[R] lasso cross-validation
Dear all, I am using cv.glmnet in r and I have the following question: The default is 10-fold cross-validation, but it is not clear to me how many times are repeated? Is it 50 repeats? I am sore if me question will be very easy for some people! Many thanks in advance, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] glm
Dear all, I am using glm with quasibinomial. What does the following error message mean: Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1 Does it mean that the predictor variable should only have zero and one or it is also possible to have continuous values between zero and one? Many thanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] UniCox in R
Thank you for your reply. My question was how to create Fig. 2? I am using UniCox; the aa=uniCoxCV gives list of aa$ devcvm aa$ncallcvm aa$se.devcvm, aa$devcv, aa$ ncallcv and aa$ folds, which data I should plot here to create the graph in Fig. 2? Many thanks, Sam --- On Wed, 8/12/10, jim holtman wrote: From: jim holtman Subject: Re: [R] UniCox in R To: "Samuel Okoye" Cc: r-help@r-project.org Date: Wednesday, 8 December, 2010, 5:25 Do a little reading on how to use the graphics commands. I would look at plot lines segments a combination of those will let you easily create the output. It would seem you need some data object that has the dimensions of the bar lengths you want to create, but given that, it is not much of a problem to solve. On Wed, Dec 8, 2010 at 8:14 AM, Samuel Okoye wrote: > > > > > Hello, > > I am interested in Figure 2 in > > http://www-stat.stanford.edu/~tibs/ftp/cus.pdf > > Can anyone tell please how to create this plot? > > Many thanks > Samuel > > > > > > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] UniCox in R
Hello, I am interested in Figure 2 in http://www-stat.stanford.edu/~tibs/ftp/cus.pdf Can anyone tell please how to create this plot? Many thanks Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] AUC
Hello, Is there is any R function computes the AUC for paired data? Many thanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm
Thank you ver much.
Is there is a function in R which is doing penalized cubic regression, say
spl.plr(), that if I have weeks = 1:9 I can use somthing like pp <-
spl.plr(weeks,c(1,3,5,7)) and for 8 and 9 will be linear? Is rcs()
library(Design) doing this?
Many thanks,
Samuel
--- On Tue, 22/6/10, Joris Meys wrote:
From: Joris Meys
Subject: Re: [R] glm
To: "Samuel Okoye"
Cc: r-help@r-project.org
Date: Tuesday, 22 June, 2010, 9:50
On Tue, Jun 22, 2010 at 1:00 AM, Samuel Okoye wrote:
> Hi,
>
> I have the following data
>
> data1 <- data.frame(count = c(0,1,1,2,4,5,13,16,14), weeks = 1:9,
> treat=c(rep("1mg",3),rep("5mg",3),rep("10mg",3)))
> and I am using
>
> library(splines)
>
> to fit
>
> glm.m <- glm(count~weeks)+as.factor(treat),family=poisson,data=data1)
>
> and I am interested in predicting the count variale for the weeks 10, 11 and
> 12 with treat 10mg and 15mg.
bad luck for you.
newdat <-data.frame(
weeks=rep(10:12,each=2),
treat=rep(c("5mg","10mg"),times=3)
)
preds <- predict(glm.m,type="response",newdata=newdat,se.fit=T)
cbind(newdat,preds)
gives as expected :
Warning message:
In bs(weeks, degree = 3L, knots = numeric(0), Boundary.knots = c(1L, :
some 'x' values beyond boundary knots may cause ill-conditioned bases
weeks treat fit se.fit residual.scale
1 10 5mg 5.934881 5.205426 1
2 10 10mg 12.041639 9.514347 1
3 11 5mg 4.345165 6.924663 1
4 11 10mg 8.816168 15.805171 1
5 12 5mg 2.781063 8.123436 1
6 12 10mg 5.642667 18.221007 1
Watch the standard errors on the predicted values. No, you shouldn't
predict outside your data space, especially when using splines. And
when interested in 15mg, well, you shouldn't put treatment as a factor
to start with.
Cheers
Joris
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
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[R] glm
Hi,
I have the following data
data1 <- data.frame(count = c(0,1,1,2,4,5,13,16,14), weeks = 1:9,
treat=c(rep("1mg",3),rep("5mg",3),rep("10mg",3)))
and I am using
library(splines)
to fit
glm.m <- glm(count~bs(weeks)+as.factor(treat),family=poisson,data=data1)
and I am interested in predicting the count variale for the weeks 10, 11 and
12 with treat 10mg and 15mg.
Thanks in advance.
Regards,
Samuel
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[R] Power calculation
Hello, Is there any R function which does power calculation for unbalanced groups (n1 neq n2)? Since power.t.test has n Number of observations (per group). Many thanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with library(SSPA)
Dear Maarten,
I have problem to use your package and I would be very thankful if you could
help me to solve this.
Regards,
Samuel
--- On Wed, 9/6/10, Uwe Ligges wrote:
From: Uwe Ligges
Subject: Re: [R] Problem with library(SSPA)
To: "Samuel Okoye"
Cc: r-help@r-project.org
Date: Wednesday, 9 June, 2010, 6:43
On 09.06.2010 15:19, Samuel Okoye wrote:
> I can't find his email
packageDescription("SSPA")
>and I have asked the same question to
>
> bioconduc...@stat.math.ethz.ch
>
> Regards,
> Samuel
>
> --- On Wed, 9/6/10, Uwe Ligges wrote:
>
> From: Uwe Ligges
> Subject: Re: [R] Problem with library(SSPA)
> To: "Samuel Okoye"
> Cc: r-help@r-project.org
> Date: Wednesday, 9 June, 2010, 5:43
>
> Same for me, but since this is a BioC package, why do you ask here?
> First you may report to the package maintainer or if that fails to the
> BioC mailing list.
>
> Best,
> Uwe Ligges
>
>
> On 09.06.2010 12:01, Samuel Okoye wrote:
>>
>> Hello,
>>
>> I have the fellowing problem and I am thankful for any advice!
>>
>> Regards,
>> Samuel
>>
>>
>>> source("http://bioconductor.org/biocLite.R";)
>> BioC_mirror = http://www.bioconductor.org
>> Change using chooseBioCmirror().
>>> biocLite("SSPA")
>> Using R version 2.11.0, biocinstall version 2.6.7.
>> Installing Bioconductor version 2.6 packages:
>> [1] "SSPA"
>> Please wait...
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.6/bioc/bin/windows/contrib/2.11/SSPA_1.4.0.zip'
>> Content type 'application/zip' length 305310 bytes (298 Kb)
>> opened URL
>> downloaded 298 Kb
>>
>> package 'SSPA' successfully unpacked and MD5 sums checked
>>
>>> library(SSPA)
>> Loading required package: qvalue
>> Loading
>> required package: tcltk
>> Loading Tcl/Tk interface ... done
>> Error : .onAttach failed in attachNamespace() for 'SSPA', details:
>> call: fun(...)
>> error: could not find function "addVigs2WinMenu"
>> Error: package/namespace load failed for 'SSPA'
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
>> [4] LC_NUMERIC=C LC_TIME=English_United
>> Kingdom.1252
>>
>> attached base packages:
>> [1] tcltk stats graphics grDevices utils datasets
>> methods base
>>
>> other attached
>> packages:
>> [1] qvalue_1.22.0
>>
>> loaded via a namespace (and not attached):
>> [1] limma_3.4.3 SSPA_1.4.0 tools_2.11.0
>>
>> ##
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
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Re: [R] Problem with library(SSPA)
I can't find his email and I have asked the same question to
bioconduc...@stat.math.ethz.ch
Regards,
Samuel
--- On Wed, 9/6/10, Uwe Ligges wrote:
From: Uwe Ligges
Subject: Re: [R] Problem with library(SSPA)
To: "Samuel Okoye"
Cc: r-help@r-project.org
Date: Wednesday, 9 June, 2010, 5:43
Same for me, but since this is a BioC package, why do you ask here?
First you may report to the package maintainer or if that fails to the
BioC mailing list.
Best,
Uwe Ligges
On 09.06.2010 12:01, Samuel Okoye wrote:
>
> Hello,
>
> I have the fellowing problem and I am thankful for any advice!
>
> Regards,
> Samuel
>
>
>> source("http://bioconductor.org/biocLite.R";)
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>> biocLite("SSPA")
> Using R version 2.11.0, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "SSPA"
> Please wait...
>
> trying URL
> 'http://www.bioconductor.org/packages/2.6/bioc/bin/windows/contrib/2.11/SSPA_1.4.0.zip'
> Content type 'application/zip' length 305310 bytes (298 Kb)
> opened URL
> downloaded 298 Kb
>
> package 'SSPA' successfully unpacked and MD5 sums checked
>
>> library(SSPA)
> Loading required package: qvalue
> Loading
> required package: tcltk
> Loading Tcl/Tk interface ... done
> Error : .onAttach failed in attachNamespace() for 'SSPA', details:
> call: fun(...)
> error: could not find function "addVigs2WinMenu"
> Error: package/namespace load failed for 'SSPA'
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> Kingdom.1252
>
> attached base packages:
> [1] tcltk stats graphics grDevices utils datasets methods base
>
> other attached
> packages:
> [1] qvalue_1.22.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.4.3 SSPA_1.4.0 tools_2.11.0
>
> ##
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Problem with library(SSPA)
Hello,
I have the fellowing problem and I am thankful for any advice!
Regards,
Samuel
> source("http://bioconductor.org/biocLite.R";)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite("SSPA")
Using R version 2.11.0, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] "SSPA"
Please wait...
trying URL
'http://www.bioconductor.org/packages/2.6/bioc/bin/windows/contrib/2.11/SSPA_1.4.0.zip'
Content type 'application/zip' length 305310 bytes (298 Kb)
opened URL
downloaded 298 Kb
package 'SSPA' successfully unpacked and MD5 sums checked
> library(SSPA)
Loading required package: qvalue
Loading
required package: tcltk
Loading Tcl/Tk interface ... done
Error : .onAttach failed in attachNamespace() for 'SSPA', details:
call: fun(...)
error: could not find function "addVigs2WinMenu"
Error: package/namespace load failed for 'SSPA'
> sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United
Kingdom.1252
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods
base
other attached
packages:
[1] qvalue_1.22.0
loaded via a namespace (and not attached):
[1] limma_3.4.3 SSPA_1.4.0 tools_2.11.0
##
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[R] simulation of censoring data
Dear all,
I would like to understand the effect of censoring in a linear model therefore
I am doing the following
n <- 20
cen <- sample(x=c(0,1), size=n-1, replace=TRUE, prob=c(0.8,0.2))
cen <- c(cen,0)
x <- rnorm(n,0,1)
tt <- -1+x+log(-log(1-runif(n)))+0.5767
y <- c()
for(i in 1:n){
y[i] <- min(tt[i],cen[i])
}
moda <- lm(tt~x)
modb <- lm(y~x)
Is this simulation correct? Thank you in advance!
Samuel
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[R] variation in one variable
Hello, Could you please tell me wether there is any function in R that tell me how many subgroup in one variable I have? So for example if my data are x <- c(rnorm(50,50,3),rgamma(50,2,1),runif(50,0,1)) I want to know how many group I have? Many thank in advance, Samuel --- On Thu, 9/17/09, Samuel Okoye wrote: From: Samuel Okoye Subject: SVM To: r-h...@stat.math.ethz.ch Date: Thursday, September 17, 2009, 4:39 AM Hello, I have 12 sample each sample has got 1000 observation, i.e I have a matrix X with 1000 rows and 12 columns! m <- svm(t(X)) p <- predict (m) Can anyone tell me how to use svmtrain() in R! Many Yhanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SVM
Thank you again for your reply! What I would like to do is to class my sample into two group (0,1). I am not sure which method to apply and whether the svm is the correct one! However, when I apply the below R code I get two group the samples in TRUE and FALSE. Can I take this result to put TRUE samples in group A and FALSE samples in group B? Best wishes, Samuel PS: I will not give up to understand statistics! --- On Thu, 9/17/09, Steve Lianoglou wrote: From: Steve Lianoglou Subject: Re: [R] SVM To: "Samuel Okoye" Cc: r-h...@stat.math.ethz.ch Date: Thursday, September 17, 2009, 2:47 PM Hi, On Sep 17, 2009, at 5:34 PM, Samuel Okoye wrote: > Thank you for your reply! Yes, I am using the svm and I do not have new data > (how do you create new data?), all I have these 12 samples which I want to > classify (predict) these into two group so that I do have six sample in each > group? I'm not really sure where to begin ... what are you trying to do, exactly? Why do you think you want to build an SVM? What do you expect it to do for you? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SVM
Thank you for your reply! Yes, I am using the svm and I do not have new data (how do you create new data?), all I have these 12 samples which I want to classify (predict) these into two group so that I do have six sample in each group? Many thanks, Samuel --- On Thu, 9/17/09, Steve Lianoglou wrote: From: Steve Lianoglou Subject: Re: [R] SVM To: "Samuel Okoye" Cc: r-h...@stat.math.ethz.ch Date: Thursday, September 17, 2009, 8:36 AM Hi, On Sep 17, 2009, at 7:39 AM, Samuel Okoye wrote: > Hello, > > I have 12 sample each sample has got 1000 observation, i.e I have a matrix X > with 1000 rows and 12 columns! > > m <- svm(t(X)) > p <- predict (m) > > Can anyone tell me how to use svmtrain() in R! I guess you're using the svm in the e1071 package? What's svmtrain? The call to "svm" trains the svm. The call to predict uses it on new data, but you need to give it new data to predict on. You have: p <- predict(m) What exactly do you want your model to do? Predict on what? Please see the code in the Examples section of ?svm .. it's pretty straight forward. Let us know what problems you're having understanding those examples and we can try to offer some insight. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SVM
Hello, I have 12 sample each sample has got 1000 observation, i.e I have a matrix X with 1000 rows and 12 columns! m <- svm(t(X)) p <- predict (m) Can anyone tell me how to use svmtrain() in R! Many Yhanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ANCOVA
Hello, Could you please help me in the following question: I have 16 persons 6 take 0.5 mg, 6 take 0.75 mg and 4 take placebo! Can I use the ANCOVA and t-test in this case? Is it possible in R? Thank you in advance, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SAS data
Hello, I am trying to read the SAS file MyData.sa7bdat in R! This file is saved under D:\data! I therefore wrote > path <-"D:/SasData" > sashome <- "C/Progra, Files/SAS Institute/9_1/SAS" > sascmd <- file.path(sashome, "sas.exe") > MyData <- read.ssd(path, "MyData", sascmd=sascmd) The results what I get: SAS failed. SAS program at C:\DOCUME~1\Temp\RtmpcTlKtb\file4eb43288.sas The log file will be file4eb43288.log in the current directory NULL Warning message: SAS return code was 2 in: read.ssd(path, "MyData", sascmd = sascmd) Thank you in advance! Sam - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] y_hat
Hello, suppose one has the following values x1 <- rnorm(10,5,1) x2 <- rgamma(10,5,1) y <- rnorm(10,4,1) mydat <- data.frame(y,x1,x2) then one can use glm like mod <- glm(y~x1+x2, data=mydat, family=gaussian) But how could I estimate y_hat? Thanks alot! Sam - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with times
Hello, I have got the following problem:
> times <- c("02.07.2007", "03.07.2007","03.09.2007", "04.07.2007","05.07.2007")
> mode(times)
[1] "numeric"
> tim <- as.character(times)
> mode(tim)
[1] "character"
> sort(times)
[1] "02.07.2007" "03.07.2007" "03.09.2007" "04.07.2007" "05.07.2007"
Is it possible to get
> function(sort(times))
[1] "02.07.2007" "03.07.2007" "04.07.2007" "05.07.2007" "03.09.2007"
Thank you very much in advance,
Sam
-
Pinpoint customers who are looking for what you sell.
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[R] sort time
Hello, I have got the following problem:
> times <- c("02.07.2007", "03.07.2007","03.09.2007",
"04.07.2007","05.07.2007")
> mode(times)
[1] "numeric"
> tim <- as.character(times)
> mode(tim)
[1] "character"
> sort(times)
[1] "02.07.2007" "03.07.2007" "03.09.2007" "04.07.2007" "05.07.2007"
Is it possible to get
> function(sort(times))
[1] "02.07.2007" "03.07.2007" "04.07.2007" "05.07.2007" "03.09.2007"
Thank you very much in advance,
Sam
-
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[R] plot or boxplot!
Hello,
if we suppose that
times <- c("2006-05-14", "2006-06-12", "2006-06-12", "2006-05-14",
"2006-05-14", "2006-06-12")
value <- c(2,3,1,4,3,1)
then with
plot(times, value)
we have two boxplots in one graph for 2006-05-14 and 2006-06-12 respectively!
Is it possible to have them in a scatterplot? and if I sort the data as
x <- data.frame(times, value)
x <- x[order(times),]
Is it possible to create a new variable which contains 1 for 2006-05-14 and 2
for 2006-06-12?
Thank you very much in advance!
-
Luggage? GPS? Comic books?
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[R] date
Hello,
I have got the following problem:
> setwd("C:/temp")
> library(xlsReadWrite)
> MyData <- read.xls(file="Mappe1.xls", colNames = TRUE,dateTimeAs =
> "isodatetime")
> attach(MyData)
> MyData
name value times
1 A1 2 2006-05-12
2 A2 3 2006-05-16
3 A3 1 2006-05-12
4 A4 4 2006-05-12
5 A5 2 2006-05-16
6 A6 1 2006-05-12
> plot(times,value)
Error
Could you help me please?
Thanks alot,
Samuel
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
