Adaikalavan Ramasamy cancer.org.uk> writes:
:
: There was a BioConductor thread today where the poster wanted to find
: pairwise difference between columns of a matrix. I suggested the slow
: solution below, hoping that someone might suggest a faster and/or more
: elegant solution, but no other
On Fri, 2004-07-30 at 18:30, Adaikalavan Ramasamy wrote:
> There was a BioConductor thread today where the poster wanted to find
> pairwise difference between columns of a matrix. I suggested the slow
> solution below, hoping that someone might suggest a faster and/or more
> elegant solution, but n
There was a BioConductor thread today where the poster wanted to find
pairwise difference between columns of a matrix. I suggested the slow
solution below, hoping that someone might suggest a faster and/or more
elegant solution, but no other response.
I tried unsuccessfully with the apply() family
Patrick,
Here is one additional option for you.
I happened to be doing some searching on the OO.org site today for some
printing related issues in their Bugzilla equivalent.
There was a reference to a MS Office PDF import filter available from
ScanSoft that would enable you to create PDF vector
> I'm a biologist, so please forgive me
Biologists are hard to forgive! :-)
>if my question sounds absurd!
The only absurd question is the one that is not asked.
> I have 3 parameters x1, x2, x3 and a response variable y.The
> sample size
Hi;
Is there a faster way to run this code?
Ab<- matrix(numeric(1),nrow=2,ncol=1000)
Bb<- matrix(numeric(1),nrow=2,ncol=1000)
for(j in 1:1000) {
for(i in 1:1000) {
eq<- sample(stud,replace=T)
ystar<- beta.r*x+eq+b0
Ab[,i]<- wwfit(x,ystar)$coef
Hi,
I'm a biologist, so please forgive me if my question sounds absurd! I have 3
parameters x1, x2, x3 and a response variable y.The sample size is 75. I tried
to do the following:
mylm<-lm(y~ x1 + x2 + x3, data="mydata")
but i can only get stats from anova for the first 2 variables. The third c
You have to have postscript("foo.eps", ..) before you issue the plot
commands and isuue a dev.off() at the end.
If you want to copy the plot graph to a postscript driver use
dev.copy2eps(file="foo.eps")
?dev.print
?postscript
Hope this helps.
On Fri, 30 Jul 2004, marzban wrote:
>
> Hi,
Hi,
I'm running the latest version of R on a linux box.
plot() does produce a grahpics window. But is it
"normal" for that window to not respond to a left
or right mouse click?
What I'm really trying to do is the save the graphics
to a postscript file, but postscript() produces an "empty posts
Have a look at
?par
You need to have par(xpd = TRUE) and then use par("usr") to get the
coordinates for the edges of the plot. Also make sure you have enough
space around the plot to put the legend. For that, have a look at par(oma)
or par(mar) etc.
HTH.
Partha
Jean Eid <[EMAIL PROTECTE
I am trying to put legends underneath the plot (in the outer margins). Is
there an easy way to do this. I have been tinkering with split..screen but
I could not make it work.
Thank in advance
Jean
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Hi,
Sorry to bother those who are not interested in the
question.
I am using R to run a multiphase mixed-effects model. I
simulated a data set by using the following model. And now
I want to use R to estimate the parameters and compare the
results with the true values.
The equations of the mo
Surely it's simply just to use as.numeric() to stop them being integers?
This is fixed in r-devel anyway -- you have a choice of a bunch of
deparsing options.
-thomas
On Fri, 30 Jul 2004, Sundar Dorai-Raj wrote:
>
>
> Jack Tanner wrote:
>
> > Sundar Dorai-Raj wrote:
> >
> >> Not sure
On Fri, 30 Jul 2004 [EMAIL PROTECTED] wrote:
> Dear R-help,
>
> I have a question on subsetting a dataframe and I searched all of R-help to no
> avail. Please view the following example dataframe:
>
> # Example
> > x <- factor(rep(c(1,2,3,4),2))
> > y <- c(1,4,3,2,1,2,5,1,2)
> > z <- c(10,12,18,
Gabor Grothendieck myway.com> writes:
:
: Adair, Laurence parsons.com> writes:
:
: > Here is something that sounds simple, but I'm having trouble getting it. I
: > have a data frame with two columns, the first is date and the second is
: > employee ID. I'd like to plot date on the horizontal
Jack Tanner wrote:
Sundar Dorai-Raj wrote:
Not sure about what sqlQuery is doing but you can wrap your return
value in a eval(parse(text = x)) to evaluate the "as.integer(.)"
string. As in,
a <- eval(parse(text = a))
This works, except it doesn't.
> a <- sqlQuery(irrdb, "select count(field) f
Thank all of you. That's exactly what I want.
Best,
Frank
Quoting Gavin Simpson <[EMAIL PROTECTED]>:
> F Duan wrote:
> > Dear All,
> >
> > I am sorry if this question has been asked before. Below is my Question:
> >
> > I want to put several plots in the same window, but I dont want the bla
Adair, Laurence parsons.com> writes:
> Here is something that sounds simple, but I'm having trouble getting it. I
> have a data frame with two columns, the first is date and the second is
> employee ID. I'd like to plot date on the horizontal axis, employee ID on
> the vertical axis, and the nu
Dear R-help,
I have a question on subsetting a dataframe and I searched all of R-help to no avail.
Please view the following example dataframe:
# Example
> x <- factor(rep(c(1,2,3,4),2))
> y <- c(1,4,3,2,1,2,5,1,2)
> z <- c(10,12,18,21,24,32,34,12,23)
> test <- data.frame(x, y, z)
> test
x y
On Friday 30 July 2004 10:13, Adair, Laurence wrote:
> Hi All,
>
> Here is something that sounds simple, but I'm having trouble getting
> it. I have a data frame with two columns, the first is date and the
> second is employee ID. I'd like to plot date on the horizontal axis,
> employee ID on the
F Duan wrote:
Dear All,
I am sorry if this question has been asked before. Below is my Question:
I want to put several plots in the same window, but I don’t want the blank
space between plots (like par(mfrow=)) --- that makes the plots too small.
Could anyone tell me how to do it?
Thanks a lot.
Sundar Dorai-Raj wrote:
Not sure about what sqlQuery is doing but you can wrap your return value
in a eval(parse(text = x)) to evaluate the "as.integer(.)" string. As in,
a <- eval(parse(text = a))
This works, except it doesn't.
> a <- sqlQuery(irrdb, "select count(field) from mytable where field
Sorry!, by "TeX" I meant the PicTeX option for graphics devices (which
in anycase produces bulky files!).
-Original Message-
From: Uwe Ligges
To: Roy, Supratik
Cc: '[EMAIL PROTECTED]'
Sent: 7/30/2004 3:58 PM
Subject: Re: [R] LaTeX in R
Roy, Supratik wrote:
> I tried to include LaTeX expr
On Fri, 30 Jul 2004 08:13:05 -0700 (PDT) bob mccall wrote:
> Greetings:
>
> Is there an simple way to do dynamic regressions in R?
> >From what I've seen, one must use arima() and construct the X matrix
> >with lagged values etc. and modify Y as well.
If you want OLS regression with lagged reg
On Fri, 2004-07-30 at 10:41, F Duan wrote:
> Dear All,
>
> I am sorry if this question has been asked before. Below is my Question:
>
> I want to put several plots in the same window, but I dont want the blank
> space between plots (like par(mfrow=)) --- that makes the plots too small.
> Could
Dear R Development Team,
I compile R-1.9.1 on AIX 5.2 under 2.9-aix51-020209, and xlf 7.1. In
order to let R compile successfully under gcc 2.9, I have to change one
C statement of file(RHOME//src/modules/X11/devX11.c) line 1768 from
"retrun FALSE" to "retrun NULL", following is C code snapshot
Frank,
Why not try using grid graphics? You can open arbitrary viewports into
which to place plots.
Sean
On Jul 30, 2004, at 11:41 AM, F Duan wrote:
Dear All,
I am sorry if this question has been asked before. Below is my
Question:
I want to put several plots in the same window, but I don’t wa
F Duan wrote:
Dear All,
I am sorry if this question has been asked before. Below is my Question:
I want to put several plots in the same window, but I don’t want the blank
space between plots (like par(mfrow=)) --- that makes the plots too small.
Could anyone tell me how to do it?
E.g. with par(m
Lattice graphics may be the answer depending on your exact problem.
Here is an example of four traditional plots without space:
par(mfrow=c(2,2), omi=c(.5, .5, .5, .5))
par(mar=c(0, 2, 2, 0))
plot(rnorm(10), rnorm(10), axes=FALSE)
box(); axis(2); axis(3)
par(mar=c(0, 0, 2, 2))
plot(rnorm(10
On Fri, 30 Jul 2004, F Duan wrote:
> Dear All,
>
> I am sorry if this question has been asked before. Below is my Question:
>
> I want to put several plots in the same window, but I dont want the blank
> space between plots (like par(mfrow=)) --- that makes the plots too small.
> Could anyone tel
F Duan wrote:
Dear All,
I am sorry if this question has been asked before. Below is my Question:
I want to put several plots in the same window, but I don’t want the blank
space between plots (like par(mfrow=)) --- that makes the plots too small.
Could anyone tell me how to do it?
Thanks a lot.
Hello,
I want to compute the P-value from the joint cumulative distribution of an
n-dimensional
order statistic in R, using the formula found on
http://cmgm.stanford.edu/%7Ekimlab/multiplespecies/Supplement/methods_network.html
My data consists of three different techniques (G2D, POCUS and RANDO
On Fri, 30 Jul 2004, Roy, Supratik wrote:
>
> I tried to include LaTeX expressions in the header of a plot in R.
> (1) Using PlotMath, LaTeX type expressions, e.g., R^x is possible, however,
> dist<-"" (some string)
> main=expression(R^x,dist)
> does not substitute the value of dist, a
Could someone kindly help me with the following question:
when I analyze microarray data I need to fit multiple linear regression
models between genes and clinical patameters followed by estimation of
the p-values.
What's the solution to implement Westfall and Young's algorithm +
resampling into
Dear Bob,
If you mean regression with autocorrelated errors, take a look at the gls
(generalised least squares) function in the nlme package.
I hope this helps,
John
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of bob mccall
> Sent: Friday, July
Dear All,
I am sorry if this question has been asked before. Below is my Question:
I want to put several plots in the same window, but I dont want the blank
space between plots (like par(mfrow=)) --- that makes the plots too small.
Could anyone tell me how to do it?
Thanks a lot.
Frank
On Fri, 30 Jul 2004, Adair, Laurence wrote:
> Hi All,
>
> Here is something that sounds simple, but I'm having trouble getting it. I
> have a data frame with two columns, the first is date and the second is
> employee ID. I'd like to plot date on the horizontal axis, employee ID on
> the vertica
Could someone kindly help me with the following question:
when I analyze microarray data I need to fit multiple linear regression
models between genes and clinical patameters followed by estimation of
the p-values.
What's the solution to implement Westfall and Young's algorithm +
resampling into
On Fri, Jul 30, 2004 at 11:37:32AM +0200, Dewez Thomas wrote:
> Dear R-users,
>
> Thanks to Roger Bivand, it appears that the real problem is coming from the
> way R talks to X11 under cygwin. Both other invocations of Rterm, either in
> a bash window without Xwindow capability or from the DOS com
Hi All,
Here is something that sounds simple, but I'm having trouble getting it. I
have a data frame with two columns, the first is date and the second is
employee ID. I'd like to plot date on the horizontal axis, employee ID on
the vertical axis, and the number of times the employee appears for
Greetings:
Is there an simple way to do dynamic regressions in R?
>From what I've seen, one must use arima() and construct the X matrix with lagged
>values etc. and modify Y as well.
Thanks,
Bob
-
[[alternative HTML version deleted
Two things to try:
1. Try transforming the parameters. It may be that one or more
parameters transformed by log or reciprocal, say, will improve the
objective function from the optimizer's viewpoint.
2. specify the gradient explicitly. If its complicated but not
too complicated you might try
Roy, Supratik wrote:
I tried to include LaTeX expressions in the header of a plot in R.
(1) Using PlotMath, LaTeX type expressions, e.g., R^x is possible, however,
dist<-"" (some string)
main=expression(R^x,dist)
does not substitute the value of dist, as well do the proper superscriptin
Stephan Moratti wrote:
Trying following example from Pinheiro and Bates in order to fit an
ARMA(1,1) model:
library(nlme)
fm1Ovary.lme<-lme(follicles~sin(2*pi*Time)+cos(*pi*Time),data=Ovary,random=p
dDiag(~sin(2*pi*Time)))
fm5Ovary.lme<-update(fm1Ovary.lme,corr=corARMA(p=1,q=1))
I get follwing erro
I tried to include LaTeX expressions in the header of a plot in R.
(1) Using PlotMath, LaTeX type expressions, e.g., R^x is possible, however,
dist<-"" (some string)
main=expression(R^x,dist)
does not substitute the value of dist, as well do the proper superscripting.
Also within an ex
Dear Uwe and Jordi,
It is possible to get close to what Jordi wants using the tcltk package:
IDPoints <- function(x, y, labels){
top <- tktoplevel()
tkwm.title(top, "Coordinates")
coords <- tclVar("")
coordsEntry <- tkentry(top, width="25", textvariable=coords)
Stop <- tclVar(
Molins, Jordi wrote:
Hello,
I use R 1.9.1 on Windows 2000. I have a chart that I am looking. I use
identify() and locator() to find out the (x,y) values of interesting points
in the chart, but these functions are not always helpful (e.g., sometimes
identify() prints on top of the chart, making the
[EMAIL PROTECTED] wrote:
I'm working with S-Plus 6 in Windows. Does anyone know if the prune.tree or
prune.misclass function automatically cross-validates or do you have to use
cv.tree if you want to do cross-validation?
This mailing list is about R. There is, e.g., the s-news lists for
questions
Dear all again,
Here is a wrap-up of the fact finding mission Roger and I led over the last
two days (see his reply below my email).
The issue was the following:
---
1. Rterm breaks down when invoked from Xwindow under Cygwin. This is a
typical Cygwin problem and does not
[EMAIL PROTECTED] wrote on 30/07/2004 05:34:32:
> Are the Windows recipients of the R graphics involved in
> creating/editing the resultant documents, or do they simply require
> "read only" access of a final document?
>
> If the latter, then let me suggest that you generate EPS based grap
Gunnar Wrobel wrote:
>
> Dear list,
>
> is there any way to debug the S4 methods using the debug() function in
> R1.9.1?
>
> I am able to use browser() inside a S4 method but I wondered if there is
> a way to debug the function without recompiling the package.
Yes. Use the trace() function to
Dear R-friends,
I use
optim(par=c(mystartingpoints), fn=myloglikelihoodfunction, gr=NULL,
method=c("L-BFGS-B"), ## I would like to do not use any
bounds
control=list(trace=6, ## just to see what it's going on
maxit=c(2))
I'm working with S-Plus 6 in Windows. Does anyone know if the prune.tree or
prune.misclass function automatically cross-validates or do you have to use
cv.tree if you want to do cross-validation?
Heather
__
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https://www.st
Trying following example from Pinheiro and Bates in order to fit an
ARMA(1,1) model:
library(nlme)
fm1Ovary.lme<-lme(follicles~sin(2*pi*Time)+cos(*pi*Time),data=Ovary,random=p
dDiag(~sin(2*pi*Time)))
fm5Ovary.lme<-update(fm1Ovary.lme,corr=corARMA(p=1,q=1))
I get follwing error message:
Error in
Hello,
I use R 1.9.1 on Windows 2000. I have a chart that I am looking. I use
identify() and locator() to find out the (x,y) values of interesting points
in the chart, but these functions are not always helpful (e.g., sometimes
identify() prints on top of the chart, making the number illegible).
Dewez Thomas <[EMAIL PROTECTED]> writes:
> + Rterm dies when hitting return after correcting typos
> the error message then is:
> ---
> Error: syntax error
> Execution halted
> ---
>
> This suggests that Rterm is by-passing fvwm2 and the X11 environment to talk
> to windows directly. This is also
On Fri, 30 Jul 2004, Dewez Thomas wrote:
> Dear R-users,
>
> Thanks to Roger Bivand, it appears that the real problem is coming from the
> way R talks to X11 under cygwin. Both other invocations of Rterm, either in
> a bash window without Xwindow capability or from the DOS command, work just
> fi
Dear R-users,
Thanks to Roger Bivand, it appears that the real problem is coming from the
way R talks to X11 under cygwin. Both other invocations of Rterm, either in
a bash window without Xwindow capability or from the DOS command, work just
fine.
Rterm breaks down every time it is invoked from a
Jason Sinnwell wrote:
Dear useRs-
I am developing a package that uses output from stand-alone unix software
programs. I use multiple perl scripts to process the output and make it ready
for reading into R. I would like to keep the perl scripts in the designated
place for such files, exec/, but
I suspect sqlQuery() returns a data frame, is that correct? Then try to
convert it into a matrix before you paste() it. Example:
> x <- data.frame(a=1:3, b=1:3+0.5)
> as.character(x)
[1] "as.integer(c(1, 2, 3))" "c(1.5, 2.5, 3.5)"
> as.character(as.matrix(x))
[1] "1" "2" "3" "1.5" "2.5" "3.5
[EMAIL PROTECTED] wrote:
dear R wizards: I would like to write a function that roughly places
the equivalent of the following latex text into the current plot:
\newcommand{ \placesigma }[4]{ \put(\#1,\#2){ \sigma_{A , #3} = #4 }
???
You are "just" defining a new LaTeX command ... nothing will
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