[R] problem loading package Hmisc
Hi, I installed the package Hmisc with the command install.packages(Hmisc) without errors. When I try to load the library with command library(Hmisc) I get the error library(Hmisc) Error in library(Hmisc) : there is no package called 'Hmisc' version _ platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) Any help is appreciated. Unfortunately the RSiteSearch is not working now, so the question may not be well researched. Thanks Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem loading package Hmisc
Sorry about the question. I had installed the package locally and hence the library command was not working as stated. library(Hmisc, lib.loc=~/R/) did the trick. On 11/25/06, Ritwik Sinha [EMAIL PROTECTED] wrote: Hi, I installed the package Hmisc with the command install.packages(Hmisc) without errors. When I try to load the library with command library(Hmisc) I get the error library(Hmisc) Error in library(Hmisc) : there is no package called 'Hmisc' version _ platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) Any help is appreciated. Unfortunately the RSiteSearch is not working now, so the question may not be well researched. Thanks Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Problems with plot and X11 in ubuntu
Hi Everyone, Thanks for the question and the answer. It helped me solve the problem which I too faced. Ritwik. On 11/11/06, Oscar [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Take a look at this link: http://www.ubuntuforums.org/showthread.php?t=268024 HTH Oscar On Nov 11, 2006, at 04:19, Bagatti Davide wrote: About Ubuntu, it's a new installation (ubuntu 6.10, code name Edgy Eft). About R, it's a new installation. Thank you very much 2006/11/10, [EMAIL PROTECTED] [EMAIL PROTECTED]: A few questions before I may help. Is this a NEW installation or an upgrade? If an upgrade, what version are you upgrading from? Regards, Oscar From: Bagatti Davide [EMAIL PROTECTED] Date: 2006/11/10 Fri AM 09:22:24 CST To: r-help@stat.math.ethz.ch Subject: [R] Problems with plot and X11 in ubuntu Hello, I am an italian student, who is trying to use R 2.3.1 with Ubuntu 6.10 (last version). When I try to use the plot command, I get the error: could not find any X11 fonts Check that the Font Path is correct How can I solve this problem? Thank you very much Davide [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Multivariate regression
You can use gee ( http://finzi.psych.upenn.edu/R/library/geepack/html/00Index.html) or maybe the function gls in nlme. Ritwik. On 10/27/06, Ravi Varadhan [EMAIL PROTECTED] wrote: Hi, Suppose I have a multivariate response Y (n x k) obtained at a set of predictors X (n x p). I would like to perform a linear regression taking into consideration the covariance structure of Y within each unit - this would be represented by a specified matrix V (k x k), assumed to be the same across units. How do I use lm to do this? One approach that I was thinking of is as follows: Flatten Y to a vector, say, Yvec (n*k x 1). Create Xvec (n*k, p*k) such that it is made up of block matrices Bij (k x k), where Bij is a diagonal matrix with X_ij as the diagonal (i = 1,.n, and j = 1,.,p). Now I can use lm in a univariate mode to regress Yvec against Xvec, with covariance matrix Vvec (n*k x n*k). Vvec is a block-diagonal matrix with blocks of V along the diagonal. This seems like a valid approach, but I still don't know how to specify the covariance structure to do weighted least squares. Any help is appreciated. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Replacing for loop with apply type function.
Hi Everyone, I want to replace the following for loop with an apply type function to (possibly) speed up the process. # The for loop I want to replace x - numeric(10) for(i in 2:10) x[i] - x[i-1]+1 x To give you some more background, I am running a Metropolis Hastings MCMC chain with k parameters. So, if x represents the sample from the chain, the ith row (representing the ith iteration) depends on the (i-1)th row. Thanks in advance, Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] lattice: adding text to plots
Hi Gabor,
Thanks for your reply. The solution you gave me and the one that I had
attempted have the same problem. The plots don't differentiate between
y1 and y2, in other words, they loose the groups attribute. This is
what 'does not work' means. I am attaching a ps file (I hope that does
not get stripped). In each panel there should be two lines, but this
has just one (group lost).
This plot was produced with R 2.4 on windows and lattice 0.14-9.
Thanks and regards,
Ritwik.
On 10/9/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Could you explain what does not work means. It seems to produce a
graph with x-y numbers on it in R 2.4.0 on Windows.
At any rate, I would have done it like this although I think you can
leave off the [1] on subscripts and it will still work.
library(lattice)
library(grid)
xyplot(y1 + y2 ~ x | g * h, data = DF, type = l,
panel = function(x, y, subscripts, groups, ...) {
panel.xyplot(x, y, ...)
grid.text(DF$f[subscripts[1]], .1, .9)
})
On 10/9/06, Ritwik Sinha [EMAIL PROTECTED] wrote:
Hi Everyone,
I know there was a thread recently that dealt with a similar issue,
but this one is a little different.
I have the following data frame
DF - data.frame(x = 1:12, y1 = rnorm(12), y2 = rnorm(12), g =
gl(2,6), h = rep(c(1, 2), 6), f = c(rep(c(1-1,1-2),3),
rep(c(2-1,2-2),3)))
I essentially want this plot
xyplot(y1+y2~x|g*h, data=DF, type=l)
However, now I want to add a different text to each panel, the text
being from column f of the data frame. In other words, I want text
1-1 in the panel where g=1 and h=1 and so on. I tried to pass groups
and subscript to the panel function but could not get what I was
looking for. The following attempt does not work.
xyplot(y1+y2~x|g*h, data=DF, type=l, auto.key=TRUE,
panel=function(x,y,..., groups, subscripts){panel.xyplot(x,y,...);
panel.text(x=4,y=0, labels=DF$f[subscripts])})
My R version is 2.2.1 and lattice version is 0.12-11 (sorry they are
not the latest ones, these are on the server).
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
[EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha
__
R-help@stat.math.ethz.ch 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.
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
[EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha
Rplots.ps
Description: PostScript document
__
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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] lattice: adding text to plots
On 10/9/06, Deepayan Sarkar [EMAIL PROTECTED] wrote:
Just out of curiosity, what's wrong with
xyplot(y1 + y2 ~ x | interaction(g, h, sep = -), data = DF, type =
l, auto.key = TRUE)
The reason would be that I want to add information to the plot that is
not of the form i-j. My example happens to be an over
simplification.
? Not having to do the other sort of callisthenics is the whole point
of having strips.
I should point out a subtle effect here (even hinted at in the
documentation, miraculously), which can be seen with
xyplot(y1 + y2 ~ x | g * h, data=DF,
+ panel = function(x, y, ..., subscripts) print(subscripts) )
[1] 1 3 5 13 15 17
[1] 7 9 11 19 21 23
[1] 2 4 6 14 16 18
[1] 8 10 12 20 22 24
Note that the last three values of 'subscripts' in each panel is 12 +
i, where i is the true subscript (DF has only 12 rows). This is a
consequence of the fact that DF is internally 'reshape()'d. Gabor's
solution avoids this by using subscripts[1] in each panel (and also
because 'x' and 'y' are not recycled to be as long as the labels in
grid.text), but it's something to be generally aware of.
Thanks for the clarification. I had realized that the internal reshape
makes this change.
-Deepayan
Thanks and regards,
Ritwik.
On 10/9/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Could you explain what does not work means. It seems to produce a
graph with x-y numbers on it in R 2.4.0 on Windows.
At any rate, I would have done it like this although I think you can
leave off the [1] on subscripts and it will still work.
library(lattice)
library(grid)
xyplot(y1 + y2 ~ x | g * h, data = DF, type = l,
panel = function(x, y, subscripts, groups, ...) {
panel.xyplot(x, y, ...)
grid.text(DF$f[subscripts[1]], .1, .9)
})
On 10/9/06, Ritwik Sinha [EMAIL PROTECTED] wrote:
Hi Everyone,
I know there was a thread recently that dealt with a similar issue,
but this one is a little different.
I have the following data frame
DF - data.frame(x = 1:12, y1 = rnorm(12), y2 = rnorm(12), g =
gl(2,6), h = rep(c(1, 2), 6), f = c(rep(c(1-1,1-2),3),
rep(c(2-1,2-2),3)))
I essentially want this plot
xyplot(y1+y2~x|g*h, data=DF, type=l)
However, now I want to add a different text to each panel, the text
being from column f of the data frame. In other words, I want text
1-1 in the panel where g=1 and h=1 and so on. I tried to pass groups
and subscript to the panel function but could not get what I was
looking for. The following attempt does not work.
xyplot(y1+y2~x|g*h, data=DF, type=l, auto.key=TRUE,
panel=function(x,y,..., groups,
subscripts){panel.xyplot(x,y,...);
panel.text(x=4,y=0, labels=DF$f[subscripts])})
My R version is 2.2.1 and lattice version is 0.12-11 (sorry they are
not the latest ones, these are on the server).
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
[EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] lattice: adding text to plots
Hi Everyone,
I know there was a thread recently that dealt with a similar issue,
but this one is a little different.
I have the following data frame
DF - data.frame(x = 1:12, y1 = rnorm(12), y2 = rnorm(12), g =
gl(2,6), h = rep(c(1, 2), 6), f = c(rep(c(1-1,1-2),3),
rep(c(2-1,2-2),3)))
I essentially want this plot
xyplot(y1+y2~x|g*h, data=DF, type=l)
However, now I want to add a different text to each panel, the text
being from column f of the data frame. In other words, I want text
1-1 in the panel where g=1 and h=1 and so on. I tried to pass groups
and subscript to the panel function but could not get what I was
looking for. The following attempt does not work.
xyplot(y1+y2~x|g*h, data=DF, type=l, auto.key=TRUE,
panel=function(x,y,..., groups, subscripts){panel.xyplot(x,y,...);
panel.text(x=4,y=0, labels=DF$f[subscripts])})
My R version is 2.2.1 and lattice version is 0.12-11 (sorry they are
not the latest ones, these are on the server).
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
[EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha
__
R-help@stat.math.ethz.ch 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] Plotting text with lattice
Hi,
On a related note, if I wanted to add different texts to different
panels, should I stick to using trellis.focus() for each text in each
panel? I cannot figure out a way to do it using a panel function.
Ritwik.
On 9/29/06, Deepayan Sarkar [EMAIL PROTECTED] wrote:
On 9/29/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Here are two possibilities. The first use trellis.focus/trellis/unfocus to
add text subsequent to drawing the xyplot and the second uses a
custom panel:
xyplot(x ~ x, data = data.frame(x = 1:10))
trellis.focus(panel, 1, 1)
panel.text(x=2, y=4, labels=Text)
trellis.unfocus()
xyplot(x ~ x, data = data.frame(x = 1:10), panel = function(...) {
panel.xyplot(...)
panel.text(x=2, y=4, labels=Text)
})
Right, on a more general note, this is necessary because it is not clear what
ltext(x=2, y=4, labels=Text)
should do for a multi-panel plot. On an even more general note, you
will keep getting in trouble when using lattice if you (1) try to
follow the incremental addition approach of standard graphics or (2)
use the par() system in any way.
Deepayan
On 9/29/06, McGehee, Robert [EMAIL PROTECTED] wrote:
Hello,
I've decided to take the leap and try my hand at the lattice package,
though I am getting stuck at what one might consider a trivial problem,
plotting text at a point in a graph. Apologies in advance if (that) I'm
missing something extremely basic.
Consider in base graphics:
plot(1:10)
text(2, 4, Text)
In the above you will see text centered at the point (2, 4) on the
graph.
Now I would like to try to do the same thing using the lattice package:
xyplot(x ~ x, data = data.frame(x = 1:10))
ltext(x=2, y=4, labels=Text)
panel.text(x=2, y=4, labels=Text)
grid.text(label=Text, x=2, y=4)
grid.text(label=Text, x=unit(2, native), y=unit(4, native))
None of the above four commands puts the Text at the (2, 4) point on
the graph. Any help with this would be appreciated! Also, if I have more
than one panel and would like to place text at different points on
different panels how would I do this?
Also, note that I'm hoping to use text to label interesting points in a
levelplot, but am using the above xyplot as an example.
Thanks,
Robert
Robert McGehee
Quantitative Analyst
Geode Capital Management, LLC
53 State Street, 5th Floor | Boston, MA | 02109
Tel: 617/392-8396Fax:617/476-6389
mailto:[EMAIL PROTECTED]
This e-mail, and any attachments hereto, are intended for us...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch 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.
--
http://www.stat.wisc.edu/~deepayan/
__
R-help@stat.math.ethz.ch 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.
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
[EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha
__
R-help@stat.math.ethz.ch 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] Plotting text with lattice
Thanks Gabor,
I realized I could also use this code
xyplot(x ~ x | g, data = data.frame(x = 1:12, g = gl(3,4)), groups=g,
panel = function(..., groups, subscripts) {
panel.xyplot(...)
panel.text(x=2, y=4, labels=groups[subscripts])
})
Which is essentially a rewrite of one of the examples of xyplot.
Ritwik.
On 10/5/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
I seem to have omitted g
library(lattice)
xyplot(x ~ x | g, data = data.frame(x = 1:12, g = gl(3,4)), panel =
function(...) {
panel.xyplot(...)
panel.text(x=2, y=4, labels=which.packet())
})
On 10/5/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
This requires R 2.4.0. Its the same as my earlier example except
the labels= arg has been changed to labels=which.packet().
xyplot(x ~ x | g, data = data.frame(x = 1:12), panel = function(...) {
panel.xyplot(...)
panel.text(x=2, y=4, labels=which.packet())
})
On 10/5/06, Ritwik Sinha [EMAIL PROTECTED] wrote:
Hi,
On a related note, if I wanted to add different texts to different
panels, should I stick to using trellis.focus() for each text in each
panel? I cannot figure out a way to do it using a panel function.
Ritwik.
On 9/29/06, Deepayan Sarkar [EMAIL PROTECTED] wrote:
On 9/29/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Here are two possibilities. The first use
trellis.focus/trellis/unfocus to
add text subsequent to drawing the xyplot and the second uses a
custom panel:
xyplot(x ~ x, data = data.frame(x = 1:10))
trellis.focus(panel, 1, 1)
panel.text(x=2, y=4, labels=Text)
trellis.unfocus()
xyplot(x ~ x, data = data.frame(x = 1:10), panel = function(...) {
panel.xyplot(...)
panel.text(x=2, y=4, labels=Text)
})
Right, on a more general note, this is necessary because it is not
clear what
ltext(x=2, y=4, labels=Text)
should do for a multi-panel plot. On an even more general note, you
will keep getting in trouble when using lattice if you (1) try to
follow the incremental addition approach of standard graphics or (2)
use the par() system in any way.
Deepayan
On 9/29/06, McGehee, Robert [EMAIL PROTECTED] wrote:
Hello,
I've decided to take the leap and try my hand at the lattice
package,
though I am getting stuck at what one might consider a trivial
problem,
plotting text at a point in a graph. Apologies in advance if (that)
I'm
missing something extremely basic.
Consider in base graphics:
plot(1:10)
text(2, 4, Text)
In the above you will see text centered at the point (2, 4) on the
graph.
Now I would like to try to do the same thing using the lattice
package:
xyplot(x ~ x, data = data.frame(x = 1:10))
ltext(x=2, y=4, labels=Text)
panel.text(x=2, y=4, labels=Text)
grid.text(label=Text, x=2, y=4)
grid.text(label=Text, x=unit(2, native), y=unit(4, native))
None of the above four commands puts the Text at the (2, 4) point
on
the graph. Any help with this would be appreciated! Also, if I have
more
than one panel and would like to place text at different points on
different panels how would I do this?
Also, note that I'm hoping to use text to label interesting points
in a
levelplot, but am using the above xyplot as an example.
Thanks,
Robert
Robert McGehee
Quantitative Analyst
Geode Capital Management, LLC
53 State Street, 5th Floor | Boston, MA | 02109
Tel: 617/392-8396Fax:617/476-6389
mailto:[EMAIL PROTECTED]
This e-mail, and any attachments hereto, are intended for
us...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch 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.
--
http://www.stat.wisc.edu/~deepayan/
__
R-help@stat.math.ethz.ch 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.
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Re: [R] only need the p-value
This is how you go about doing this. summary(results)$coefficients[1,5] You will have to check this for you code. But the idea is that summary(results) is a list (?) and one of its components is called coefficients, which is a matrix. So the problem is just to extract one element of this matrix. I am not well versed with coxph so there may be some minor details I am missing, but that is the general idea (same as with lm, glm etc.). Ritwik. On 9/30/06, Boks, M.P.M. [EMAIL PROTECTED] wrote: Dear R users, I am calculating several cox proportional hazard models after each other (I know this is unusual, but I am just exploring the data). For the purpose of multiple testing correction I need to construct an array of these p-values. However since the output is not an array in itself, I cannot find a way to obtain the p-value only. attach(tms) goal-rep(0.7*FREQUENC[1:13],6) event- Surv(TIJD,FREQUENCgoal) results-coxph(event~ TYPETREA) summary(results) Call: coxph(formula = event ~ TYPETREA) n=76 (2 observations deleted due to missing) coef exp(coef) se(coef) z p TYPETREAnon-guided -0.826 0.4380.484 -1.71 0.088 exp(coef) exp(-coef) lower .95 upper .95 TYPETREAnon-guided 0.438 2.28 0.169 1.13 Rsquare= 0.041 (max possible= 0.829 ) Likelihood ratio test= 3.2 on 1 df, p=0.0737 Wald test= 2.91 on 1 df, p=0.088 Score (logrank) test = 3.08 on 1 df, p=0.0794 Does anyone now how to extract the p-value? Many thanks!, Marco __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Print/Save/Cat/Write list
Hi, I would like to write a list to an ascii file. I tried the following y - list(a = 1, b = c(TRUE,FALSE), c = oops) save(y, file=y.data, ascii=TRUE) # Not satisfactory print does not have a file= option cat cannot handle lists. write does not handle lists write.table converts it to a d.f Perhaps I could loop through the elements of a list and keep appending its elements to a file, but that will have a problem if any of the elements of the list is a list. I suppose there must be a simple function that does what I need. Sorry if I have missed anything obvious, my searches did not return anything useful. Thanks and regards, Ritwik. Here is my version platform i686-redhat-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor2.1 year 2005 month12 day 20 svn rev 36812 language R -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Print/Save/Cat/Write list
thanks. Ritwik. On 9/30/06, jim holtman [EMAIL PROTECTED] wrote: try: sink(y.data) y sink() On 9/30/06, Ritwik Sinha [EMAIL PROTECTED] wrote: Hi, I would like to write a list to an ascii file. I tried the following y - list(a = 1, b = c(TRUE,FALSE), c = oops) save(y, file=y.data, ascii=TRUE) # Not satisfactory print does not have a file= option cat cannot handle lists. write does not handle lists write.table converts it to a d.f Perhaps I could loop through the elements of a list and keep appending its elements to a file, but that will have a problem if any of the elements of the list is a list. I suppose there must be a simple function that does what I need. Sorry if I have missed anything obvious, my searches did not return anything useful. Thanks and regards, Ritwik. Here is my version platform i686-redhat-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor2.1 year 2005 month12 day 20 svn rev 36812 language R -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Heteroskedasticity test
you may also try to levene test. Once again i think it is for a known change point. http://finzi.psych.upenn.edu/R/library/car/html/levene.test.html On 9/30/06, Achim Zeileis [EMAIL PROTECTED] wrote: On Fri, 29 Sep 2006, Alberto Monteiro wrote: Is there any heteroskedasticity test in the package? Something that would flag a sample like x - c(rnorm(1000), rnorm(1000, 0, 1.2)) The package lmtest contains several tests for heteroskedasticity, in particular the Breusch-Pagan test (and also the Goldfeld-Quandt test for known change point). Furthermore, some of the structural change tests in strucchange can be used to test for non-constant variances, e.g, the Nyblom-Hansen test. Z Alberto Monteiro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Histogram
Hi, There may be an easier way but here is one way you can do it. # create vector that has Y[i] X[i]s new.data - rep(X,Y) hist(new.data, breaks=c(0,.1,.4,.6)) # or something like that look at what exactly breaks should be. Ritwik. On 9/27/06, Mohsen Jafarikia [EMAIL PROTECTED] wrote: Dear all, I want to design a histogram and I need to have the frequency at certain points. For example I have the following 2 columns: *X Y* 0.125 0.422 0.45 11 0.55 21 I want the chart to have 4 columns. First column is from 0.0-0.1 (on X) and frequency is 25. Next colum is wider and form 0.1-0.4 with 22 frequency. Next column is narrow with 11 frequency and the last column is the same as the first one with 21 frequency. Can anybody tell me how I can have this chart. Thanks, Mohsen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University [EMAIL PROTECTED] | +12163682366 | http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] creation of new variables
Depends on what these variables are. Are these vectors? if so a simple a*b etc should work. If they are columns of a data frame DF? then DF$a*DF$b. If these variables are part of a function then also a*b should work. On 9/26/06, nalluri pratap [EMAIL PROTECTED] wrote: Hello All, I have 8 variables named a b c d e f g h I need to create four variables from these 8 vraibles in R. the new variables are ab,cd,ef,gh. Can anyone pleas help me thanks, Pratap - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Statitics Textbook - any recommendation?
How about this book by Julian Faraway. http://www.stat.lsa.umich.edu/~faraway/book/ It covers only regression and anova, but I really like the book. It gives a good overview of the important topics in linear regression and anova. Also it is on the web and hence free. Ritwik On 9/22/06, Wolfgang Lindner [EMAIL PROTECTED] wrote: Iuri Gavronski schrieb: Other text I am trying to find is multivariate data analysis (EFA, cluster, mult regression, MANOVA, etc.) with examples with R. Hi Iuri, for your second answer I would recommend B. Everitt: An R and S-PLUS Companion to Multivariate Analysis. Springer 2005. isbn 1-85233-882-2. Best Wolfgang -- privat: Wolfgang Lindner, Stieglitzweg 6, D-42799 Leichlingen __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] how to delete some columns from a matrix based on some other indicator variable
Hi, The problem might be mode of the vector r. Try this D[,as.character(r)==1] But I am not sure that is the problem. Sometimes factors tend to complicate things. Look for factor in the R FAQ page. Ritwik. On 9/20/06, David Barron [EMAIL PROTECTED] wrote: You don't need a loop. You could try r - c(0,0,1,1) matD - matrix(1:12,nrow=3) matD [,1] [,2] [,3] [,4] [1,]147 10 [2,]258 11 [3,]369 12 matD[,r==1] matD[,r==1] [,1] [,2] [1,]7 10 [2,]8 11 [3,]9 12 On 20/09/06, Ya-Hsiu Chuang [EMAIL PROTECTED] wrote: Hello, I am not very familiar with R and need help in deleting a few columns in a matrix. Suppose I have a indicator variable called r and it's defined as r = (0, 0, 1, 1). A matrix D is a 3X4 matrix. If I want a new matrix which contains only the columns of D corresponding to the elements of r that equal to 1. how can i write a loop which creat a new matrix that contains only the last 2 columns of D in this case? thanks __ R-help@stat.math.ethz.ch 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 Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] About truncated distribution
However, if you know the point(s) of truncation then you should be able to work your way back. Look for the mean and variance of a truncated normal, it will involve mu, sigma and c (point of truncation). You will need to solve for mu and sigma from two equation. For example look at the wikipedia page on normal distribution, it has the mean of a truncated normal distribution. Many standard statistics books should have the rest of the information. On 9/12/06, Berton Gunter [EMAIL PROTECTED] wrote: But my question is a bit different. What I know is the mean and sd after truncation. If I assume the distribution is normal, how I am gonna develope the original distribution using this two parameters? You can't, as they are plainly not sufficient (you need to know the amount of truncation also). If you have only the mean and sd and neither the actual data nor the truncation point you're through. -- Bert Gunter Genentech Could anybody give me some advice? Thanks in advance! Jen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] covariance matrix of predictions
Hi,
If I understand correctly the
Var(X \hat{\beta}) = X (X'X)^{-1}X' \sigma^2, where X will now be x.pred.
Which should be easily obtained by performing the matrix computation and
multiplying it with the estimate of the variance.
For more details about different aspects of the estimate and variance of the
predictor refer to page 39 of http://www.stat.lsa.umich.edu/~faraway/book/
Ritwik Sinha
On 8/23/06, Arnab mukherji [EMAIL PROTECTED] wrote:
Hi !
I am trying to get at the covariance of the predictions of a linear model.
Suppose the we have:
x-runif(1000)
y-2 + 25x*x +rnorm(1000)
lm1 -lm(y~x, data = data.frame(y = y, x=x))
x.pred -runif(10)
y.hat - predict(lm1, newdata = data.frame(x=x.pred))
I was wondering how to get an estimate of the covariance of y.hat which
would be a 10 x 10 matrix telling be the uncertainty in each of the
predictions.
thanks
Arnab
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--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
http://darwin.cwru.edu/~rsinha
[[alternative HTML version deleted]]
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Re: [R] two density curves in one plot?
Hi Gabor and Dimitris, I was wondering if this question was frequent enough to be in the R FAQ under R Miscellanea and thought of something like this Q. How do I plot two curves on the same graph? A. Plot the first curve using the plot() command and add lines using lines(). For example d1 - density(rnorm(100)) d2 - density(rnorm(100)) plot(range(d1$x, d2$x), range(d1$y, d2$y), type = n, xlab = x, ylab = Density) lines(d1, col = red) lines(d2, col = blue) Alternatively one can use points() to add points to the plot. If you think this question should be in the FAQ and if you have any comments/changes to the QA then I can request the maintainer of the FAQ to include it. We could also include a lattice solution but I was thinking of not complicating things. Ritwik Sinha On 8/27/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: Not sure who maintains the FAQ but its not me. On 8/27/06, Ritwik Sinha [EMAIL PROTECTED] wrote: This seems to be a common question for new commers to R, does it make sense to add it to the R FAQ page? I checked it is not currently there. Ritwik On 8/23/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: With lattice graphics: library(lattice) d1 - rnorm(100) d2 - runif(100) densityplot(~ d1 + d2, auto.key = TRUE) On 8/23/06, Antje [EMAIL PROTECTED] wrote: Hello, I was wondering if I can plot two curves I get from density(data) into one plot. I want to compare both. With the following commad, I just get one curve plotted: plot( density(mydata) ) Sorry for this stupid question but I could not find a solution until now... Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Implementing EM Algorithm in R!
Implementing the EM algorithm will be easy if you know what the algorithm is for your particular problem. This will be very specific to your problem. The trick is to augment your data to get something for which there is an easy ML estimate. I do not believe there is a unique recipe to perform the EM algorithm for any problem. On 8/26/06, Pushkar Kumar [EMAIL PROTECTED] wrote: Hi All, I need some help in how one can implement maximumlikelihood estimation for models with discrete hidden variables in EM in R. Regards [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] plotting picture data
Just a suggestion. It seems like each square can be denoted by x and y coordinates. Then you essentially have a two dimensional histogram/density that you need to plot. You can use the lattice functions cloud/wireframe. You can also go for a heat map/contour plot, the lattice functions for that will be levelplot/contourplot. In case the number of squares are small, you might prefer a two-dimensional histogram, cloud in lattice has an option to plot the point as histogram. Ritwik. On 8/4/06, Gichangi, Anthony [EMAIL PROTECTED] wrote: Hi R users I have a dataset which represents points that are market by patients as the source of pain. Basically the patients indicates by a cross on a chest pictures where he/she thinks is the source of pain. The data was then digitalized by divinding the chest into small squares and each square was give value 1 if it was the center 2 if it was touched by the markings and 3 if it was not touched. I would like to plot this data on the chest like graph showing the intesities of different points and later stratify the grouping variables to see the difference. Has anybody got an idea how I can go around this ? Help is highly appreciated. Regards Anthony Gichangi, M. sc. Department of Statistics. JB. Winsløvej 9B, DK 5000 Odense C. Tel: 00 45 6550 3379 Mobile: 00 45 61105805 __ R-help@stat.math.ethz.ch 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. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rearrange data.
Hi,
I am trying to rearrange the following data
d.f - data.frame(x=c(1,1,2,2), y=c(1,2,1,2), vals=c(a11, a12,
a21, a22))
to look like a table with x as the rows and y as the columns, something like
y 1 2
x
1a11 a12
2a21 a22
I tried doing this
funny - function(x,y){d.f[d.f$x==x d.f$y==y,3]}
outer(1:2,1:2, FUN=funny)
But get the error
Error in outer(1:2, 1:2, FUN = funny) : dim- : dims [product 4] do
not match the length of object [2]
What am I doing wrong? I am sure there are a hundred different ways of
doing this.
version
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
http://darwin.cwru.edu/~rsinha
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Re: [R] FW: Large datasets in R
Hi, I have a related question. How differently do other statistical softwares handle large data? The original post claims that 350 MB is fine on Stata. Some one suggested S-Plus. I have heard people say that SAS can handle large data sets. Why can others do it and R seem to have a problem? Don't these softwares load the data onto RAM. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha __ R-help@stat.math.ethz.ch 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] Saving R graphics with version 2.3.1
Hi, Have a jpeg() your plot function dev.off() That will direct your graphs to a file called Rplots.jpg. Look for function jpeg and png. On 6/14/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: HI ! I´ve installed the latest R version (2.3.1) and I´ve had problems to save my graphics as JPEG, PNG and the others available formats. R saves the file with no extension. Then, I have to open this file using an image visualizer and save it as PNG, for instance. Previous R versions work without problems. Has everyone had a similar problem? Is it a bug of R 2.3.1? Thanks in advance. Ilka Afonso Reis __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] negative binomial: expected number of events?
Hi, This page should answer your questions. http://mathworld.wolfram.com/NegativeBinomialDistribution.html Ritwik Sinha http://darwin.cwru.edu On 6/5/06, Werner Tell [EMAIL PROTECTED] wrote: Hi I'm fitting poisson and negative binomial distributions to event data. I'm interested in the expected number of events occuring in a time period. For the poisson this is determined by the parameter lambda only. For the neg. binomial, is the expected number of events determined by the parameter mu only or does parameter size influence the first moment as well? thank you, wt _ Die MSN Homepage liefert Ihnen alle Infos zu Ihren Lieblingsthemen. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] negative binomial: expected number of events?
Hi, The wikipedia page http://en.wikipedia.org/wiki/Negative_binomial also does a great job of explaining the negative binomial distribution. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fastest way to do HWE.exact test on 100K SNP data?
Hi Anna, I am not really answering your question, but, here goes my (unsolicited) suggestion. Some time back I did some simulations to see how the HWE tests performed. In particular I compared the exact test and the chi squared test. Look at the attached figure Rplots.ps. I saw that for null simulations with 40 individuals, the HWE chi squared test was reasonably close to the (expected) uniform distribution. However this was obtained using the function HWE.chisq(X, simulate.p.value=F), the default seemed to have some issues. Hence my suggestion would be, if you feel comfortable, to replace the exact test with a chi sq test, at least at the screening level. Once you identify a set of SNPs with small p-values, you could follow them up with the exact test. -- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha http://darwin.cwru.edu/%7Ersinha Rplots.ps Description: PostScript document __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lm() variance covariance matrix of coefficients.
Thanks Everybody, I found it moments after I posted the question. Ritwik. On 03 Jun 2006 01:34:48 +0200, Peter Dalgaard [EMAIL PROTECTED] wrote: Rolf Turner [EMAIL PROTECTED] writes: Peter Dalgaard wrote: Rolf Turner [EMAIL PROTECTED] writes: summary(object)$cov.unscaled You need to multiply that with sigma. However, vcov(object) is easier. Well, I thought unscaled meant unscaled --- the plain unvarnished covariance matrix! I figure that multiplying the *covariance* matrix by something would be scaling it. Silly me. Think (quasi-)binomial glm() and things become clearer. Unscaled corresponds to a scale factor of 1. Also: (a) Shouldn't that be ``multiply by sigma^2'' rather than by sigma? Yup (b) Wouldn't it be helpful to have a pointer (``see also'') to vcov() in the help on summary.lm()? Well, it *is* in ?lm ... -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] lm() variance covariance matrix of coefficients.
Hi, I am running a simple linear model with (say) 5 independent variables. Is there a simple way of getting the variance-covariance matrix of the coeffcient estimates? None of the values of the lm() seem to provide this. Thanks in advance, Ritwik Sinha [EMAIL PROTECTED] Grad Student Case Western Reserve University [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is there a way to draw 3d plot?
Hi, I am not aware what this function does in matlab, but I was wondering why cloud or wireframe in the lattice package has not entered the discussion. Sorry if I am being naive. Ritwik. http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] uniform and clumped point plots
Hi, If you are looking for data clustered in two dimenstions you can use the multivariate normal package. Ritwik Sinha http://darwin.cwru.edu/~rsinha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] plot with abscissa in hours/weekdays
Hi, You can use the axis() command. For example plot(xvec,yvec, xaxt=n) axis(side=1, labels=c(Mon, Tue), at=c(0,1)) The xaxt sets up the axis but does not plot it. And axis does the rest. Ritwik. Case Western Reserve University http://darwin.cwru.edu/~rsinha m p wrote: Hello, How can I use plot and have abscissa in hours say (20:00,22:00,00:00,02:00 etc) and also weekdays say (Mon, Tue, Wed, ...) ? Is there a command that I can put into plot(xvec,yvec...,axes=...) that would enable that? Thanks for help, Mark __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
