Re: [R] Tcl\tk not supported on this system
This is covered in the "R Installation and Administration" manual. You need to
specify the location of your tclConfig.sh and tkConfig.sh files.
Patrick Richardson
Biostatistician - Laboratory of Translational Medicine
Van Andel Research Institute
Grand Rapids, MI 49503
ph. 616-234-5787
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Michael Gormley
Sent: Friday, August 08, 2008 1:29 PM
To: r-help@r-project.org
Subject: [R] Tcl\tk not supported on this system
trying to install the pbatR package, I was greeted with the error
Error: package 'tcltk' does not have a name space
Execution halted
Directly installing the package tcltk2 returned the following error:
Loading required package: tcltk
Error in firstlib(which.lib.loc, package) :
Tcl/Tk support is not available on this system
I have seen from previous posts that tcl/tk must be present when R is
installed.
I tried reinstalling R from source using
./configure
make
and although the installation went fine I received the same errors.
Typing rpm -qa|grep tcl returns:
tclx-8.3.5-4
tcl-8.4.7-2
tcl-8.4.7-2
Typing rpm -qa|grep tk returns:
gtkspell-2.0.7-2
atk-1.8.0-2
gtk+-1.2.10-33
gtk2-2.4.13-22
authconfig-gtk-4.6.10-rhel4.3
gtkhtml2-2.6.2-1
gtk-engines-0.12-6.el4
tk-8.4.7-2
gtksourceview-1.1.0-4
gtk-engines-0.12-6.el4
tk-8.4.7-2
gnome-python2-gtkhtml2-2.6.0-3
gtkglarea-1.2.2-16
gtk2-engines-2.2.0-7.el4
gtkhtml3-3.3.2-6.EL
usermode-gtk-1.74-1
atk-1.8.0-2
gtk2-2.4.13-22
pygtk2-libglade-2.4.0-1
gtk+-1.2.10-33
gtkhtml2-2.6.2-1
pygtk2-2.4.0-1
So it seems that tcl and tk are present on the system. I saw a post
suggesting that I may need some development packages? What is a good place
to find these packages?
I am running R version 2.5.1 on a Linux machine running Redhat Enterprise 3.
Let me know if you need any more info on the operating system and if there
are any ideas on how to resolve these issues.
Thanks,
Michael Gormley
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Re: [R] Test of Homogeneity of Variances
What are your hypotheses? Once you state what they are, interpretation should
be straightforward.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daren Tan
Sent: Friday, August 22, 2008 11:18 AM
To: [EMAIL PROTECTED]
Subject: [R] Test of Homogeneity of Variances
I am testing the homogeneity of variances via bartlett.test and fligner.test.
Using the following example, how should I interpret the p-value in order to
accept or reject the null hypothesis ?
set.seed(5)
x <- rnorm(20)
bartlett.test(x, rep(1:5, each=4))
Bartlett test of homogeneity of variances
data: x and rep(1:5, each = 4)
Bartlett's K-squared = 1.7709, df = 4, p-value = 0.7778
fligner.test(x, rep(1:5, each=4))
Fligner-Killeen test of homogeneity of variances
data: x and rep(1:5, each = 4)
Fligner-Killeen:med chi-squared = 1.0819, df = 4, p-value = 0.8971
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Re: [R] XP/Vista/Office 2007/IE Compatibility question
http://cran.r-project.org/bin/windows/base/rw-FAQ.html (for the first two
questions anyway)
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED]
Sent: Monday, August 25, 2008 10:31 AM
To: r-help@r-project.org
Subject: [R] XP/Vista/Office 2007/IE Compatibility question
Good morning. My client currently has Windows 2000 and Office 2000.
They are planning to upgrade to Windows XP/Vista/Office 2007. Some
computers have R installed. I don't have a version number. I'm
working off of a spreadsheet. Please respond to the following
questions at your earliest convenience:
1) What versions, if any, of R are compatible with XP? If no
compatible version exists on our machines, what is the cost involved in
upgrading?
1) What versions, if any, of R are compatible with Vista? If no
compatible version exists on our machines, what is the cost involved in
upgrading?
1) What versions, if any, of R are compatible with Office 2007? If no
compatible version exists on our machines, what is the cost involved in
upgrading?
1) If applicable, which versions of Internet Explorer are compatible
with R? If no compatible version exists on our machines, what is the
cost involved in upgrading?
Thanks,
Isabe
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Re: [R] Help understanding lrm function of Design library
I found Professor Harrell's book answered most of my questions as it contains
discussion of both Hmisc and Design libraries
.
http://www.amazon.com/Regression-Modeling-Strategies-Frank-Harrell/dp/0387952322/ref=sr_1_2?ie=UTF8&qid=1250596657&sr=8-2
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Noah Silverman
Sent: Monday, August 17, 2009 5:21 PM
To: r help
Subject: [R] Help understanding lrm function of Design library
Hi,
I'm developing an experiment with logistic regression.
I've come across the lrm function in the Design library.
While I understand and can use the basic functionality, there are a ton
of options that go beyond my knowledge.
I've carefully read the help page for lrm, but don't understand many of
the arguments and optional return values.
(penalty, penalty.matrix, strata.penalty, var.penalty, weights)
Additionally, there are several items returned in the model that I don't
understand.
(Max Derriv, Model L.R, C, Dxy, Gamma, Tau-a, R2, Briar, Wald Z)
1) Could someone point me to an online resource where I could learn
more? (I'm big on trying to teach myself.)
2) Or, alternately, does anybody want to explain a few things for me?
Thanks!
--
Noah
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[R] Transform data for repeated measures
I have a dataset that I'm trying to rearrange for a repeated measures analysis:
It looks like:
patient basefev1 fev11h fev12h fev13h fev14h fev15h fev16h fev17h fev18h drug
201 2.46 2.68 2.76 2.50 2.30 2.14 2.40 2.33 2.20a
202 3.50 3.95 3.65 2.93 2.53 3.04 3.37 3.14 2.62a
203 1.96 2.28 2.34 2.29 2.43 2.06 2.18 2.28 2.29a
204 3.44 4.08 3.87 3.79 3.30 3.80 3.24 2.98 2.91a
And I want to make it look like:
Patient FEV time drug
201 2.460 a
201 2.681 a
201 2.762 a
201 2.503 a
And so on . . . . . There would be 9 "time" and drug is a factor variable.
I know there is a way to do this in R but I cannot remember the function. I've
looked at the transpose function in (base) but that doesn't seem to be what I
want. Can something like this be done easily from within package functions or
would it require writing something custom? Another program would use something
like the transpose procedure, but I'm trying to stay away from that program.
Thanks,
Patrick
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets tcltk splines graphics stats utils
methods base
other attached packages:
[1] svSocket_0.9-43 svMisc_0.9.48 TinnR_1.0.3 R2HTML_1.59-1 Hmisc_3.6-1
survival_2.35-4
loaded via a namespace (and not attached):
[1] cluster_1.12.0 grid_2.9.2 lattice_0.17-25 tools_2.9.2
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[R] Error message in Design library
This was working a few weeks ago, but perhaps the package has been updated
since then.
model.1 <- lrm(response ~ p_value, data=c_abl_oncogene_1_RTK)
When I run the following command . . . .
prediction.1 <- predict(model.1, type=c("fitted"))
I get the following error message. . . .
Error in predictDesign(object, ..., type = "lp", se.fit = FALSE) :
could not find function "Varcov"
It seems like a required function of "predict" may be missing in the Design
package (although I doubt Professor Harrell would have overlooked this).
Perhaps its my own stupidity with something. Any ideas what could be causing
this? I'm sorry I didn't post a reproducable example, but it a lot of code.
Any help would be appreciated.
Best regards,
Patrick
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid datasets tcltk grDevices splines graphics utils
stats methods base
other attached packages:
[1] Design_2.2-0ROCR_1.0-2 gplots_2.7.1caTools_1.9
bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1svSocket_0.9-43 svMisc_0.9.48
TinnR_1.0.3 R2HTML_1.59-1
[12] Hmisc_3.7-0 MASS_7.2-48 survival_2.35-7
loaded via a namespace (and not attached):
[1] cluster_1.12.0 lattice_0.17-25 tools_2.9.2
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Re: [R] Bartlett Test
?bartlett.test
>From the help page "If x is a list, its elements are taken as the samples or
>fitted linear models to be compared for homogeneity of variances. In this
>case, the elements must either all be numeric data vectors or fitted linear
>model objects, g is ignored, and one can simply use bartlett.test(x) to
>perform the test. If the samples are not yet contained in a list, use
>bartlett.test(list(x, ...)).
Otherwise, x must be a numeric data vector, and g must be a vector or factor
object of the same length as x giving the group for the corresponding elements
of x. "
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Amit Patel
Sent: Monday, March 01, 2010 9:26 AM
To: r-help@r-project.org
Subject: [R] Bartlett Test
Hi
I am trying to conduct a Bartlett test between two groups Samp 1 and Samp 2,
both of which are vectors of equal length. I cant find any information on how
to do this. Does the data need to be in a structured list.
Thanks in advance
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The information transmitted is intended only for the per...{{dropped:8}}
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Re: [R] Normal distribution
?shapiro.test
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Noela Sánchez
Sent: Thursday, October 01, 2009 12:47 PM
To: r-help@r-project.org
Subject: [R] Normal distribution
Hi,
I am dealing with how to check in R if some data that I have belongs to a
normal distribution or not. I am not interested in obtaining the theoreticall
frequencies. I am only interested in determing if (by means of a test as
Kolmogorov, or whatever), if my data are normal or not.
But I have tried with ks.test() and I have not got it.
--
Noela
Grupo de Recursos Marinos y Pesquerías
Universidad de A Coruña
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Re: [R] Normal distribution
I don't disagree. And to that end one could probably look at the skewness and
kurtosis values as well. A combination of several techniques would probably be
a good idea.
Best regards,
Patrick
-Original Message-
From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com]
Sent: Thursday, October 01, 2009 1:18 PM
To: Richardson, Patrick
Cc: Noela Sánchez; r-help@r-project.org
Subject: Re: [R] Normal distribution
Hi,
I think you can also use a qq-plot to do the same, no? You won't get a
statistic score + p.value, but perhaps you're more of a visual person?
:-)
-steve
On Thu, Oct 1, 2009 at 12:56 PM, Richardson, Patrick
wrote:
> ?shapiro.test
>
>
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of Noela Sánchez
> Sent: Thursday, October 01, 2009 12:47 PM
> To: r-help@r-project.org
> Subject: [R] Normal distribution
>
> Hi,
>
> I am dealing with how to check in R if some data that I have belongs to a
> normal distribution or not. I am not interested in obtaining the theoreticall
> frequencies. I am only interested in determing if (by means of a test as
> Kolmogorov, or whatever), if my data are normal or not.
>
> But I have tried with ks.test() and I have not got it.
>
>
> --
> Noela
> Grupo de Recursos Marinos y Pesquerías
> Universidad de A Coruña
>
>[[alternative HTML version deleted]]
>
> This email message, including any attachments, is for ...{{dropped:25}}
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[R] Greater than less than in "ifelse"
I'm trying to categorize a continuous variable (yes, I know that's horrible,
but I'm trying to reproduce some exercises from a textbook) and don't really
know an efficient way to do this.
I have a data frame that looks like:
surv_time relapse sex log_WBC rx
1 35 0 11.45 0
2 34 0 11.47 0
3 32 0 12.20 0
4 32 0 12.53 0
And I'm trying to categorize log_WBC into:
(0-2.30) = "low"
(2.31-3.00)= "medium"
(>3.00) = "high"
I've used an ifelse statement such as:
anderson$log_WBC <- ifelse(anderson$log_WBC<2.30,"low",anderson$log_WBC)
Is there a way to use "greater than" "less than" syntax within the context of
an ifelse statement? Or can someone point me to a function that will do this
easier.
Many Thanks,
Patrick
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Re: [R] Warning message when Loading package svMisc in R 2.10.0
svMisc was built and submitted to CRAN under 2.9.2. If you are trying to use it
within TINN, TINN will still work. The package needs to be built under 2.10 and
resubmitted. I'm sure Phillipe will get to it in due time.
Best regards,
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Orvalho Augusto
Sent: Tuesday, October 27, 2009 3:14 AM
To: r-help@r-project.org
Subject: Re: [R] Warning message when Loading package svMisc in R 2.10.0
I did not try. But you try to update all the packages with:
update.packages()
Good luck
Caveman
On Tue, Oct 27, 2009 at 6:28 AM, Qi Li wrote:
> Hi,
>
> I have a problem when using R 2.10.0,
>
> Loading required package: svMisc
> Warning message:
> package 'svMisc' was built under R version 2.9.1 and help will not work
> correctly
>
> HOW to fix it?
> __
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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.
>
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[R] Setting Repositories in the .Rprofile file
Is there any way to select (during startup) all repositories by modifying the
Rprofile.site file? If so, could someone let me know the syntax to use (or
direct me to where I can find it)?
Thank you,
Patrick
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Re: [R] how to import data from excel to R
Well, first of all it doesn't look like you're trying to read an excel file as
the file you are trying you specify is "data.txt" not "data.xls".
Try:
library(gdata)
?read.xls
HTH,
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of sta_2...@spectrum.net.in
Sent: Thursday, December 17, 2009 12:25 PM
To: r-help@r-project.org
Subject: [R] how to import data from excel to R
Hi,
I am using R and I want to know how data can be transferred from Excel
Spread sheet to R for analyzing. I have done like this
mydata<-read.table("C:\Documents and Settings\admin\Desktop\data.txt");
but its not working how can i do it
regards
Sarath Sankar V
Spectrum Softtech Solution
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Re: [R] glm fit
Interesting. Now the fifth homework question you have posted here. As was stated before (by several members) this is not a homework forum. Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of mathallan Sent: Friday, May 08, 2009 5:50 AM To: r-help@r-project.org Subject: [R] glm fit Hi, I try to ask here, because I hope someone will help me understand this problem- I have fittet a glm in R with the results > glm1 <- > glm(log(claims)~log(sum)*as.factor(grp),family=gaussian(link="identity")) > summary(glm1) Call: glm(formula = log(claims) ~ log(sum) * as.factor(grp), family = gaussian(link = "identity")) Deviance Residuals: Min 1Q Median 3Q Max -6.6836 -1.3626 -0.2576 1.2038 8.2480 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 3.525657 0.436102 8.084 8.18e-16 *** log(sum)0.334288 0.025668 13.024 < 2e-16 *** as.factor(grp)2 0.434262 0.976240 0.445 0.6565 as.factor(grp)3 3.666490 1.436471 2.552 0.0107 * as.factor(grp)4 0.040782 1.024730 0.040 0.9683 log(sum):as.factor(grp)2 0.007719 0.061914 0.125 0.9008 log(sum):as.factor(grp)3 -0.209986 0.091578 -2.293 0.0219 * log(sum):as.factor(grp)4 0.059342 0.067320 0.881 0.3781 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for gaussian family taken to be 3.693731) Null deviance: 15839 on 4035 degrees of freedom Residual deviance: 14878 on 4028 degrees of freedom AIC: 16737 Number of Fisher Scoring iterations: 2 But i'm not sure what I get out of the summary. What does it tell me? How should the formula for Y look like, out from the summary? Is it something like Y=0.334288*X_sum+0.434262*X_2+ ?? And when I get a expression for Y, what does it tell me? Is it an expected expression? Can anyone help me please? -- View this message in context: http://www.nabble.com/glm-fit-tp23443121p23443121.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. __ 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] Why can't I use ADF.test?
Since you provided no code, the following is just a guess, Try:
install.packages("uroot")
library(uroot)
Then try your analysis again.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of DongHongwei
Sent: Wednesday, June 24, 2009 3:06 PM
To: r-help@r-project.org
Subject: [R] Why can't I use ADF.test?
Greetings!
I'm trying to use R to test the unit root for a univariate data. By this link:
http://rss.acs.unt.edu/Rdoc/library/uroot/html/ADF.test.html
it tells me that I can use the function ADF.test(). However, when I tried this
in R, I got this message:
"Error: could not find function "ADF.test"".
I'm confused by this. Anyone could give me some hints? Thanks.
Hongwei
_
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Re: [R] install.package("TinnR") - there is no package called 'TinnR'
Hi Martin,
If all else fails, you could download the package from
http://cran.r-project.org/web/packages/TinnR/index.html
and install as a .zip file from within R.
That is bizarre that R cannot find the package. I've had no problems
downloading and installing.
Best regards,
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Martin Tomko
Sent: Tuesday, March 24, 2009 8:25 AM
To: David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] install.package("TinnR") - there is no package called 'TinnR'
David,
that is not helpful. I KNOW that TinnR is a standalone editor. If you
had a look at the Rprofile.site required by TinnR, you would notice the
part of the code I send earlier:
# check necesary packages
necessary = c('TinnR', 'svSocket')
installed = necessary %in% installed.packages()[, 'Package']
if (length(necessary[!installed]) >=1)
install.packages(necessary[!installed], dep=T).
These are executed by the TinnR editor upon start. The TinnR package
MUST therefore exist, and is required.
Hope that someone else can REALLY help.
Martin
David Winsemius wrote:
> Tinn-R is not an R package. It is a standalone text editor:
>
> http://www.lmgtfy.com/?q=tinn-r
>
>
> -- David Winsemius
>
> On Mar 24, 2009, at 7:05 AM, Martin Tomko wrote:
>
>> I have troubles make TinnR 2.2.0.2 work, it seems that the dependency
>> on the package TinnR that cannot be found (I tried also manual
>> downloads, but I cannot find the package anywhere on any CRAN mirror).
>>
>> I even set a default cran mirror in the Rprofile.site file, so that
>> the later command can find it:
>> # check necesary packages
>> necessary = c('TinnR', 'svSocket')
>> installed = necessary %in% installed.packages()[, 'Package']
>> if (length(necessary[!installed]) >=1)
>> install.packages(necessary[!installed], dep=T).
>>
>> No luck. Even manually issuing the comand in Rterm fails, package
>> 'TinnR' is not available.
>> Any idea how I could make my TinnR work? I googled extensively, but
>> without luck...
>>
>> Thanks
>> Martin
>>
>> __
>> 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.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>
>
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[R] Separating variables in read.table
If I have a table (we'll call it, "test") containing two columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables without
having to code:
i <- test$i
x1 <- test$x1
x2 <- test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
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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] Separating variables in read.table
If I have a table (we'll call it, "test") containing seven columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables without
having to code:
i <- test$i
x1 <- test$x1
x2 <- test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
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Re: [R] Separating variables in read.table
Yes. attach() was what I was needing. Thanks to all those who replied. Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Johannes Huesing Sent: Friday, April 17, 2009 4:18 PM To: r-help@r-project.org Subject: Re: [R] Separating variables in read.table Richardson, Patrick [Fri, Apr 17, 2009 at 09:31:35PM CEST]: > If I have a table (we'll call it, "test") containing seven columns (as below): > > i x1 x2 x3 x4 x5 y > 0 1.125 0.232 7.160 0.0859 8.905 1.5563 > 7 0.920 0.268 8.804 0.0865 7.388 0.8976 > 150.835 0.271 8.108 0.0852 5.348 0.7482 > 221.000 0.237 6.370 0.0838 8.056 0.7160 > 291.150 0.192 6.441 0.0821 6.960 0.3130 > 370.990 0.202 5.154 0.0792 5.690 0.3617 > 440.840 0.184 5.896 0.0812 6.932 0.1139 > 580.650 0.200 5.336 0.0806 5.400 0.1139 > > > Is there a simple command to break this table into individual variables > without having to code: > > i <- test$i > x1 <- test$x1 > x2 <- test$x2 ?attach Does this do what you want? -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:johan...@huesing.name from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, "Life on the Mississippi") __ 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. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. __ 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] Rhelp
Please read the posting guide at http://www.R-project.org/posting-guide.html
and repost your question.
You have not provided the information need to properly address your
difficulties.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Slusher, Nicole
Sent: Wednesday, April 22, 2009 3:49 PM
To: r-help@r-project.org
Subject: [R] Rhelp
Hello,
I am trying to run R on my Mac (OS10.5.6) and am having trouble installing
and running packages (genefilter in particular in Bioconductor)
I've tried re-installing R and it hasn't solved the issue.
Thanks,
~Nicole Slusher
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and provide commented, minimal, self-contained, reproducible code.
[R] Cannot update.packages (error message)
When trying to update (various) packages using update.packages() I get the
following error message for various packages
package 'fBasics' successfully unpacked and MD5 sums checked
Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
>
This happens with other packages besides fBasics (Matrix, as well as others)
and I have switched mirrors and the same thing occurs.
Any suggestions?
Best regards,
Patrick
Win XP SP3
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods base
other attached packages:
[1] svSocket_0.9-5 TinnR_1.0.3R2HTML_1.59-1 Hmisc_3.5-2
loaded via a namespace (and not attached):
[1] cluster_1.11.13 grid_2.9.0 lattice_0.17-22 svMisc_0.9-5tools_2.9.0
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and provide commented, minimal, self-contained, reproducible code.
[R] R-2.9.0 malformed bundle DESCRIPTION file, no Contains field
When trying to update (various) packages using update.packages() I get the
following error message for various packages
package 'fBasics' successfully unpacked and MD5 sums checked Error in
unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
>
This happens with other packages besides fBasics (Matrix, as well as others)
and I have switched mirrors and the same thing occurs.
Any suggestions?
Best,
Patrick
Win XP SP3
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods base
other attached packages:
[1] svSocket_0.9-5 TinnR_1.0.3R2HTML_1.59-1 Hmisc_3.5-2
loaded via a namespace (and not attached):
[1] cluster_1.11.13 grid_2.9.0 lattice_0.17-22 svMisc_0.9-5tools_2.9.0
This email message, including any attachments, is for th...{{dropped:9}}
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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.
Re: [R] Cannot update.packages (error message)
Hi Uwe,
I was able to reinstall every package you suggested except for "gregmisc" (see
below)
package 'gregmisc' successfully unpacked and MD5 sums checked
Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
I've again tried update.packages() and the ones that fail are:
fBasics
Matrix
plm
R2HTML
timeSeries
zoo
When trying to install the above packages I receive the same error are
originally reported (same as in "gregmisc").
Any ideas?
Thanks,
Patrick
-Original Message-
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Tuesday, April 28, 2009 10:01 AM
To: Richardson, Patrick
Cc: r-help@r-project.org
Subject: Re: [R] Cannot update.packages (error message)
Richardson, Patrick wrote:
> When trying to update (various) packages using update.packages() I get the
> following error message for various packages
>
> package 'fBasics' successfully unpacked and MD5 sums checked
> Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
> malformed bundle DESCRIPTION file, no Contains field
Can you try to reinstall (with install.packages()) all your installed
package *bundles* (the 8 on CRAN are VR, CoCo, dse, hoa, gregmisc,
BACCO, empiricalBayes, forecasting). I hope update packages will work
again afterwards.
Best wishes,
Uwe Ligges
> This happens with other packages besides fBasics (Matrix, as well as others)
> and I have switched mirrors and the same thing occurs.
>
> Any suggestions?
>
> Best regards,
>
> Patrick
> Win XP SP3
>
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets tcltk utils methods base
>
> other attached packages:
> [1] svSocket_0.9-5 TinnR_1.0.3R2HTML_1.59-1 Hmisc_3.5-2
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.13 grid_2.9.0 lattice_0.17-22 svMisc_0.9-5
> tools_2.9.0
>
> This email message, including any attachments, is for ...{{dropped:15}}
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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.
Re: [R] Cannot update.packages (error message)
Uwe,
I deleted "gregmisc" from by library folder and ran update.packages() again and
I still get the same error:
package 'fBasics' successfully unpacked and MD5 sums checked
Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
>
Best regards,
Patrick
-Original Message-
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Tuesday, April 28, 2009 11:01 AM
To: Richardson, Patrick
Cc: r-help@r-project.org
Subject: Re: [R] Cannot update.packages (error message)
Richardson, Patrick wrote:
> Hi Uwe,
>
> I was able to reinstall every package you suggested except for "gregmisc"
> (see below)
>
> package 'gregmisc' successfully unpacked and MD5 sums checked
> Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
> malformed bundle DESCRIPTION file, no Contains field
>
> I've again tried update.packages() and the ones that fail are:
> fBasics
> Matrix
> plm
> R2HTML
> timeSeries
> zoo
>
> When trying to install the above packages I receive the same error are
> originally reported (same as in "gregmisc").
>
> Any ideas?
Arrrgh, I made anoter mistake with gregmisc which is now fixed.
Can you try in 24 hours to reinstall gregmisc and try update.packages()
after that?
Or for even better for now: Please delete the gregmisc folder in your
library and try to run update.packages after that. Still problems?
Uwe
> Thanks,
>
> Patrick
>
>
> -Original Message-
> From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
> Sent: Tuesday, April 28, 2009 10:01 AM
> To: Richardson, Patrick
> Cc: r-help@r-project.org
> Subject: Re: [R] Cannot update.packages (error message)
>
>
>
> Richardson, Patrick wrote:
>> When trying to update (various) packages using update.packages() I get the
>> following error message for various packages
>>
>> package 'fBasics' successfully unpacked and MD5 sums checked
>> Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
>> malformed bundle DESCRIPTION file, no Contains field
>
>
> Can you try to reinstall (with install.packages()) all your installed
> package *bundles* (the 8 on CRAN are VR, CoCo, dse, hoa, gregmisc,
> BACCO, empiricalBayes, forecasting). I hope update packages will work
> again afterwards.
>
> Best wishes,
> Uwe Ligges
>
>
>
>
>> This happens with other packages besides fBasics (Matrix, as well as others)
>> and I have switched mirrors and the same thing occurs.
>>
>> Any suggestions?
>>
>> Best regards,
>>
>> Patrick
>> Win XP SP3
>>
>> R version 2.9.0 (2009-04-17)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets tcltk utils methods
>> base
>>
>> other attached packages:
>> [1] svSocket_0.9-5 TinnR_1.0.3R2HTML_1.59-1 Hmisc_3.5-2
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.13 grid_2.9.0 lattice_0.17-22 svMisc_0.9-5
>> tools_2.9.0
>>
>> This email message, including any attachments, is for th...{{dropped:9}}
>>
>> __
>> 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.
> This email message, including any attachments, is for ...{{dropped:11}}
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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.
Re: [R] Kolmogorov-Smirnov test
This is the third homework question you have asked the list to do for you. How
many more should we expect?
The posting guide is pretty clear in that: " Basic statistics and classroom
homework: R-help is not intended for these."
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of mathallan
Sent: Wednesday, April 29, 2009 10:52 AM
To: r-help@r-project.org
Subject: [R] Kolmogorov-Smirnov test
I got a distribution function and a empirical distribution function. How do I
make to Kolmogorov-Smirnov test in R.
Lets call the empirical distribution function >Fn on [0,1]
and the distribution function >F on [0,1]
ks.test( )
thanks for the help
--
View this message in context:
http://www.nabble.com/Kolmogorov-Smirnov-test-tp23296096p23296096.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Variable Combinations in Regression
Let's say I have 8 variables and I want to generate all combinations of those
variables (In pairs, threes fours, etc) to run in multiple linear regression.
Is there a built-in function to do that in R?
Or at a minimum, how could I take those variables and generate all possible
combinations.
Thank you for any assistance.
Patrick
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and provide commented, minimal, self-contained, reproducible code.
[R] Selective Plot Color
Is there a way (with a simple plot) to select all observations greater than a
certain value and plot them with a different color than the rest of the
observations in the plot? (i.e. for all observations greater than 10, I want to
plot them in red, but the rest of the observations remain black. Where can I
find how to do this?
Patrick
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[R] Multiple Ploting Colors
I'm trying to use multiple plotting colors in my code. My first "ifelse"
statement successfully does what I want. However, now I want anything less than
-4.5 to be green and the rest black. I want another "col" argument but can only
use one. How could I go about getting separate colors for anything above 4.5
and less than -4.5?
plot(three, type="h", col=ifelse(three > 4.5, "red", "black"), xlim=c(0,500),
ylim=range(three), lwd=2,
xlab="Chromosome", ylab="Z-Score", font.lab=2, font=2, main="Upregulated
Genes in Patient Sample")
Thanks in advance,
Patrick
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple Ploting Colors
Steve,
That worked perfectly. Thank You!
Best regards,
Patrick
-Original Message-
From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com]
Sent: Monday, July 12, 2010 12:55 PM
To: Richardson, Patrick
Cc: r-help@r-project.org
Subject: Re: [R] Multiple Ploting Colors
Hi,
On Mon, Jul 12, 2010 at 12:02 PM, Richardson, Patrick
wrote:
> I'm trying to use multiple plotting colors in my code. My first "ifelse"
> statement successfully does what I want. However, now I want anything less
> than -4.5 to be green and the rest black. I want another "col" argument but
> can only use one. How could I go about getting separate colors for anything
> above 4.5 and less than -4.5?
>
> plot(three, type="h", col=ifelse(three > 4.5, "red", "black"), xlim=c(0,500),
> ylim=range(three), lwd=2,
> xlab="Chromosome", ylab="Z-Score", font.lab=2, font=2, main="Upregulated
> Genes in Patient Sample")
How about:
my.colors <- ifelse(three > 4.5, "red", "black")
my.colors[three < -4.5] <- 'green'
plot(three, type='h', col=my.colors, ...)
--
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Extreme Value Regression model
Well, RSiteSearch("extreme value regression) turns up quite a few relevant
posts including one on package "XReg". . . for extreme value regression.
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Shubha Vishwanath Karanth
Sent: Thursday, July 15, 2010 2:27 AM
To: r-help@r-project.org; r-h...@stat.math.ethz.ch
Subject: [R] Extreme Value Regression model
Hi R,
Just like a Poisson regression model, is there a package in R to do
Extreme Value Regression model? Thanks.
Thanks and Regards,
Shubha Karanth
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Re: [R] Intel i7 utilization
Costas,
Take a look at this post that I found to be very helpful. The walkthrough is
very easy to follow.
http://psyccomputing.blogspot.com/2010/04/compiling-64-bit-r-2101-with-mkl-in.html
I'm not sure if the i7 is supported however you can always replace
export FFLAGS="-march=core2 -O3"
export CFLAGS="-march=core2 -O3"
export CXXFLAGS="-march=core2 -O3"
export FCFLAGS="-march=core2 -O3"
with. .
export FFLAGS="-march=native -O3"
export CFLAGS="-march=native -O3"
export CXXFLAGS="-march=native -O3"
export FCFLAGS="-march=native -O3"
Best,
Patrick
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Costas
Sent: Tuesday, October 05, 2010 6:42 AM
To: r-help@r-project.org
Subject: [R] Intel i7 utilization
Hello,
Is there a way to force through R the amount of the cpu's cores (or the
cpu's utilization level) used under Windows 7 or Linux?
Thanks,
Costas
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Re: [R] how to analyze time series structures?
would you like coffee with that?
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of ensark [EMAIL PROTECTED]
Sent: Sunday, June 01, 2008 5:30 PM
To: r-help@r-project.org
Subject: [R] how to analyze time series structures?
hı, I am preparing undergraduate thesis If you help me this would make me
feel good.
First I need to analyze effect of Dow Jones Industrial average(DJIA)'s
return on Istanbul Stock Exchange(ISE). I want to use Markov-Switching
Bayesian Vector Autoregression Models (MSBVAR) that is used to examine the
effect of a large economy’s stock exchange movement on a small economy’s
stock exchange movement. The foreign stock exchange index follows its own
dynamics (an AR process is used as a proxy).
Turkish stock exchange movements are affected by its own lag and movements
of the foreign stock exchange. Therefore, the foreign stock exchange can be
thought to have an exogenous affect on the Turkish stock exchange. None of
the lag variables of the Turkish stock exchange determine foreign stock
exchange; however, lag values and spot values of the foreign stock exchange
affect Turkish stock exchange movement.
To calculate the standard errors of the impulse response functions, I
should use the modified error bands of Bernanke, Hall, Leeper, Sims and Zha
(1996) for the maximum likelihood estimation (MLE).
Data structure(time series);
for ISE and DJIA
daily closing prices from 01.01.1989 to 01.01.2008 in excel format.
Also I should provide following spec.;
*should fill the missing variables.
*the lag order of the identified VAR model is 5 as suggested by Bayesian
information criteria.
*All error bands for this paper should generated with 2000 Monto Carlo
draws. The corresponding impulse responses should reported in the
figures(use one-standard deviation shock in order to see impulses.).
and I need these outputs;
*plot impluse-response figures and should define level of confidence bonds
in the figures for every sub-periods
*t values of responses from ISE to DJIA.(for 10 days)
Finally, I am not good at R statistics(inexperienced) so I need explanations
in detailed also need resources and ready-made codes. How I use MSBVAR model
in R and Can you prepare me toDo list? thank you
--
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Re: [R] print and read.table commands
?read.table
And don't forget the " at the end of your filename
HTH
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Adams
Sent: Monday, June 02, 2008 2:34 PM
To: r-help@r-project.org
Subject: [R] print and read.table commands
Hello to everyone,
I am new to programming in R and am having trouble with the following
two commands
1.I am running a simple 1 line script "read.table(file="C:\\Document and
Settings\\All Users\\Desktop\\colon cancer.txt) and the error message I get is
"Error in file (file, "r"): cannot
open the connection In addition warning message In file (file, "r"): cannot
open file'C:\Document and
Settings\All Users\Desktop\colon cancer..txt
2.I am running the simple 1 line script print (file="C:\\Document and
Settings\\All Users\\Desktop\\colon cancer.txt) and the error message I get is
"error in print.default (file="C:\\
Document and Settings\\All Users\\Desktop\\colon cancer.txt"): argument x is
missing,with no default
I am not sure what I am supposed to enter as argument x.
Any help would be greatly appreciated
paul
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Re: [R] samr result
Could you post your code so we can see what you are trying to do?
Thanks,
Patrick
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Eleni Christodoulou
[EMAIL PROTECTED]
Sent: Tuesday, June 10, 2008 11:20 AM
To: r-help@r-project.org
Subject: [R] samr result
Hello list!
I have a proble trying to perform a SAM analysis using the function samr
from the samr package. I have put the option *center.arrays=TRUE *in order
to scale all the experiments to median=0. I would like to retrieved the
scaled data but it seems that samr does not return it...Does anyone have any
idea on this?
Thanks a lot!!!
E.
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Re: [R] p-value
Something like. . .
> midpoint <- c(132968364, 135945080, 156539568, 157817896,
+ 162399496, 168344072, 173146584, 176302744,
+ 182878168, 183946152, 185068720, 190791232,
+ 84317660, 93708872, 106810172, 12684,
+ 148519056, 150945112, 155771432, 181069984,
+ 87104384
+ )
> shapiro.test(midpoint)
HTH,
Patrick
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mohamed nur
anisah
Sent: Thursday, June 12, 2008 9:56 AM
To: r-help@r-project.org
Subject: [R] p-value
Dear R User,
say I have this sample of data ( attach with). What i'm going to do is to
test whether this data is uniformly distributed or not by finding the p-value.
I've tried using the punif command but it gave me the value of 1 of all the
data. Any suggestion on R command to find the p-value??Thanks in advance!!
Cheers,
Anisah
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Re: [R] 3D histogram
Try
?hist
-and-
?plot.histogram
You should find what you need there.
Cheers,
Patrick
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sumit gupta
Sent: Friday, June 20, 2008 8:46 AM
To: r-help@r-project.org
Subject: [R] 3D histogram
Hii..
Could anyone please tell me how to draw 3D histogram in R
I have a 20X3 matirx. Now I want 2 of the variable on X and Y axis .And
Height of the bar should denote the value of third variable.
Thanx
Sumit
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Re: [R] 3D histogram
Actually, have a look at the rgl package and this link
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/3d_bar_chart/
It points to bar charts, but there is some valuable info on 3D histograms as
well.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sumit gupta
Sent: Friday, June 20, 2008 8:46 AM
To: r-help@r-project.org
Subject: [R] 3D histogram
Hii..
Could anyone please tell me how to draw 3D histogram in R
I have a 20X3 matirx. Now I want 2 of the variable on X and Y axis .And
Height of the bar should denote the value of third variable.
Thanx
Sumit
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Re: [R] Insurance data in library(MASS)
Try ?relevel
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of choonhong ang
Sent: Tuesday, February 24, 2009 2:33 PM
To: r-help@r-project.org
Subject: Re: [R] Insurance data in library(MASS)
Hi,
In the result shown, the District 1 is used as the base category. How to
change to make District 4 as a base category ?
On Mon, Feb 23, 2009 at 11:05 AM, choonhong ang wrote:
> I have used the insurance data from R library and I have 2 questions:
> I use the following:
> >library(MASS)
> >data(Insurance)
> > m1=glm(Claims ~ District + Group + Age + offset(log(Holders)),data =
> Insurance, family = poisson)
> >summary(m1)
>
> Call:
> glm(formula = Claims ~ District + Group + Age + offset(log(Holders)),
> family = poisson, data = Insurance)
> Deviance Residuals:
> Min1QMedian3Q Max
> -2.46558 -0.50802 -0.03198 0.5 1.94026
> Coefficients:
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -1.810508 0.032972 -54.910 < 2e-16 ***
> District20.025868 0.043016 0.601 0.547597
> District30.038524 0.050512 0.763 0.445657
> District40.234205 0.061673 3.798 0.000146 ***
> Group.L 0.429708 0.049459 8.688 < 2e-16 ***
> Group.Q 0.004632 0.041988 0.110 0.912150
> Group.C -0.029294 0.033069 -0.886 0.375696
> Age.L -0.394432 0.049404 -7.984 1.42e-15 ***
> Age.Q -0.000355 0.048918 -0.007 0.994210
> Age.C -0.016737 0.048478 -0.345 0.729910
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> (Dispersion parameter for poisson family taken to be 1)
> Null deviance: 236.26 on 63 degrees of freedom
> Residual deviance: 51.42 on 54 degrees of freedom
> AIC: 388.74
> (1) In the result above, what is Group.L, Group.Q, Group.C, Age.L, Age.Q,
> Age.C ?
>
> (2) When I copy the Insurance data in csv format (as shown in the
> attachement) and run the same procedure the result shown is different from
> above result, why ?
>
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Re: [R] Sort help
http://www.ats.ucla.edu/stat/R/faq/sort.htm
A great tutorial about sorting data in R.
HTH,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
Grand Rapids, MI 49503
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rajasekaramya
Sent: Wednesday, November 05, 2008 2:03 PM
To: r-help@r-project.org
Subject: [R] Sort help
Geneset_name #Chromosome #Hit_in_Biomart
original_geneset_len Missing.genes
[1,] "AGUIRRE_PANCREAS_CHR12" "1" "51"
"59" "8"
[3,] "AGUIRRE_PANCREAS_CHR9" "1" "24"
"24" "0"
[4,] "AGUIRRE_PANCREAS_CHR1""1" "30"
"31" "1"
[5,] "AGUIRRE_PANCREAS_CHR18" "1" "17"
"17" "0"
[6,] "AGUIRRE_PANCREAS_CHR7" "1" "35"
"48" "13"
[7,] "AGUIRRE_PANCREAS_CHR8" "1" "55"
"61" "6"
Above is a dataframe information.
i need to sort the entire dataframe based on the 3rd colum. in decending
order.
I tried using order
information[order(information[,3])] but it gives me only the ordered first
coulmn that too i am not sure that it really works.
Kindly let me know with any suggestions.
Regards
Ramya
--
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http://www.nabble.com/Sort-help-tp20346314p20346314.html
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Re: [R] read SAS file
Did you load the "foreign" library first?
Try:
library(foreign)
read.xport("cft2008R")
HTH,
Patrick
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of b g
Sent: Monday, November 10, 2008 1:29 PM
To: r-help@r-project.org
Subject: [R] read SAS file
Looked at a lot of documentation and listserv postings and still can't solve
this problem. I need to get a SAS dataset into R. I've converted it to an
.xpt file and when I try to read it I get:
> read.xport("cft2008R")
Error: could not find function "read.xport"
>
Not sure what I'm doing wrong. I'm running SAS 9.1.3 on an UNIX box. I ftp'd
the file over to my C:\Program Files\R\R-2.8.0\ directory on my local machine
running WinXP. Suggestions appreciated.
_
l.
ty_112008
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[R] Legend Position
List,
Is there any way to specify the position of the legend from within the
following code? If so, how can I do it. As it stands it in the bottom left
corner and I want to move it to the top right. I'm not sure if I can use the
default "plot" or if I need to go with the lattice package. Suggestions much
appreciated.
plot(y, xlab="Survival Time (Months)", ylab="Survival Probability",
mark.time=TRUE, col = c("red", "blue"),legend.text = c("Locally Advanced",
"Metastatic"),
main="Kaplan-Meier Curve of Survival Times - Stratified by Group", lwd=3)
Thanks,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
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[R] Dendrogram labels
Is there any way to change the orientation of the labels on the end of the
dendrograms to horizontal rather than vertical? If so, how can I do that.
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
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and provide commented, minimal, self-contained, reproducible code.
[R] Dendrogram labels
Is there any way to change the orientation of the labels on the end of the
dendrograms to horizontal rather than vertical? If so, how can I do that.
Below is my code, but I'm not sure which argument(s) I can use to change the
label(s) (if it is possible to do).
a <- hclust(z, method = "complete")
# Plots hclust dendrogram #
plot(a, frame.plot=TRUE, lwd=2)
Many thanks,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
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Re: [R] Dendrogram labels
This does work, but also orients the entire dendrogram as horizontal. If I
could, I'd like the dendrogram to stay vertical and just orient the labels as
horizontal.
Many thanks,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
ph. 616.234.5787
-Original Message-
From: Fan Yang [mailto:[EMAIL PROTECTED]
Sent: Friday, November 21, 2008 2:28 PM
To: Richardson, Patrick
Cc: 'r-help@r-project.org'
Subject: Re: [R] Dendrogram labels
Try:
b<-as.dendrogram(a); plot(b, horiz=TRUE).
that should help.
fan
On Nov 21, 2008, at 2:14 PM, Richardson, Patrick wrote:
> Is there any way to change the orientation of the labels on the end
> of the dendrograms to horizontal rather than vertical? If so, how
> can I do that. Below is my code, but I'm not sure which argument(s)
> I can use to change the label(s) (if it is possible to do).
>
> a <- hclust(z, method = "complete")
>
> # Plots hclust dendrogram #
> plot(a, frame.plot=TRUE, lwd=2)
>
> Many thanks,
>
> _
> Patrick Richardson
> Biostatistician - Program of Translational Medicine
> Van Andel Research Institute - Webb Lab
> 333 Bostwick Avenue NE
> Grand Rapids, MI 49503
> ph. 616.234.5787
>
>
> This email message, including any attachments, is for th...{{dropped:
> 9}}
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
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[R] Comparing survival curves with "survdiff" "strata" help
ExpeRts,
I'm trying to compare three survival curves using the function "survdiff" in
the survival package. Following is my code and corresponding error message.
> survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata)
Error in survdiff(Surv(st_months, status) ~ strata(BOR), data = mydata) :
No groups to test
When I check the "strata" of the variable. I get . . .
> strata(BOR)
Levels: BOR=PD BOR=PR BOR=SD
So I know there are levels associated with the BOR variable, but I can't seem
to get the strata statement to work within "survdiff". I checked ?strata and
(unless I am not understanding) the help, it seems to be working as I get the
following output
> levels(strata(BOR))
[1] "BOR=PD" "BOR=PR" "BOR=SD"
I can get the survival tables and KM plot with no problem, but I can't seem to
be able to compare the survival curves. I can get an overall comparison if I
remove the "strata" statement
> survdiff(Surv(st_months, status) ~ BOR, data=mydata)
Call:
survdiff(formula = Surv(st_months, status) ~ BOR, data = mydata)
n=35, 5 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
BOR=PD 13 13 6.51 6.464 8.87
BOR=PR 10 1018.48 3.888 10.59
BOR=SD 12 1210.01 0.395 0.61
Chisq= 13.5 on 2 degrees of freedom, p= 0.00117
But when I use survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata) it
doesn't want to work. Any suggestions?
Many thanks for your assistance!
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
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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] Comparing survival curves with "survdiff" "strata" help
ExpeRts,
I'm trying to compare three survival curves using the function "survdiff" in
the survival package. Following is my code and corresponding error message.
> survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata)
Error in survdiff(Surv(st_months, status) ~ strata(BOR), data = mydata) :
No groups to test
When I check the "strata" of the variable. I get . . .
> strata(BOR)
Levels: BOR=PD BOR=PR BOR=SD
So I know there are levels associated with the BOR variable, but I can't seem
to get the strata statement to work within "survdiff". I checked ?strata and
(unless I am not understanding) the help, it seems to be working as I get the
following output
> levels(strata(BOR))
[1] "BOR=PD" "BOR=PR" "BOR=SD"
I can get the survival tables and KM plot with no problem, but I can't seem to
be able to compare the survival curves. I can get an overall comparison if I
remove the "strata" statement
> survdiff(Surv(st_months, status) ~ BOR, data=mydata)
Call:
survdiff(formula = Surv(st_months, status) ~ BOR, data = mydata)
n=35, 5 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
BOR=PD 13 13 6.51 6.464 8.87
BOR=PR 10 1018.48 3.888 10.59
BOR=SD 12 1210.01 0.395 0.61
Chisq= 13.5 on 2 degrees of freedom, p= 0.00117
But when I use survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata) it
doesn't want to work. Any suggestions?
Many thanks for your assistance!
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
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[R] Clustering with Mahalanobis Distance
Dear R ExpeRts,
I'm having memory difficulties using mahalanobis distance to trying to cluster
in R. I was wondering if anyone has done it with a matrix of 6525x17 (or
something similar to that size). I have a matrix of 6525 genes and 17 samples.
I have my R memory increased to the max and am still getting "cannot allocate
vector of size" errors. My matrix "x" is actually a transpose of the original
matrix (as I want to cluster by samples and not genes). "y" is a vector of the
mean gene expression levels and "z" is the covariance matrix of "x" (I think
this is where the problem lies as the covariance matrix is enormous.
I can't really provide a reproducible example as I would have to attach my data
files, which I don't think anyone would appreciate.
rm(list=ls()) #removes everything from memory#
gc() #collects garbage#
memory.limit(size = 4095) #increases memory limit#
x <- as.matrix(read.table("x.txt", header=TRUE, row.names=1))
y <- as.matrix(read.table("y.txt", header=TRUE, row.names=1))
z <- as.matrix(read.table("z.txt", header=TRUE, row.names=1))
mal <- mahalanobis(x, y, z)
The ultimate goal is to run "hclust" with the mahalanobis distance matrix.
If anyone knows where I could find a more "memory friendly" function or any
advise as to what I might try to optimize my code, I would appreciate it.
sessionInfo() is below.
Many Thanks,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods base
other attached packages:
[1] svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59svMisc_0.9-5 svIDE_0.9-5
loaded via a namespace (and not attached):
[1] tools_2.8.0
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[R] Error message when starting TINN-R
When R starts I get the following error message
Warning message:
In grep(paste("[{]TclEval ", topic, "[}]", sep = ""), tclvalue(.Tcl("dde
services TclEval {}")), :
argument 'useBytes = TRUE' will be ignored
Has anyone else run into this issue and is there any way to can fix this?
Thanks,
Patrick
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message when starting TINN-R
I have asked the maintainer for a fix and didn't get a reply, which is why I
posted to the list to see if there were any other ideas.
Sorry to bother. . . with my warning message.
Patrick
-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
Sent: Friday, December 12, 2008 9:34 AM
To: Richardson, Patrick
Cc: 'r-help@r-project.org'
Subject: Re: [R] Error message when starting TINN-R
And the *Error* message was (that was a warning)?
The warning comes from some contributed code, probably in Tinn-R. Please
find out where it is and ask the maintainer for a fix. But it looks
harmless enough.
On Fri, 12 Dec 2008, Richardson, Patrick wrote:
> When R starts I get the following error message
>
> Warning message:
> In grep(paste("[{]TclEval ", topic, "[}]", sep = ""), tclvalue(.Tcl("dde
> services TclEval {}")), :
> argument 'useBytes = TRUE' will be ignored
>
> Has anyone else run into this issue and is there any way to can fix this?
>
> Thanks,
>
> Patrick
>
>
>
> This email message, including any attachments, is for ...{{dropped:27}}
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and provide commented, minimal, self-contained, reproducible code.
