Uwe Ligges
Heiko Strathmann wrote:
I tried out the code you wrote, it also works for me, but it lacks a
parameter i use in my code.
The problem (at this computer) seems to be this "cross"-parameter of
ksvm - if I, for example, add the parameter cross=10, i get the old
problem:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(10, ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", C=2, cross=10))
gets me a frozen R process, CTRL-C does not work anymore, and the only thing left is to kill it.
(for cross < 4, the thing still works)
(I also just reinstalled my Ubuntu and R)
Heiko Strathmann
Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe Ligges:
Heiko Strathmann wrote:
Hello uwe, Thanks for trying out. the freeze happens after about 10 to 20 iterations. Did you try as many?
I just tried again:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(100, ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc", C=2))
and everything is still fine (same on Linux).
Uwe Ligges
Am Sonntag, den 29.11.2009, 17:22 +0100 schrieb Uwe Ligges:
I just tried ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", cross=10, C=2) several times on both workspaces and both returned some results after a couple of seconds under the same versions (R version 2.10.0 and kernlab 0.9-9.) under Windows XP. There mist be something else going on... Best wishes, Uwe Ligges Heiko Strathmann wrote:
Hello again, the freeze seems to depend on the kernel matrix. With another kernel matrix of similiar size, gernerated with the same kernel, but on another dataset, there is no freeze. I have put a workspace with the working matrix and one with the freezing matrix online for testing (see old email) http://www-stud.uni-due.de/~sfhestra/ In my eyes this behavior is really strange, and i have no clue, what to do to solve this. Regards, Heiko Strathmann Am Sonntag, den 29.11.2009, 14:21 +0100 schrieb Heiko Strathmann:
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point, everything works fine.
But now, i want to do a search for a good C Parameter, so I call the
ksvm method multiple times in a loop, with changing parameters.
This loop freezes after a few iterations.
The following simple example also freezes after few iterations (the
number varies). See that the ksvm call is always the same in every
iteration:
for (i in c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody have an idea what causes this? I am new to R and kernlab,
perhaps i missed something?
I put my workspace online, which contains the kernel matrix and the
training labels. Simply load workspace, kernlab library and paste the
example code to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R version 2.10.0 and kernlab 0.9-9.
Thanks for your help!
Regards,
Heiko Strathmann
______________________________________________ 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.
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20091130/cba5ef09/attachment-0001.pl>
Hi, I have an experiment with 5 treatments, of which 2 with 10 repetitions and 2 with 7 replications. I conducted the test of Bartlett step-by-step and compared with the value calculated directly by the R and the values are different. Anyone know tell me why? #------------------- n = length(trat) I = 4 (M = 2.3026*((n-I)*log10(mean(tapply(valor,trat,var))) - (9*log10(vari[1])+9*log10(vari[2])+6*log10(vari[3])+6*log10(vari[4])))) (C = 1 + 1/(3*(4-1))*((1/9 + 1/9 + 1/6 + 1/6) - 1/(9+9+6+6))) (B = M/C)
B
1.748670
qchisq(.05, 3, lower.tail=F) # Valor tabelado
[1] 7.814728
#-----------------------------------------
# Teste de Bartlett de forma direta no R -
#-----------------------------------------
bartlett.test(valor,trat)
Bartlett test of homogeneity of variances
data: valor and trat
Bartlett's K-squared = 0.7845, df = 3, p-value =
0.8532
Thanks,
--------------------------------------
Silvano Cesar da Costa
Departamento de Estat?stica
Universidade Estadual de Londrina
Fone: 3371-4346
Silvano wrote:
Hi, I have an experiment with 5 treatments, of which 2 with 10 repetitions and 2 with 7 replications. I conducted the test of Bartlett step-by-step and compared with the value calculated directly by the R and the values are different. Anyone know tell me why?
The first term in M looks wrong when group sizes differ, but it would be much easier to check if you gave the actual group variances. (and PLEASE don't hijack other threads. This has nothing to do with kernlab's ksvm!)
#------------------- n = length(trat) I = 4 (M = 2.3026*((n-I)*log10(mean(tapply(valor,trat,var))) - (9*log10(vari[1])+9*log10(vari[2])+6*log10(vari[3])+6*log10(vari[4])))) (C = 1 + 1/(3*(4-1))*((1/9 + 1/9 + 1/6 + 1/6) - 1/(9+9+6+6))) (B = M/C)
B
1.748670
qchisq(.05, 3, lower.tail=F) # Valor tabelado
[1] 7.814728
#-----------------------------------------
# Teste de Bartlett de forma direta no R -
#-----------------------------------------
bartlett.test(valor,trat)
Bartlett test of homogeneity of variances
data: valor and trat
Bartlett's K-squared = 0.7845, df = 3, p-value =
0.8532
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Silvano wrote:
Hi, I have an experiment with 5 treatments, of which 2 with 10 repetitions and 2 with 7 replications. I conducted the test of Bartlett step-by-step and compared with the value calculated directly by the R and the values are different. Anyone know tell me why?
Yes. Is mean(tapply(valor,trat,var)) the pooled variance estimate? Maybe you should look at the code of bartlett.test.default. -Peter Ehlers
#------------------- n = length(trat) I = 4 (M = 2.3026*((n-I)*log10(mean(tapply(valor,trat,var))) - (9*log10(vari[1])+9*log10(vari[2])+6*log10(vari[3])+6*log10(vari[4])))) (C = 1 + 1/(3*(4-1))*((1/9 + 1/9 + 1/6 + 1/6) - 1/(9+9+6+6))) (B = M/C)
B
1.748670
qchisq(.05, 3, lower.tail=F) # Valor tabelado
[1] 7.814728
#-----------------------------------------
# Teste de Bartlett de forma direta no R -
#-----------------------------------------
bartlett.test(valor,trat)
Bartlett test of homogeneity of variances
data: valor and trat
Bartlett's K-squared = 0.7845, df = 3, p-value =
0.8532
Thanks,
--------------------------------------
Silvano Cesar da Costa
Departamento de Estat?stica
Universidade Estadual de Londrina
Fone: 3371-4346
______________________________________________ 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.
Hello again, i got this message from the maintainer: Am Montag, den 30.11.2009, 11:22 +0100 schrieb Heiko Strathmann:
Ok, i reported it.
thanks for trying it out again.
Am 30. November 2009 11:06 schrieb Uwe Ligges
<ligges at statistik.tu-dortmund.de>:
My apologies, that must have been a copy&paste error and the
essential argument got lost. I can reproduce it now under
R-2.10.0 both Windows and Linux.
Please report your findings to the package maintainer who
might be able to debug this under Linux (probably easier than
under Windows).
Best,
Uwe Ligges
Heiko Strathmann wrote:
I tried out the code you wrote, it also works for me,
but it lacks a
parameter i use in my code.
The problem (at this computer) seems to be this
"cross"-parameter of
ksvm - if I, for example, add the parameter cross=10,
i get the old
problem:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(10, ksvm(kernel="matrix", kernelMatrix,
trainingDataYs, type="C-svc", C=2, cross=10))
gets me a frozen R process, CTRL-C does not work
anymore, and the only thing left is to kill it.
(for cross < 4, the thing still works)
(I also just reinstalled my Ubuntu and R)
Heiko Strathmann
Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe
Ligges:
Heiko Strathmann wrote:
Hello uwe,
Thanks for trying out.
the freeze happens after about 10 to
20 iterations. Did you try as many?
I just tried again:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(100, ksvm(kernel="matrix",
kernelMatrix, trainingDataYs, type="C-svc",
C=2))
and everything is still fine (same on Linux).
Uwe Ligges
Am Sonntag, den 29.11.2009, 17:22
+0100 schrieb Uwe Ligges:
I just tried
ksvm(kernel="matrix",
kernelMatrix, trainingDataYs,
type="C-svc", cross=10, C=2)
several times on both
workspaces and both returned
some results after a couple of
seconds under the same
versions (R version 2.10.0 and
kernlab 0.9-9.) under Windows
XP.
There mist be something else
going on...
Best wishes,
Uwe Ligges
Heiko Strathmann wrote:
Hello again,
the freeze seems to
depend on the kernel
matrix.
With another kernel
matrix of similiar
size, gernerated with
the same
kernel, but on another
dataset, there is no
freeze.
I have put a workspace
with the working
matrix and one with
the freezing
matrix online for
testing (see old
email)
http://www-stud.uni-due.de/~sfhestra/
In my eyes this
behavior is really
strange, and i have no
clue, what to
do to solve this.
Regards,
Heiko Strathmann
Am Sonntag, den
29.11.2009, 14:21
+0100 schrieb Heiko
Strathmann:
Hello,
I am using
kernlab to do
some binary
classification
on aminoacid
strings.
I am using a
custom kernel,
so i use the
kernel="matrix" option of the
ksvm method.
My
(normalized)
kernel matrix
is of size
1309*1309, my
results vector
has the same
length.
I am using
C-svc.
My kernlab
call is
something
similiar to
this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point,
everything
works fine.
But now, i
want to do a
search for a
good C
Parameter, so
I call the
ksvm method
multiple times
in a loop,
with changing
parameters.
This loop
freezes after
a few
iterations.
The following
simple example
also freezes
after few
iterations
(the
number
varies). See
that the ksvm
call is always
the same in
every
iteration:
for (i in
c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody
have an idea
what causes
this? I am new
to R and
kernlab,
perhaps i
missed
something?
I put my
workspace
online, which
contains the
kernel matrix
and the
training
labels. Simply
load
workspace,
kernlab
library and
paste the
example code
to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R
version 2.10.0
and kernlab
0.9-9.
Thanks for
your help!
Regards,
Heiko
Strathmann
______________________________________________
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.
Sorry, heres the message: Hi yes the freeze is rather a result of the kernelMatrix being non-positive definite, have a look at the eigenvalues of kernelMatrix with eigs and you will see even small negative values. This is usualy the result of small numerical inacuracies in the computation of the kernel matrix that normally do not have an effect but can cause problems. The issue is amplified by the fact that you are doing 10-fold cross validation and in effect training 220 models (sampled from the kernelMatrix) in a 20 fold loop. You can get around this issue by adding a small epsilon to the diagonal of your kernelMatrix thus making sure that all sampled kernelMatrices are positive semidefinite i.e. diag(kernelMatrix) <- diag(kernelMatrix) + 0.05 seems to do the trick for me. regards Alexandros Am Montag, den 30.11.2009, 11:22 +0100 schrieb Heiko Strathmann:
Ok, i reported it.
thanks for trying it out again.
Am 30. November 2009 11:06 schrieb Uwe Ligges
<ligges at statistik.tu-dortmund.de>:
My apologies, that must have been a copy&paste error and the
essential argument got lost. I can reproduce it now under
R-2.10.0 both Windows and Linux.
Please report your findings to the package maintainer who
might be able to debug this under Linux (probably easier than
under Windows).
Best,
Uwe Ligges
Heiko Strathmann wrote:
I tried out the code you wrote, it also works for me,
but it lacks a
parameter i use in my code.
The problem (at this computer) seems to be this
"cross"-parameter of
ksvm - if I, for example, add the parameter cross=10,
i get the old
problem:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(10, ksvm(kernel="matrix", kernelMatrix,
trainingDataYs, type="C-svc", C=2, cross=10))
gets me a frozen R process, CTRL-C does not work
anymore, and the only thing left is to kill it.
(for cross < 4, the thing still works)
(I also just reinstalled my Ubuntu and R)
Heiko Strathmann
Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe
Ligges:
Heiko Strathmann wrote:
Hello uwe,
Thanks for trying out.
the freeze happens after about 10 to
20 iterations. Did you try as many?
I just tried again:
library("kernlab")
load("freeze_workspace.RDATA")
replicate(100, ksvm(kernel="matrix",
kernelMatrix, trainingDataYs, type="C-svc",
C=2))
and everything is still fine (same on Linux).
Uwe Ligges
Am Sonntag, den 29.11.2009, 17:22
+0100 schrieb Uwe Ligges:
I just tried
ksvm(kernel="matrix",
kernelMatrix, trainingDataYs,
type="C-svc", cross=10, C=2)
several times on both
workspaces and both returned
some results after a couple of
seconds under the same
versions (R version 2.10.0 and
kernlab 0.9-9.) under Windows
XP.
There mist be something else
going on...
Best wishes,
Uwe Ligges
Heiko Strathmann wrote:
Hello again,
the freeze seems to
depend on the kernel
matrix.
With another kernel
matrix of similiar
size, gernerated with
the same
kernel, but on another
dataset, there is no
freeze.
I have put a workspace
with the working
matrix and one with
the freezing
matrix online for
testing (see old
email)
http://www-stud.uni-due.de/~sfhestra/
In my eyes this
behavior is really
strange, and i have no
clue, what to
do to solve this.
Regards,
Heiko Strathmann
Am Sonntag, den
29.11.2009, 14:21
+0100 schrieb Heiko
Strathmann:
Hello,
I am using
kernlab to do
some binary
classification
on aminoacid
strings.
I am using a
custom kernel,
so i use the
kernel="matrix" option of the
ksvm method.
My
(normalized)
kernel matrix
is of size
1309*1309, my
results vector
has the same
length.
I am using
C-svc.
My kernlab
call is
something
similiar to
this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
cross=10, C=2)
To this point,
everything
works fine.
But now, i
want to do a
search for a
good C
Parameter, so
I call the
ksvm method
multiple times
in a loop,
with changing
parameters.
This loop
freezes after
a few
iterations.
The following
simple example
also freezes
after few
iterations
(the
number
varies). See
that the ksvm
call is always
the same in
every
iteration:
for (i in
c(1:20)) {
print(i)
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
type="C-svc",
cross=10, C=2)
}
Does anybody
have an idea
what causes
this? I am new
to R and
kernlab,
perhaps i
missed
something?
I put my
workspace
online, which
contains the
kernel matrix
and the
training
labels. Simply
load
workspace,
kernlab
library and
paste the
example code
to reproduce:
http://www-stud.uni-due.de/~sfhestra/
I am using R
version 2.10.0
and kernlab
0.9-9.
Thanks for
your help!
Regards,
Heiko
Strathmann
______________________________________________
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.