Hi,
coxfilter function in genefilter package uses coxph to fit a model to filter
genes. how come that coxfilter could converge to find a solution in cox model
fitting using a data matrix of 8000 variables and 600 samples but coxph doesn't
converge with the same matrix?
regards,
carol
On Tue, 22 May 2007, hadley wickham wrote:
On 5/22/07, Rolf Turner [EMAIL PROTECTED] wrote:
On 22/5/07 6:48 AM, hadley wickham [EMAIL PROTECTED] wrote:
Two possible solutions:
* DISPLAY=0.0.0.0:0 R - and then X11() should work without having to use
xterm
*
Hi,
I have been trying many of the suggested options
to place a legend outside plotting area, including
something like this:
par(xpd=T,
oma=par()$oma+c(4.5,0,1.5,0),mar=par()$mar+c(1,0,1,0)
But the aspect of the four plots gets compromised
when I change the margin settings. I cannot
Well, i had this problem too, but with Edy edge 5.06.
I fixed the problem after reading this.
http://ubuntuforums.org/archive/index.php/t-248750.html
http://ubuntuforums.org/archive/index.php/t-248750.html
But I also updated to Feisty Fawn (5.10) and there the problem didn't
occur. I'm not sure
李俊杰 klijunjie at gmail.com writes:
Hi, Lynch,
Thank you for attention first.
I am also not a statistician and have just taken several statistics classes.
So it is natral for us to ask some question seeming naive to statisticans.
I am sorry that I cannot agree with your point that we
On Tue, 2007-05-22 at 00:35 +, [EMAIL PROTECTED] wrote:
I'd like to get a measure of goodness of fit for a heirarchical
clustering result from hclust. Something that would indicate the
extent to which the dendrogram accurately represents the original
dissimilarity matrix. Is there an
This gives you a GUI that runs R without you having to run it yourself on your
machine:
http://rss.acs.unt.edu/cgi-bin/R/Rprog
You could upload your data to a webspace if you have one, and catch it from
there in that service they provide.
You could provide to whomever you like such a service
I'm in need of information with regard to Stochastic Kernel.
I would like to know if I can use R to compute stochastic Kernels according
to Quah methodology.
Best wishes,
Oriana
-
-
[[alternative HTML
good morning,
I have some SAS code to translate in R code and when I export data from Excel
to R I have to read formula writed as follow
C604=(C181/S181)*(100-C182)*(100/85)
or
if C325=. then C740=(C346/C103)*100| else C740=(C346/C325)*100
I find some difficulties to write a good program to
You want to select two subplots for each DL value. Try:
df - data.frame( DL=gl(3,4), subplot=rep(1:4,3) )
df$index - 1:nrow(df)
ind - tapply( df$index, df$DL, function(x) sample(x,2) )
df[ unlist(ind), ]
You could also have used rownames(df) instead of creating df$index.
OR
tmp -
Assuming the R packages have been downloaded locally and end with
tar.gz, then how about simply changing to where the files are located
and typing the following command?
ls *.tar.gz | while read x; do echo R CMD INSTALL $x; done | bash
Alternatively, you can use the install.packages()
I am not sure if R can read formulas and if it does, it probably as
characters. I would suggest you Copy and Paste Special (as values) onto
a new sheet and save it a tab delimited files.
elyakhlifi mustapha wrote:
good morning,
I have some SAS code to translate in R code and when I export
Hello everyone,
I get (reproducible) segfaults when I try to update my packages, and
was wondering whether anyone knows why this might be happening.
I am trying to update my packages:
1. I start R via sudo in a terminal
2. I type update.packages() - a Tcl/Tk list pops up, I select a mirror
3. R
Hi,Oksanen,
Thanks for your reply.
I agree with you at the point that if we misjudge none-zero intercept to be
zero, there will be loss still or even great loss as you and Venables
emphasized in your practical research work. If there won't be any loss when
we misjudge
zero intercept to be
Dear R-help,
I'm building a package which will contain a data set. I was wondering if it's
possible to make a message appear on the console whenever a user loads the
data. So the console would look like
data(mydata)
Please do not use these data in any publication without permission of the
Dear Chuck,
This solution works reasonably well for me. Although it occasionally
produces an error, I'm able to trap that.
Thank you -- and to everyone else who responded.
John
John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario
[EMAIL PROTECTED] wrote:
Hello everyone,
I get (reproducible) segfaults when I try to update my packages, and
was wondering whether anyone knows why this might be happening.
I am trying to update my packages:
1. I start R via sudo in a terminal
2. I type update.packages() - a Tcl/Tk
here is my address [EMAIL PROTECTED]
-
[[alternative HTML version deleted]]
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
RSiteSearch(legend outside plot)
will bring you many links to the discussions of this question.
layout perfectly allows everything.
typical sequence looks like this
This divides the device region by two parts one below another:
layout(matrix(c(1,2),byrow=TRUE), heights=[blah-blah-blah], [some
Judith,
you might try split.screen() and related functions, see ?screen.
Example:
split.screen(c(1,2)) # 1 row, 2 columns
split.screen(c(2,2), screen = 1) # split left column into 2x2
for(i in 3:6) { screen(i); plot(1:10) }
screen(2)
plot(1, type=n, axes=F, ann=F) # empty plot
legend(center,
?par
There are several parameters can only be set by a call
to par(): new
You just were lucky enough to find one.
--- jiho [EMAIL PROTECTED] wrote:
Hello everybody,
This is probably a classic but I cannot find an
answer to this on the
mailing list (i.e. with a google search restricted
Dear all:
I read in a tab delimited dataset, and then write it out as another
file as following: I did this simply to make sure I understand the
behavior of this command.
data-read.table(file,header=F,sep=\t,fill=T,colClasses=character);
On 2007-May-22 , at 13:51 , John Kane wrote:
?par
There are several parameters can only be set by a call
to par(): new
You just were lucky enough to find one.
Yes sorry about that, I saw this afterwards. I read the help pages a
while ago and it seems it's time to take a re-read tour.
If you write out unquoted fields, how do you know they do not contain
tabs?
The default is quote=TRUE for a good reason.
On Tue, 22 May 2007, Yong Wang wrote:
Dear all:
I read in a tab delimited dataset, and then write it out as another
file as following: I did this simply to make sure I
Hi,
after reading the archives I found some methods... adopted and
modified one of them to the following. I think it is correct after
checking and comparing the results with other software... but if
possible someone could have a look and spot any mistakes I would be
grateful. Thanks
pcor3 -
Dear Wolfgang,
I agree that it's preferable to compute the two-sided p-value without
assuming symmetry. Another, equivalent, way of thinking about this is to use
t^2 for the two-sided test in place of t.
BTW, the formula used in my appendix (for the one-sided p-value) is from
Davison and
You will have to be more clear about what exactly you are trying to do.
I, at least, am quite unsure about what you want.
fit - coxph(Surv(time, status) ~ x1 + strata(x2))
The hazard ratio(s) wrt x1 have the same meaning for a stratified or an
unstratified model. If you are asking about
Is it possible to conduct part (also called semi-partial correlation)
with R. The help.search produces no results and there is also nothing
into the archive, well one post asking what is part correlation. Just
quickly from Field [Discovering statistics using spss]:
When we do a partial
Dear all,
Is it possible to add a list in the data folder when creating a new package?
In other words, is data in packages restricted to data.frame only?
Thank you,
Adrian
--
Adrian Dusa
Romanian Social Data Archive
1, Schitu Magureanu Bd
050025 Bucharest sector 5
Romania
Tel./Fax: +40 21
Hi,
Without trying to print 100 points (see http://
finzi.psych.upenn.edu/R/Rhelp02a/archive/42105.html), I often print
maps for which I do not want to loose too much of coastline detail,
and/or plots with 1000-5000 points (yes, some are on top of each
other, but using transparency
This is a time series\optimization rather than an R question : Suppose I
have an ARMA(1,1) with
restrictions such that the coefficient on the lagged epsilon_term is
related to the coefficient on
The lagged z term as below.
z_t =[A + beta]*z_t-1 + epsilon_t - A*epsilon_t-1
So, if I don't have a
Thank you for the suggestion, Dr. Ripley
However, I am a little bit confused. My understanding is that you
suspect the should-be-quoted fields (factor or character fields)
contains tabs.
if this is the case, count.fields() should detect the tab,
read.table(sep=t\) should read with the same
On Tue, 22 May 2007, Yong Wang wrote:
Thank you for the suggestion, Dr. Ripley
I made no suggestion: I asked a question you have not answered.
However, I am a little bit confused. My understanding is that you
suspect the should-be-quoted fields (factor or character fields)
contains tabs.
Ich werde ab 22.05.2007 nicht im Büro sein. Ich kehre zurück am
28.05.2007.
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R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide
On 5/21/07, Alberto Monteiro [EMAIL PROTECTED] wrote:
Paul Lynch wrote:
I don't think it makes sense to compare models with
and without an intercept term. (Also, I don't know what the point of
using a model without an intercept term would be, but that is
probably just my ignorance.)
Thanks.
This appears to do the trick.
Best regards,
Costas
-Original Message-
From: Armstrong, Whit [mailto:[EMAIL PROTECTED]
Sent: Tuesday, May 22, 2007 6:14 PM
To: Vorlow Constantinos
Cc: [EMAIL PROTECTED]
Subject: RE: [R-SIG-Finance] readcsvIts
I believe you need:
Hello,
I am trying to read a .CSV file from Bloomberg of prices (for an its
series) of the following format:
Date Price
23/10/2006 09:59 57.291
23/10/2006 10:01 57.221
23/10/2006 10:02 57.201
23/10/2006 10:03 57.231
23/10/2006
Your approach obviously won't give you the same result as when the
likelihood is optimized jointly with A and \beta. However, you can maximize
the likelihood over \beta for different values of A, which would give you a
profiled likelihood. Then you pick the \beta and A corresponding to
maximum
In my previous email, I meant to say:
P1 - A
P2 - atanh(A + beta)
So that the model becomes:
z_t = tanh(P2)*z_t-1 + epsilon_t - P1*epsilon_t-1
Although I am not sure, how readily the likelihood of the above model can be
maximized.
Ravi.
Hi everyone!
I am beginner in using R, so please excuse easy questions in advance.
I want to reproduce results from the data available in the lmtest-package.
That’s the failure code I get:
data(bondyield)
Warning message:
file 'bondyield.rda' has magic number 'RDX1'
Use of save versions
Dear R gurus,
I would like to use the ccf function on two matrices that are each 196000 x
12. Ideally, I want to be able to go row by row for the two matrices using
apply for the ccf function and get one 196000 X 1 array output. The apply
function though wants only one array, no? Basically, is
You could combine them with cbind, and then split the rows again inside
the function you're calling with apply.
Mat - cbind(mat1, mat2)
apply(Mat, 1, function(x){
row.mat1 - x[seq_len(length(x)/2)]
row.mat2 - x[length(x)/2 + seq_len(length(x)/2)]
cor(row.mat1, row.mat2)
})
Hi,
I am trying to install the package exonmap and RMySQL however I keep
getting the following error:
Error in library(pkg, character.only = TRUE) :
'RMySQL' is not a valid package -- installed 2.0.0?
I have R version 2.4.1 so I know its not a version issue. I deleted and
reinstalled
On Mon, 21 May 2007, carol white wrote:
Hi, coxfilter function in genefilter package uses coxph to fit a model
to filter genes. how come that coxfilter could converge to find a
solution in cox model fitting using a data matrix of 8000 variables and
600 samples but coxph doesn't converge
Hi Simon --
?data indicates that the first file looked for is mydata.R, and then
mydata.RData and so on. So add a file mydata.R to your data directory that
contains R code to print a message and then loads the data. This hack
is used in Bioconductor, e.g., the Biobase package
On Mon, 21 May 2007, John Fox wrote:
In retrospect, I didn't specify the problem clearly: What I want to be able
to do is to place text on a background of arbitrary (but known RGB) colour
so that the text is legible. I guess that this is better described as a
contrasting than a complementary
On Tue, 22 May 2007, Henning Schoelen wrote:
Hi everyone!
I am beginner in using R, so please excuse easy questions in advance.
I want to reproduce results from the data available in the lmtest-package.
Thatâs the failure code I get:
data(bondyield)
Warning message:
file 'bondyield.rda'
John Fox [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
The object is to get contrasting colours, so that
when one is plotted over the other, the two will be readily
distinguishable.
A simple approach to contrast is to compute a mean intensity by taking the
mean of the three
On Fri, 18 May 2007, Moss, Angela (Dudley PCT) wrote:
Dear All
I am trying to use svychisq with a two-dimensional table 4 x 5. The
command I am using is
summary(svytable(~dietperception+dietstatus,dudleyls1rake,na.rm=TRUE),C
hisq)
It is throwing up an error message as follows:
Error in
Sorry, I'm stuck. :)
I am writing a function, which would fit either one linear model or another
one, depending on its argument model.type.
And I don't want to use several if's, because R allows doing it with much
more beauty.
That is I am looking for prettier alternative to the following
Porblem solved! Thanks for the fast response!
Thought I updated my packages over the menu already.
Greetings
Achim Zeileis wrote:
On Tue, 22 May 2007, Henning Schoelen wrote:
Hi everyone!
I am beginner in using R, so please excuse easy questions in advance.
I want to reproduce
I understand you to want correlations of corresponding rows (** not ccf,
which returns a vector ccf for each pair of rows). If that is so,
1) ... in theory, diag(cor(t(A), t(B)) would work without apply, except
196,000 rows is probably too large, and it is probably too inefficient to
compute and
You could use the class dispatching mechanism:
mymodel - function(a, b, method = S) {
.Class - method
NextMethod(mymodel)
}
mymodel.S - function(a, b, method = S) cat(S:, a, b, method, \n)
mymodel.HK - function(a, b, method = S) cat(HK:, a, b, method, \n)
mymodel(1:3, 1:4)
Hello,
I have a basic problem but i can't figure it out with the
table underneath. I would like to compute monthly averages.
I would like to have the average measure for month #5 for the first
three rows (the same number in the first three lines) and the average
measure for month #6 for the
From the help page
'pdf' writes uncompressed PDF. It is primarily intended for
producing PDF graphics for inclusion in other documents, and
PDF-includers such as 'pdftex' are usually able to handle
compression.
If you are able to contribute a stream compressor, R will
You need not buy Acrobat. There are two free software programs that will
compress pdf files:
http://www.cutepdf.com
http://www.cs.wisc.edu/~ghost/ (and in particular GSView)
They both allow several levels of compression.
Thanks,
--sundar
Chabot Denis said the following on 5/22/2007 3:32 AM:
Hi Karen --
This sounds like a Bioconductor question, and should be sent to the
Bioconductor list.
http://www.bioconductor.org/docs/mailList.html
Likely the complaint is about RMySQL being too old, rather than R. The
idea of 'reinstalling folders' doesn't sound like a good strategy for
updating
Dear R People:
I was wondering if there were any packages for parallel programming in R.
According to the R-help, at one time there was a package called SNOW. It
doesn't seem
to exist anymore.
Any help would be much appreciated!
Sincerely,
Erin Hodgess
mailto: [EMAIL
Thank you Prof. Ripley.
Believe me, I do not have the skills to contribute such a thing as a
stream compressor and I DO appreciate the work and usefulness of the
pdf device as it is. I do most of my plots with pdf device, the rest
with quartz (especially when I'm not sure I'll want to save
Dear Thomas,
This seems simpler than the solution that I used, so I'll give it a
try.
Thanks,
John
On Tue, 22 May 2007 09:01:01 -0700 (PDT)
Thomas Lumley [EMAIL PROTECTED] wrote:
On Mon, 21 May 2007, John Fox wrote:
In retrospect, I didn't specify the problem clearly: What I want to
be
Benoit,
Try the aggregate() function.
-Cody
Cody Hamilton, PhD
Edwards Lifesciences
Benoit
Chemineau
Only trivial if you can find it.
Will the package corpcor do you any good?
--- [EMAIL PROTECTED] wrote:
Is it possible to conduct part (also called
semi-partial correlation)
with R. The help.search produces no results and
there is also nothing
into the archive, well one post asking what
On Tue, 2007-05-22 at 19:01 +0200, Benoit Chemineau wrote:
Hello,
I have a basic problem but i can't figure it out with the
table underneath. I would like to compute monthly averages.
I would like to have the average measure for month #5 for the first
three rows (the same number in the
tapply(Measure,Month,mean)[as.character(Month)]
--
Christophe Pallier (http://www.pallier.org)
On 5/22/07, Benoit Chemineau [EMAIL PROTECTED] wrote:
Hello,
I have a basic problem but i can't figure it out with the
table underneath. I would like to compute monthly averages.
I would
Thank you Sundar,
Do plots being so reduced remain object based (i.e. not bitmaps)?
Denis
Le 07-05-22 à 13:19, Sundar Dorai-Raj a écrit :
You need not buy Acrobat. There are two free software programs that
will compress pdf files:
http://www.cutepdf.com
http://www.cs.wisc.edu/~ghost/
install.packages(RMySQL, dep=T)
should fix it for you.
b
ps: The error says RMySQL is the problem... it is not complaining
about R itself (although it would not be a bad idea, given that the
latest R is v 2.5.0, so it would be a better idea to start by
upgrading your R)
On May 22, 2007,
Hello everybody,
I'm an absolute newbe in R, so please be gentle to me.
I am looking for a german map in the package maps by Becker and Wilks.
After that I want to draw the German cities from world.cities of this package
in the map and want to draw further a line from Berlin to Munich.
Has
snow still exists, and there is one more package snowFT on CRAN (FT stands
for Fault Tolerant)
Probably, you didn't find it because of typing its name in capitals.
hodgess wrote:
According to the R-help, at one time there was a package called SNOW. It
doesn't seem
to exist anymore.
On Tue, 22 May 2007, hodgess wrote:
Dear R People:
I was wondering if there were any packages for parallel programming in R.
According to the R-help, at one time there was a package called SNOW. It
doesn't seem
to exist anymore.
??? It's available on CRAN.
Best,
luke
Any help
Erin,
There is a snow package (note the case) and also a few others.
Rlsf, is specific to grids/clusters that use the LSF queue system.
More generally, the nws package is more sophisticated and should work on
most systems. Also, there is Rmpi (which I haven't used).
Max
-Original
Hello everybody,
I'm an absolute newbe in R, so please be gentle to me.
I am looking for a german map in the package maps by Becker and Wilks.
After that I want to draw the German cities from world.cities of this
package in the map and want to draw further a line from Berlin to Munich.
Has
On Tue, May 22, 2007 at 01:06:06PM -0400, Chabot Denis wrote:
Thank you Prof. Ripley.
Believe me, I do not have the skills to contribute such a thing as a
stream compressor and I DO appreciate the work and usefulness of the
pdf device as it is. I do most of my plots with pdf device, the
aggregate(Measure, list(Month=Month), mean)
--- Benoit Chemineau [EMAIL PROTECTED]
wrote:
Hello,
I have a basic problem but i can't figure it out
with the
table underneath. I would like to compute monthly
averages.
I would like to have the average measure for
month #5 for the first
There are R interfaces to MPI and PVM on CRAN, which are Rmpi and RPVM,
respectively.
hodgess wrote:
I was wondering if there were any packages for parallel programming in R.
According to the R-help, at one time there was a package called SNOW. It
doesn't seem
to exist anymore.
My solution (after a cup of coffee :) ):
model.formula-switch(model.type,S=[s-model formula],HK=[hk-model formula])
model-lm(model.formula)
Gabor Grothendieck wrote:
You could use the class dispatching mechanism:
mymodel - function(a, b, method = S) {
.Class - method
On 5/22/07, Adrian Dusa [EMAIL PROTECTED] wrote:
Dear all,
Is it possible to add a list in the data folder when creating a new package?
Yes.
In other words, is data in packages restricted to data.frame only?
Well section 1.1.3 of the manual Writing R Extensions say, in part,
Currently, data
On Wed, 23 May 2007, Maja Schröter wrote:
Hello everybody,
I'm an absolute newbe in R, so please be gentle to me.
I am looking for a german map in the package maps by Becker and Wilks.
After that I want to draw the German cities from world.cities of this
package in the map and want to draw
You can find a decent tutorial on using RMPI here:
http://ace.acadiau.ca/math/ACMMaC/Rmpi/index.html
On 22-May-07, at 3:46 PM, Kuhn, Max wrote:
Erin,
There is a snow package (note the case) and also a few others.
Rlsf, is specific to grids/clusters that use the LSF queue system.
More
On 22/05/2007 2:58 PM, Maja Schroeter wrote:
Hello everybody,
I'm an absolute newbe in R, so please be gentle to me.
I am looking for a german map in the package maps by Becker and Wilks.
After that I want to draw the German cities from world.cities of this
package in the map and want
Hi,
I used split.screen command to creaye 5 screens,
4 screens contain a plot each, the fifth screen is
designated to a legend. I am having difficulties
setting the dimensions of the screens in a way that
would allow me to have the screen dedicated to the
legend smaller. I end up with a
Note that a significant difference between the two solutions is that
the OO solution allows new methods corresponding to method=
to be added without changing the function holding the statements.
On 5/22/07, Vladimir Eremeev [EMAIL PROTECTED] wrote:
My solution (after a cup of coffee :) ):
Vladimir Eremeev wrote:
Sorry, I'm stuck. :)
I am writing a function, which would fit either one linear model or another
one, depending on its argument model.type.
And I don't want to use several if's, because R allows doing it with much
more beauty.
That is I am looking for prettier
Do I miss here something?
dtaa =
read.table(http://www.ats.ucla.edu/stat/mplus/examples/ma_snijders/mlbook1.dat;,
sep=,)
head(dtaa) # shows the data as it should be
save(dtaa,dtaa,file=c:/dtaa)
d = load(c:/dtaa)
head(d) # all data is lost, it only shows [1] dtaa dtaa
Thanks for
On Tue, 22 May 2007, [EMAIL PROTECTED] wrote:
Do I miss here something?
Yes.
dtaa =
read.table(http://www.ats.ucla.edu/stat/mplus/examples/ma_snijders/mlbook1.dat;,
sep=,)
head(dtaa) # shows the data as it should be
save(dtaa,dtaa,file=c:/dtaa)
d = load(c:/dtaa)
From ?load
On 22/05/2007 8:25 PM, [EMAIL PROTECTED] wrote:
Do I miss here something?
dtaa =
read.table(http://www.ats.ucla.edu/stat/mplus/examples/ma_snijders/mlbook1.dat;,
sep=,)
head(dtaa) # shows the data as it should be
save(dtaa,dtaa,file=c:/dtaa)
Besides what Thomas said:
Just
I was recently asked by one of new colleagues how to combine, or catentate,
or concatentate two factors. If x and y are factors, doing c(x,y) appears
to coerce x and y to numeric mode before catenating them. So what does one
do if one wants the result to be a factor whose levels are the union
Dear all,
I try to use read.table to get the data from a tab delimited file, and some
of the data is shown below:
3185heterogeneous nuclear ribonucleoprotein F
3187heterogeneous nuclear ribonucleoprotein H1 (H)
3188heterogeneous nuclear ribonucleoprotein H2 (H')
3189
use quote= to disable the effect of '
cheers
Ben Bolker
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented,
On May 22, 2007, at 9:41 PM, Alex Tsoi wrote:
Dear all,
I try to use read.table to get the data from a tab delimited file,
and some
of the data is shown below:
[snip]
and it means that whenever read.table reads ' , it skips the next
line,
until it reads ' again
Could
On Wed, 2007-05-23 at 13:38 +1200, Rolf Turner wrote:
I was recently asked by one of new colleagues how to combine, or catentate,
or concatentate two factors. If x and y are factors, doing c(x,y) appears
to coerce x and y to numeric mode before catenating them. So what does one
do if one
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