Hello
Am Donnerstag, 3. August 2006 15.34 schrieb Thomas Lumley:
On Thu, 3 Aug 2006, Thomas Kuster wrote:
Hello
Am Mittwoch, 2. August 2006 17.11 schrieb Thomas Lumley:
...
You haven't shown anything that indicates that the C code stopped reading.
More likely R just stops displaying when
Daniel Coleman coleman.daniel at gene.com writes:
When I run gnls I get the error:
Error in nls(y ~ cbind(1, 1/(1 + exp((xmid - x)/exp(lscal, data = xy, :
step factor 0.000488281 reduced below 'minFactor' of 0.000976563
My first thought was to decrease minFactor but
Brian Lunergan ff809 at ncf.ca writes:
Evening all:
I'm taking a little time to experiment with R, Sweave, and Miktex/LaTex but
I've run up against some problems and -well- I hope that there are some on
the list who might have some suggestions. This will be kind of wordy as I
will
Hi,
has anyone ever seen implemented in R the following geodesic
distance between positive definite pxp matrices A and B?
d(A,B) = \sum_{i=1}^p (\log \lambda_i)^2
were \lambda is the solution of det(A -\lambda B) = 0
thanks
stefano
as I received few private email on the
Matthew Wilson matt at overlook.homelinux.net writes:
I'm studying R in my free time. I want to build a vector where each
element is equal to the element before it in the sequence plus some
random tweak.
You will probably get many answers to this, but
I think
vec -
Good day to everyone.
I'm working on computing correlation for several datasets (one dataset for each
chromosome). Computation is done several thousand times for each dataset which
at present takes around 13 hours. We have a HPC machine with MPI. snow package
and R 2.3.1 running in Linux
Dear All,
I have seldom needed to use loops in R, but now I need to code a loop
with a stride different from one.
In the R manual I downloaded I have the example:
xc - split(x, ind)
yc - split(y, ind)
for (i in 1:length(yc)) {
plot(xc[[i]], yc[[i]]);
abline(lsfit(xc[[i]], yc[[i]]))
}
Michael Jerosch-Herold wrote:
I have data for several rings of a left heart chamber, and which I would like
to display in concentric rings, with color-encoding of the values. Each ring
corresponds to one slice through the heart, and the rings correspond to
positions from the base to the
Hi all,
I have finally gotten the prettyR package going (many thanks to Kurt
Hornik for his patience).
prettyR is a set of functions that allows the user to produce HTML
output from R scripts. Given an R script that runs properly, an HTML
listing complete with embedded graphics can be
Thanks to all contributors for the fruitfulness of this discussion. I
am speculating about a simpler solution: to use a non-parametric
approach. To avoid the requirement of having normal residuals, Frank
Harrell has suggested here the following non-parametric procedure:
library(Design) # also
Dear All,
Can anybody tell me the syntax for User input from keyboard in R. I mean
to say that if I run the program it should ask Please enter the date at
the begining of the program. I am using R-2.2.1 for windows.
Any help will be greatly appreciated.
thanks in advance.
Regards,
Chiya
Dear R users,
When you do:
x - rnorm(10)
y - rnorm(10)
z - rnorm(10)
a - data.frame(x,y,z)
a$x
[1] 1.37821893 0.21152756 -0.55453182 -2.10426048 -0.08967880 0.03712110
[7] -0.80592149 0.07413450 0.15557671 1.22165341
Why does this not work:
a[a$y0.5,y] -1
Error in
When specifying a column name with [ the name must be quoted (unlike
when using it with $):
a[a$y 0.5, y] - 1
On 8/4/06, Sander Oom [EMAIL PROTECTED] wrote:
Dear R users,
When you do:
x - rnorm(10)
y - rnorm(10)
z - rnorm(10)
a - data.frame(x,y,z)
a$x
[1] 1.37821893
I have been trying to install R under Windows from the source by
following the instructions in R Installation and Adminstration.
Met with a list of problems along the way.
1) Recommended packages:
I tried to do
make lnik-recommended
and
make rsync-recommended
In both cases, I got the
Well nobody answered :-(
Nobody on R-help is doing anovas I guess -- I don't blame them! (It's just for
aggies.)
In the absence of any response and for no good reason I am doing:
fitn1 - aov(amplitude ~ stereo*site*stimulus + Error(subject), stereon1) This
is
Bill Venables's way.
And when the
you need to use quotes, i.e.,
a[a$y 0.5, y] - 1
you can also use
a$y[a$y 0.5] - 1
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel:
Hi
cat(\n,Enter x,\n) # prompt
y-scan(n=1)
prompts for user imput and scans 1 line from console.
HTH
Petr
On 4 Aug 2006 at 17:06, chiya sharma wrote:
Date sent: Fri, 4 Aug 2006 17:06:38 +0530
From: chiya sharma [EMAIL PROTECTED]
To:
Dear Gabor and Dimitris,
Simple, once you know! It is these little exceptions on the R notation
that get me stuck. Now I am on the loose again!
Thanks,
Sander.
Dimitris Rizopoulos wrote:
you need to use quotes, i.e.,
a[a$y 0.5, y] - 1
you can also use
a$y[a$y 0.5] - 1
I hope
Dear helpeRs,
I would like to specify a newline command in R and pass it to latex
via Sweave such that it corresponds to latex' \\ command. But that
doesn't seem to be possible. If I Sweave the \n character, it just
makes a new line in latex but not the \\ command.
Is there a way such that
On Fri, 4 Aug 2006, Petr Pikal wrote:
Hi
cat(\n,Enter x,\n) # prompt
y-scan(n=1)
prompts for user imput and scans 1 line from console.
(that scans one number: use readLines(n=1) to get a string).
But readline() is probably easier.
HTH
Petr
On 4 Aug 2006 at 17:06, chiya sharma
Jan Wijffels wrote:
Dear helpeRs,
I would like to specify a newline command in R and pass it to latex
via Sweave such that it corresponds to latex' \\ command. But that
doesn't seem to be possible. If I Sweave the \n character, it just
makes a new line in latex but not the \\ command.
Is
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
Hi
seems to me that it can be done by image. See ?image.
Just as illustration.
mat-matrix(sample(c(1,rep(2,10), rep(3,50)), 1000, replace=T),
100,100)
for(i in 1:6) mat[i,c(1:(50-5*i),(50+5*i):100)]-NA
for(i in 14:9) mat[i,c(1:(50-5*(15-i)),(50+5*(15-i)):100)]-NA
image(1:100,1:100,mat)
HTH
On Fri, 4 Aug 2006, Thomas Kuster wrote:
If I change the translatable characters (overwrite the 0 between :#@'= and
~000 with ÄÖÜäöü). I can read in the file an every ÄÖÜäöü ist a withspace:
Ok, that's the problem then. The file format says that the umlauts are
unreadable and R is believing
Hi Mr Plate,
I have a little question
How to convert a rowname vector of numbers into a real column of the matrix,
My problem is that I applied a rowsum function on a matrix.
Then I get a matrix in which the names of the columns are the values of the
group (numbers)
Now I need to make
I've tried several different ways to accomplish this, but as yet to no
avail. My y-axis for a plot has a rather long label, and thus I have
been using /n to break it into two lines. However, to make it
technically correct for publication, I also need to use superscript in
the label. For
On Fri, 2006-08-04 at 09:47 -0600, Andrew Kniss wrote:
I've tried several different ways to accomplish this, but as yet to no
avail. My y-axis for a plot has a rather long label, and thus I have
been using /n to break it into two lines. However, to make it
technically correct for
Use atop:
plot(1, main = expression(atop( ^14*C*-glyphosate line, line2)))
On 8/4/06, Andrew Kniss [EMAIL PROTECTED] wrote:
I've tried several different ways to accomplish this, but as yet to no
avail. My y-axis for a plot has a rather long label, and thus I have
been using /n to break it
Sorry, you wanted a ylab=, not a main=. Try using xyplot in lattice:
library(lattice)
xyplot(1~1, ylab = expression(atop(phantom(0)^14*C*-glyphosate line,
line2)))
On 8/4/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Use atop:
plot(1, main = expression(atop( ^14*C*-glyphosate line,
Thanks. I tried them, it works for most of those characters except * and ?.
Does regular expression work in file names in windows? e.g. I have a
machine-generated file named 021706 matrix#1479 @50.csv, of which 1479 is
kinda random. Will I be able to match 1479 with some sort of wild card
Actually Gabor, using your solution with 'atop', which I had not
considered, it will work with base graphics:
par(oma = c(0, 0, 2, 0), mar = c(5, 6, 0.25, 2), lheight = 1)
plot(1:10, ylab = expression(atop( ^14*C*-glyphosate line1,
line2)))
HTH,
Marc
On
Is there a function in R comparable to rpois that can simulate random
variables from an overdispersed poisson distribution? If there is not a
function any ideas/references on how to program one?
thanks,
Spencer Jones
Graduate Student, NLM Fellow
Dept. Biomedical Informatics
University of Utah
On Fri, 2006-08-04 at 10:33 -0600, Spencer Jones wrote:
Is there a function in R comparable to rpois that can simulate random
variables from an overdispersed poisson distribution? If there is not a
function any ideas/references on how to program one?
Take a look at
?rnbinom
or
Dear list,
I installed odesolve package (0.5-15) in R 2.3.1 in a Solaris server
(Generic_118558-11 sun4u sparc SUNW,Sun-Blade-1000). The installing
progress completed without errors, though several warnings like
Warning: Option -fPIC passed to ld, if ld is invoked, ignored
otherwise were
On Fri, 2006-08-04 at 12:46 -0400, Daniel Gerlanc wrote:
Hello all,
Consider the following problem:
There is a matrix of probabilities:
set.seed(1)
probs - array(abs(rnorm(25, sd = 0.33)), dim = c(5,5), dimnames =
list(1:5, letters[1:5]))
probs
a b c d
Hi,
When I fit a GAM model (using mgvc) with overlapping terms, such as
gam(y~s(x,z)+s(z,w))
and afterwards I pretend to plot the component smooth functions that make it up
using plot.gam, I achieve a couple of 2D plots.
My question is: What's the meaning of those 2D plots in terms of y?
Hi-
I'm seeing some weirdness with svm and tune.svm that I can't figure out- was
wondering if anyone else has seen this? Perhaps I'm failing to make
something the expected class?
Below is my repro case, though it *sometimes* doesn't repro. I'm using
R2.3.1 on WindowsXP. I was also seeing it happen
Dear List,
Why do commonly used estimator functions (such as lm(), glm(), etc.) not
allow negative case weights? I suspect that there is a good reason for this.
Yet, I can see reasonable cases when one wants to use negative case weights.
Take lm() for example:
###
n - 20
Y - rnorm(n)
X -
On Fri, 4 Aug 2006, Li,Qinghong,ST.LOUIS,Molecular Biology wrote:
Thanks. I tried them, it works for most of those characters except *
and ?.
Those are not valid characters in Windows file paths
(/ * : ? \ | are invalid in file or dir names).
Does regular expression work in file names
Looking at odesolve, src/Makevars is
PKG_LIBS=$(BLAS_LIBS)
Now, the documentation says that if you have $(BLAS_LIBS) you must also
have $(FLIBS), so please change this to
PKG_LIBS=$(BLAS_LIBS) $(FLIBS)
and take this up with the package maintainer (which is what the posting
guide asked you to
On 8/4/2006 1:26 PM, Jens Hainmueller wrote:
Dear List,
Why do commonly used estimator functions (such as lm(), glm(), etc.) not
allow negative case weights?
Residual sums of squares (or deviances) could be negative with negative
case weights. This doesn't seem like a good thing: would
Thanks Duncan Murdoch,
Why do commonly used estimator functions (such as lm(),
glm(), etc.)
not allow negative case weights?
Residual sums of squares (or deviances) could be negative
with negative case weights. This doesn't seem like a good
thing: would you really want the fit to
On 4 August 2006 at 19:26, Jens Hainmueller wrote:
| Why do commonly used estimator functions (such as lm(), glm(), etc.) not
| allow negative case weights? I suspect that there is a good reason for this.
That came up on r-sig-finance a little while ago. As usual, Gabor won the
contest for most
On Fri, 2006-08-04 at 19:37 -0400, Jim Lemon wrote:
Hi all,
I have finally gotten the prettyR package going (many thanks to Kurt
Hornik for his patience).
prettyR is a set of functions that allows the user to produce HTML
output from R scripts. Given an R script that runs properly, an
With ggplot its possible to do this too but in that case it seems
necessary to recurse through the grobs. Here we look for
grobs that have a label component which contains a colon
and grid.edit those changing the value of cex. Note that
getNames() give a single grob named pretty and we start
On Fri, 4 Aug 2006, Marc Schwartz (via MN) wrote:
On Fri, 2006-08-04 at 09:47 -0600, Andrew Kniss wrote:
I've tried several different ways to accomplish this, but as yet to no
avail. My y-axis for a plot has a rather long label, and thus I have
been using /n to break it into two lines.
* Dieter Menne wrote, On 2006-08-04 02:57:
Brian Lunergan ff809 at ncf.ca writes:
Evening all:
I'm taking a little time to experiment with R, Sweave, and Miktex/LaTex but
I've run up against some problems and -well- I hope that there are some on
the list who might have some suggestions.
On Fri, 2006-08-04 at 19:44 +0100, Prof Brian Ripley wrote:
On Fri, 4 Aug 2006, Marc Schwartz (via MN) wrote:
On Fri, 2006-08-04 at 09:47 -0600, Andrew Kniss wrote:
I've tried several different ways to accomplish this, but as yet to no
avail. My y-axis for a plot has a rather long
Hi-
I'm seeing some weirdness with svm and tune.svm that I can't figure out- was
wondering if anyone else has seen this? Perhaps I'm failing to make
something the expected class?
Below is my repro case, though it *sometimes* doesn't repro. I'm using
R2.3.1 on WindowsXP. I was also seeing it
Dear R list,
I would like to illustrate the origin of the Student t distribution using R.
So, if (sample.mean - pop.mean) / standard.error(sample.mean) has t
distribution with (sample.size - 1) degree free, what is wrong with the
simulation below? I think that the theoretical curve should
thanks Prof Ripley. dir() returns the path with full names (wildcards replaced)
that are exactly what I need.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Prof Brian Ripley
Sent: Friday, August 04, 2006 12:27 PM
To: Li,Qinghong,ST.LOUIS,Molecular
Dear Jose,
The problem is that you're using the population standard deviation (sigma)
rather than the sample SD of each sample [i.e., t[i] = (mean(amo.i) - mu) /
(sd(amo.i) / sqrt(n)) ], so your values should be normally distributed, as
they appear to be.
A couple of smaller points: (1) Even
Jose Claudio Faria [EMAIL PROTECTED] writes:
Dear R list,
I would like to illustrate the origin of the Student t distribution using R.
So, if (sample.mean - pop.mean) / standard.error(sample.mean) has t
distribution with (sample.size - 1) degree free, what is wrong with the
simulation
Prof. Ripley:
Thanks for diagnosing Wuming Gong's problem.
I'm not sure I would have recognized the solution so quickly. I have
uploaded to CRAN a new version of odesolve with Makevars fixed.
R. Woodrow Setzer, Ph. D.
National Center for Computational Toxicology
US Environmental Protection
Hi, Jose/John,
Here's an example to help Jose and highlights John's advice. Also
includes set.seed which should be included in all simulations posted to
R-help.
set.seed(42)
mu - 10
sigma - 5
n - 3
nsim - 1
m - matrix(rnorm(n * nsim, mu, sigma), nsim, n)
t - apply(m, 1, function(x)
Dears John, Peter and Sundar,
Many thanks for the quick answers!!!
.. and sorry for all..
[]s
___
Jose Claudio Faria
Brasil/Bahia/Ilheus/UESC/DCET
Estatística Experimental/Prof. Adjunto
mails: [EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
John Fox escreveu:
Dear Jose,
Dear Sundar,
Try qq.plot(t, dist=t, df=n-1) from the car package, which include a
95-percent point-wise confidence envelope that helps you judge how extreme
the outliers are relative to expectations.
Regards,
John
John Fox
Department of Sociology
McMaster
Dear R-list,
I have a statistical problem with the comparison of two short time-series of
density data in an ecological framework. I have to compare two short time
series (5 years, one value for each year) of species density data (it is the
density of fish in two different streams) to test if
How can I find out what fonts are available for
par(family=
for the postscript device?
--
Erich Neuwirth, Didactic Center for Computer Science
University of Vienna
Visit our SunSITE at http://sunsite.univie.ac.at
Phone: +43-1-4277-39464 Fax: +43-1-4277-9394
We are trying to find out how to get the variance-covariance matrix of the
MLEs out of the glm function. Can anyone help?
Thanks,
Daniel Jeske
Department of Statistics
University of California
Riverside, CA
[[alternative HTML version deleted]]
Dear all,
I get a strange error when I find polychoric correlations with the ML method,
which I have been able to reproduce using randomly-generated data.
What is wrong?
I realize that the data that I generated randomly is a bit strange, but it is
the only way that I duplicate the error
On Fri, 4 Aug 2006, Daniel Jeske wrote:
We are trying to find out how to get the variance-covariance matrix of the
MLEs out of the glm function. Can anyone help?
It can be extracted with the corresponding vcov() method.
Best,
Z
__
I got the message, Coefficients: (1 not defined because of
singularities), in the returned result of lm(). What does it mean?
And where should I start investigating why it happens?
thanks.
/// Complete result of lm()
Call:
lm(formula = durationRatio ~ isHStar + isWordFinal + oneSyllToEOW +
Hello,
I'm trying to take the correlation of two distance matrices and get
the r2 value
ex)
Ndisc PS1Ntet Nsito NcB NcA PS3 NcC
NiB NiA
PS1
0.08945
Ntet 0.08601
0.02020
Dear Janet,
Because you didn't set the value of the random-number generator seed, your
example isn't precisely reproducible, but the problem is apparent anyway:
set.seed(12345)
n-100
test.x-rnorm(n, mean=0, sd=1)
test.c-test.x + rnorm(n, mean=0, sd=.5)
thresh.x-c(-2.5, -1, -.5, .5, 1000)
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